Contacts of the strand formed by residues 1323 - 1337 (chain A) in PDB entry 5DGY


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with GLY1323 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1066A  PHE*     3.8    18.2    -      -       -      -
   1084A  LEU*     4.0     9.7    -      -       -      +
   1128A  PRO*     4.2     3.8    -      -       -      -
   1146A  VAL*     4.6     0.2    -      -       -      -
   1247A  ASN      3.9     0.5    -      -       -      +
   1249A  VAL*     2.8    39.3    +      -       -      +
   1322A  MET*     1.3    77.5    -      -       -      +
   1324A  ILE*     1.3    63.8    +      -       -      -
   1325A  LEU*     3.4     9.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1324 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1066A  PHE*     3.7    26.6    -      -       +      -
   1128A  PRO*     4.7     7.4    -      -       -      +
   1129A  CYS      5.1     0.7    +      -       -      +
   1131A  VAL*     3.8    57.1    -      -       +      +
   1133A  LEU*     4.1    33.9    -      -       +      -
   1144A  CYS*     5.3     0.2    -      -       -      -
   1145A  GLY*     4.2     8.3    -      -       -      +
   1146A  VAL*     3.9    15.5    -      -       +      +
   1246A  ALA*     5.5     2.9    -      -       +      -
   1247A  ASN      4.0     2.2    -      -       -      -
   1248A  VAL*     4.1    22.2    -      -       +      +
   1295A  ALA*     5.0     0.9    -      -       +      -
   1311A  THR*     4.2     2.8    +      -       -      +
   1323A  GLY*     1.3    68.8    -      -       -      -
   1325A  LEU*     1.3    67.4    +      -       -      +
   1326A  VAL*     4.1    10.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1325 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1128A  PRO*     4.4     8.1    -      -       +      -
   1246A  ALA      3.9     0.3    -      -       -      -
   1247A  ASN*     2.9    62.0    +      -       +      +
   1249A  VAL*     4.8     3.8    -      -       +      -
   1311A  THR*     3.8    26.5    -      -       +      +
   1313A  ILE*     4.0    24.5    -      -       +      -
   1321A  VAL*     3.9    38.8    -      -       +      +
   1323A  GLY      4.1     9.0    -      -       -      +
   1324A  ILE*     1.3    79.1    -      -       -      +
   1326A  VAL*     1.3    63.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1326 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1131A  VAL*     4.1    17.9    -      -       +      -
   1244A  GLN*     4.1    16.8    -      -       +      +
   1245A  ILE      3.8     4.9    -      -       -      +
   1246A  ALA*     5.4     2.5    -      -       -      -
   1247A  ASN*     6.1     0.2    -      -       -      -
   1295A  ALA*     4.2     8.7    -      -       +      -
   1308A  ALA*     4.0    24.0    -      -       +      -
   1309A  SER      3.6    15.0    -      -       -      +
   1310A  SER*     3.7     0.8    -      -       -      -
   1311A  THR*     3.0    36.1    +      -       -      +
   1324A  ILE*     4.2     7.0    -      -       +      +
   1325A  LEU*     1.3    80.1    -      -       -      +
   1327A  SER*     1.3    67.6    +      -       -      +
   1328A  TYR*     3.8    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER1327 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1244A  GLN*     3.9     0.5    -      -       -      -
   1245A  ILE*     3.0    48.0    +      -       -      +
   1310A  SER*     4.6     5.6    -      -       -      -
   1311A  THR      5.8     0.7    -      -       -      -
   1326A  VAL*     1.3    80.1    -      -       -      +
   1328A  TYR*     1.3    77.9    +      -       -      +
   1353A  PRO*     5.3     4.7    -      -       -      +
   1354A  PHE      4.5     2.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR1328 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1242A  VAL*     4.3    15.9    -      -       +      -
   1243A  GLU      3.7     4.5    -      -       -      -
   1244A  GLN*     3.3    41.2    +      -       +      -
   1245A  ILE*     5.4     0.2    -      -       -      -
   1260A  VAL*     4.3    10.3    -      -       +      -
   1283A  PRO*     5.7     0.7    -      -       +      -
   1307A  LEU*     3.7    12.2    -      -       +      +
   1308A  ALA      2.8    36.7    +      -       -      -
   1310A  SER*     3.4    20.1    +      -       -      +
   1326A  VAL*     3.8    14.4    -      -       +      -
   1327A  SER*     1.3    84.6    +      -       -      +
   1329A  HIS*     1.3    64.8    +      -       -      +
   1353A  PRO*     3.6     2.8    -      -       -      +
   1354A  PHE*     3.0    54.2    +      +       +      +
   1356A  LEU*     4.1    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS1329 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1242A  VAL*     4.0     0.3    -      -       -      -
   1243A  GLU*     3.0    71.6    +      -       +      +
   1245A  ILE*     4.5    20.9    -      -       +      +
   1257A  VAL*     4.2    12.6    -      -       +      -
   1328A  TYR*     1.3    77.5    -      -       -      +
   1330A  ILE*     1.3    58.1    +      -       -      +
   1331A  LYS*     3.5     7.3    +      -       +      -
   1351A  GLU*     3.3    46.6    -      -       +      +
   1352A  VAL      3.3    15.7    -      -       -      +
   1353A  PRO*     3.8     9.2    -      -       +      -
   1354A  PHE*     3.6     8.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE1330 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1208A  VAL*     5.2     1.5    -      -       +      +
   1210A  LEU*     3.9    20.4    -      -       +      -
   1221A  ILE*     3.9    16.6    -      -       +      -
   1223A  VAL*     3.7    21.8    -      -       +      -
   1240A  VAL*     3.7    26.0    -      -       +      -
   1241A  SER      3.7     1.8    -      -       -      +
   1242A  VAL*     3.7    27.1    -      -       +      -
   1329A  HIS*     1.3    69.9    -      -       -      +
   1331A  LYS*     1.3    62.6    +      -       -      +
   1332A  VAL*     3.9     2.5    +      -       -      +
   1350A  THR      4.0     0.5    -      -       -      +
   1351A  GLU*     3.5     1.4    -      -       -      -
   1352A  VAL*     2.8    45.3    +      -       +      +
   1354A  PHE*     3.4    31.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS1331 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1239A  LYS      4.0     0.3    -      -       -      +
   1240A  VAL*     3.8     1.3    -      -       -      -
   1241A  SER*     2.8    51.8    +      -       -      +
   1243A  GLU*     3.3    29.5    +      -       -      +
   1329A  HIS*     3.5    13.2    +      -       +      -
   1330A  ILE*     1.3    71.2    -      -       -      +
   1332A  VAL*     1.3    62.1    -      -       -      +
   1333A  LYS*     3.8    22.1    +      -       -      +
   1349A  ALA*     3.4    26.5    -      -       -      +
   1350A  THR      3.5     7.2    -      -       -      +
   1351A  GLU*     3.5    30.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1332 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1206A  LEU*     4.1     8.9    -      -       +      +
   1208A  VAL*     3.6    24.5    -      -       +      -
   1223A  VAL*     5.6     2.2    -      -       +      -
   1225A  VAL*     4.3    12.3    -      -       +      -
   1238A  ILE*     4.0    23.1    -      -       +      -
   1239A  LYS      3.5    10.5    -      -       -      +
   1240A  VAL*     4.0    18.2    -      -       +      +
   1330A  ILE*     3.9     3.9    +      -       +      +
   1331A  LYS*     1.3    73.3    -      -       -      +
   1333A  LYS*     1.3    63.0    +      -       -      +
   1334A  LEU*     4.3     6.3    -      -       +      -
   1349A  ALA*     3.3     3.5    -      -       -      +
   1350A  THR*     3.0    55.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS1333 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1238A  ILE*     3.9     0.9    -      -       -      -
   1239A  LYS*     2.8    72.7    +      -       +      +
   1241A  SER*     4.4    16.6    +      -       -      -
   1243A  GLU*     4.7     8.2    +      -       -      -
   1331A  LYS*     3.8    20.8    -      -       -      +
   1332A  VAL*     1.3    74.4    -      -       -      +
   1334A  LEU*     1.3    66.0    +      -       -      +
   1335A  THR*     3.8     6.6    +      -       -      +
   1347A  GLU*     5.4    15.7    -      -       +      +
   1348A  VAL      3.4     5.4    -      -       -      +
   1349A  ALA*     3.5    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1334 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1195A  TRP*     4.8     1.1    -      -       +      -
   1204A  LEU*     4.7    13.5    -      -       +      -
   1206A  LEU*     3.9    39.3    -      -       +      -
   1225A  VAL*     5.3     0.2    -      -       +      -
   1227A  VAL*     4.5    14.6    -      -       +      -
   1235A  VAL*     4.4    10.8    -      -       +      -
   1237A  LYS      3.7     2.9    -      -       -      -
   1238A  ILE*     3.7    37.5    -      -       +      -
   1332A  VAL*     4.3     9.0    -      -       +      -
   1333A  LYS*     1.3    73.7    -      -       -      +
   1335A  THR*     1.3    58.8    +      -       -      +
   1336A  VAL*     3.2    14.9    +      -       +      +
   1347A  GLU*     3.5     3.1    -      -       -      -
   1348A  VAL*     2.7    52.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR1335 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1235A  VAL*     3.3     2.6    -      -       -      +
   1236A  LYS*     2.5    47.0    +      -       +      -
   1237A  LYS*     3.0    38.5    +      -       +      +
   1239A  LYS*     5.5     2.4    -      -       -      +
   1333A  LYS*     3.8     8.5    +      -       -      +
   1334A  LEU*     1.3    69.7    -      -       -      +
   1336A  VAL*     1.3    53.8    +      -       -      +
   1345A  SER*     4.4    15.7    -      -       -      -
   1346A  SER      4.0     2.0    -      -       -      -
   1347A  GLU*     4.2    28.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1336 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1197A  PHE*     4.4    20.0    -      -       +      -
   1204A  LEU*     4.7     7.9    -      -       +      -
   1231A  THR*     6.1     0.2    -      -       -      +
   1233A  LYS*     4.2    19.5    -      -       +      -
   1234A  VAL      3.4    18.4    -      -       -      +
   1235A  VAL*     3.8    15.3    -      -       +      +
   1236A  LYS*     4.6     0.9    -      -       -      -
   1334A  LEU*     3.5    26.2    -      -       +      +
   1335A  THR*     1.3    73.5    -      -       -      +
   1337A  SER*     1.4    60.5    +      -       -      +
   1338A  GLY*     2.9     9.2    +      -       -      +
   1345A  SER*     3.6     4.6    -      -       -      -
   1346A  SER*     2.9    39.2    +      -       -      +
   1348A  VAL*     4.1    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER1337 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1233A  LYS*     4.0     2.4    -      -       -      +
   1234A  VAL*     2.4    64.6    +      -       -      +
   1236A  LYS*     3.3    34.1    -      -       -      +
   1336A  VAL*     1.4    70.0    -      -       -      +
   1338A  GLY*     1.4    61.8    +      -       -      +
   1344A  THR      4.9     0.7    -      -       -      -
   1345A  SER*     4.6     8.5    -      -       -      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il