Contacts of the strand formed by residues 1244 - 1255 (chain B) in PDB entry 3GIL


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 SER1244 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1242B  ARG*     3.1    23.6    -      -       -      -
   1243B  LYS*     1.3    79.9    -      -       -      +
   1245B  ILE*     1.3    64.8    +      -       -      +
   1336B  ARG*     4.2    25.2    -      -       -      +
   1337B  PHE      3.2    10.1    -      -       -      -
   1338B  SER*     4.4     6.3    -      -       -      -
   1340B  PHE*     4.0     1.3    -      -       -      -
   1908J    T      3.8    17.7    +      -       -      +
   1909J    A      2.7    22.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE1245 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1242B  ARG*     3.5    35.7    -      -       +      +
   1244B  SER*     1.3    74.1    -      -       -      +
   1246B  GLY*     1.3    61.2    +      -       -      +
   1272B  SER*     4.3     6.5    -      -       -      +
   1275B  LYS*     3.8    37.2    -      -       +      -
   1276B  LEU*     4.1    24.2    -      -       +      +
   1279B  ARG*     4.0    17.5    -      -       -      +
   1336B  ARG*     4.3     2.2    -      -       -      -
   1337B  PHE*     2.7    44.1    +      -       -      +
   1340B  PHE*     4.0     7.2    -      -       +      -
   1908J    T      3.7    15.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY1246 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1244B  SER*     5.4     0.2    +      -       -      -
   1245B  ILE*     1.3    78.7    -      -       -      +
   1247B  ARG*     1.3    63.6    +      -       -      +
   1272B  SER*     3.4    11.1    +      -       -      -
   1275B  LYS*     5.8     2.4    -      -       -      +
   1335B  VAL      3.1    14.6    -      -       -      -
   1336B  ARG*     3.8     6.7    -      -       -      +
   1907J    C      3.6    13.8    +      -       -      +
   1908J    T      3.0    20.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG1247 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1246B  GLY*     1.3    74.8    -      -       -      +
   1248B  ILE*     1.3    80.3    +      -       -      +
   1249B  VAL*     3.8    13.3    -      -       +      +
   1267B  ARG*     6.3     0.8    -      -       -      +
   1268B  ALA*     3.5    38.5    -      -       +      +
   1271B  GLU*     2.7    36.9    +      -       +      +
   1272B  SER*     3.4     6.3    +      -       -      +
   1334B  GLY*     3.1     2.6    -      -       -      -
   1335B  VAL*     2.8    33.4    +      -       -      +
   1906J  8OG      4.1    12.5    +      -       -      -
   1907J    C      2.7    41.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE1248 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1247B  ARG*     1.3    94.6    +      -       -      +
   1249B  VAL*     1.3    64.2    +      -       -      +
   1287B  VAL*     4.3    15.9    -      -       +      +
   1289B  VAL*     4.9     4.7    -      -       +      -
   1332B  ARG*     3.7    33.2    -      -       +      +
   1333B  ILE*     3.2    37.2    -      -       -      +
   1334B  GLY*     3.5     6.1    -      -       -      +
   1906J  8OG      3.2    27.8    -      -       +      +
   1907J    C      3.0    29.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1249 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1034B  SER      5.2     4.7    -      -       -      +
   1247B  ARG*     3.8    26.0    -      -       +      +
   1248B  ILE*     1.3    85.2    -      -       -      +
   1250B  THR*     1.3    75.4    +      -       -      +
   1251B  MET*     3.8     0.9    +      -       -      +
   1264B  TYR*     4.4    23.3    -      -       +      +
   1267B  ARG*     4.9    16.6    -      -       +      +
   1268B  ALA*     4.5    13.0    -      -       +      +
   1271B  GLU*     5.5     0.7    -      -       -      +
   1332B  ARG*     3.3     5.2    -      -       -      -
   1333B  ILE*     2.8    41.5    +      -       +      +
   1906J  8OG      4.0     5.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR1250 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1034B  SER*     4.0    26.2    +      -       -      +
   1035B  GLY*     5.4     2.4    -      -       -      -
   1036B  ARG*     3.8    35.9    -      -       +      +
   1249B  VAL*     1.3    86.1    -      -       -      +
   1251B  MET*     1.3    65.7    +      -       -      +
   1264B  TYR*     4.1     5.4    -      -       -      -
   1331B  ARG*     4.2     9.6    -      -       -      +
   1332B  ARG*     3.0    25.1    -      -       +      -
   1904J    A      5.5     0.2    -      -       -      +
   1905J    C      4.0     6.9    +      -       -      +
   1906J  8OG      2.7    26.7    +      -       -      -
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Residues in contact with MET1251 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1036B  ARG*     3.0    26.0    +      -       -      +
   1249B  VAL      4.5     5.4    -      -       -      +
   1250B  THR*     1.3    77.3    -      -       -      +
   1252B  LYS*     1.3    67.0    +      -       -      +
   1253B  ARG      3.1    17.1    +      -       -      +
   1255B  SER*     4.3     6.3    -      -       -      +
   1260B  GLU*     5.0     0.9    -      -       -      +
   1261B  ILE*     4.0    30.1    -      -       +      -
   1264B  TYR*     3.6    43.5    -      -       +      -
   1330B  ILE*     3.1    49.6    -      -       +      +
   1331B  ARG      3.2    14.0    +      -       -      +
   1333B  ILE*     4.5     5.8    -      -       +      +
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Residues in contact with LYS1252 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1035B  GLY      4.6    10.1    -      -       -      +
   1036B  ARG*     3.9    37.5    +      -       -      +
   1250B  THR      4.2     0.2    +      -       -      -
   1251B  MET*     1.3    72.1    -      -       -      +
   1253B  ARG*     1.3    70.3    +      -       +      +
   1264B  TYR*     3.0    24.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG1253 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  GLU*     3.1    29.8    +      -       -      +
   1036B  ARG*     4.1    10.1    -      -       -      +
   1251B  MET*     3.1    20.9    +      -       -      +
   1252B  LYS*     1.3    90.0    -      -       +      +
   1254B  ASN*     1.3    76.9    +      -       -      +
   1255B  SER*     3.6     4.5    +      -       -      -
   1260B  GLU*     3.7    24.4    +      -       -      +
   1264B  TYR*     5.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN1254 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1036B  ARG*     3.2    33.3    +      -       -      +
   1253B  ARG*     1.3    88.4    +      -       -      +
   1255B  SER*     1.3    62.2    +      -       -      +
   1260B  GLU*     4.6     0.2    -      -       -      +
   1291B  GLU*     3.6    31.1    -      -       -      +
   1329B  LYS*     3.9    28.8    +      -       +      +
   1330B  ILE      3.2    11.1    -      -       -      +
   1331B  ARG*     4.0    13.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER1255 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1251B  MET*     4.6     3.4    -      -       -      -
   1253B  ARG      3.6     4.7    +      -       -      -
   1254B  ASN*     1.3    77.0    -      -       -      +
   1256B  ARG*     1.3    61.3    +      -       -      +
   1257B  ASN*     2.9    30.0    +      -       -      +
   1260B  GLU*     3.4    27.0    +      -       -      +
   1261B  ILE*     3.3    26.3    -      -       -      +
   1329B  LYS*     4.7     4.2    -      -       -      +
   1330B  ILE*     3.2    26.2    +      -       -      +
----------------------------------------------------------
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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