Contacts of the strand formed by residues 1219 - 1233 (chain D) in PDB entry 3CMT


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 ALA1219 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1061D  ILE*     3.3    14.8    -      -       -      +
   1062D  VAL*     4.6     0.2    -      -       -      -
   1063D  GLU*     4.3    11.0    -      -       +      +
   1215D  LEU*     2.9    21.5    +      -       +      +
   1216D  LYS      4.2     0.7    -      -       -      +
   1217D  PHE      3.4     1.1    -      -       -      +
   1218D  TYR*     1.3    76.8    -      -       -      +
   1220D  SER*     1.3    60.1    +      -       -      +
   1221D  VAL      3.8     8.7    -      -       -      +
   1222D  ARG*     3.7    29.2    -      -       +      -
   1248D  LYS*     3.0    28.1    +      -       -      -
   1250D  LYS*     4.1     1.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER1220 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98D  ALA*     4.7     2.6    -      -       -      +
   1057D  PRO*     4.4     9.4    -      -       -      -
   1060D  ARG*     3.0    53.4    +      -       -      +
   1061D  ILE      2.8    12.3    +      -       -      -
   1218D  TYR      4.0     5.7    +      -       -      -
   1219D  ALA*     1.3    74.9    -      -       -      +
   1221D  VAL*     1.3    63.2    +      -       -      +
   1248D  LYS*     4.5     2.4    -      -       -      +
   1249D  ASN*     3.5     1.9    +      -       -      -
   1250D  LYS*     2.8    43.1    +      -       -      +
   1251D  ILE*     4.4     1.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL1221 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1051D  LEU*     3.6    20.6    -      -       +      -
   1056D  LEU*     4.1     9.0    -      -       +      -
   1057D  PRO*     4.1    25.1    -      -       +      -
   1061D  ILE      3.8     1.6    +      -       -      -
   1062D  VAL*     3.4    16.1    -      -       +      +
   1063D  GLU      3.0    23.9    +      -       -      -
   1219D  ALA*     3.8     1.0    -      -       -      +
   1220D  SER*     1.3    86.2    -      -       -      +
   1222D  ARG*     1.3    69.4    +      -       -      +
   1223D  LEU*     3.6    26.9    -      -       +      -
   1246D  VAL*     4.6     0.9    -      -       +      -
   1248D  LYS      3.2     8.3    -      -       -      +
   1249D  ASN*     3.7    17.7    -      -       -      +
   1251D  ILE*     4.7     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG1222 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68D  GLU*     4.3    11.7    +      -       -      -
   1063D  GLU*     2.5    51.9    +      -       +      +
   1065D  TYR*     3.7    31.2    +      -       +      -
   1209D  THR*     4.4     8.1    +      -       -      +
   1216D  LYS*     4.1    42.3    +      -       -      +
   1219D  ALA*     3.7    19.3    -      -       +      -
   1221D  VAL*     1.3    78.8    -      -       -      +
   1223D  LEU*     1.3    66.6    -      -       -      +
   1246D  VAL*     3.7     0.5    -      -       -      -
   1247D  VAL*     2.8    41.3    +      -       +      +
   1248D  LYS*     2.9    33.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU1223 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1047D  LEU*     4.5    18.6    -      -       +      -
   1051D  LEU*     4.3     4.0    -      -       +      -
   1056D  LEU*     4.3    22.7    -      -       +      -
   1062D  VAL*     4.6     2.0    -      -       +      -
   1063D  GLU      2.7    12.2    +      -       -      +
   1064D  ILE*     3.4    31.3    -      -       +      -
   1065D  TYR*     2.9    35.4    +      -       -      +
   1075D  LEU*     4.9     4.5    -      -       +      -
   1221D  VAL*     3.6    20.4    -      -       +      -
   1222D  ARG*     1.3    78.0    -      -       -      +
   1224D  ASP*     1.3    59.3    +      -       -      +
   1225D  ILE      3.8     0.6    +      -       -      -
   1244D  VAL*     3.7    19.1    -      -       +      -
   1245D  LYS      3.5     1.8    -      -       -      +
   1246D  VAL*     4.0    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP1224 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1065D  TYR*     3.5    30.8    +      -       +      +
   1207D  GLU*     4.9     0.3    -      -       -      +
   1222D  ARG      4.2     0.4    +      -       -      -
   1223D  LEU*     1.3    69.7    -      -       -      +
   1225D  ILE*     1.3    62.1    +      -       -      +
   1226D  ARG*     2.7    41.2    +      -       -      +
   1243D  ARG      3.6     1.7    -      -       -      +
   1244D  VAL*     3.3     3.5    -      -       -      -
   1245D  LYS*     2.8    46.2    +      -       +      +
   1247D  VAL*     3.6    23.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1225 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1064D  ILE*     3.8    12.3    -      -       +      -
   1065D  TYR      2.9    19.2    +      -       -      +
   1066D  GLY*     3.4     2.6    -      -       -      -
   1067D  PRO*     3.4    14.6    -      -       -      +
   1070D  SER*     3.6    25.8    -      -       -      +
   1071D  GLY*     3.8    18.2    -      -       -      +
   1072D  LYS*     3.6    27.1    -      -       +      +
   1075D  LEU*     4.0    15.7    -      -       +      -
   1223D  LEU      3.8     0.4    -      -       -      -
   1224D  ASP*     1.3    73.3    -      -       -      +
   1226D  ARG*     1.3    72.7    +      -       -      +
   1242D  THR*     3.7    22.0    -      -       +      -
   1243D  ARG      3.5     2.9    -      -       -      -
   1244D  VAL*     3.8    19.3    -      -       +      +
   1260D  PHE*     4.6     0.9    -      -       +      -
   1262D  ILE*     4.8     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG1226 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1065D  TYR*     4.7     1.6    -      -       -      -
   1067D  PRO*     3.4    25.7    -      -       +      +
   1070D  SER*     4.2     9.6    -      -       -      -
   1195D  ILE*     3.2    18.2    -      -       -      +
   1207D  GLU*     2.6    40.7    +      -       -      -
   1224D  ASP*     2.7    34.5    +      -       -      +
   1225D  ILE*     1.3    80.7    -      -       -      +
   1227D  ARG*     1.3    65.7    +      -       -      +
   1228D  ILE*     3.6     8.8    +      -       +      +
   1242D  THR*     3.6     2.9    -      -       -      +
   1243D  ARG*     2.9    39.1    +      -       +      +
   1245D  LYS*     5.8     5.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG1227 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1067D  PRO*     5.5     1.4    -      -       -      +
   1068D  GLU      6.1     0.2    -      -       -      +
   1069D  SER      4.6     7.2    -      -       -      +
   1070D  SER*     4.2    20.0    -      -       -      +
   1226D  ARG*     1.3    74.3    -      -       -      +
   1228D  ILE*     1.3    62.7    +      -       -      +
   1229D  GLY*     3.5    26.5    +      -       -      +
   1230D  ALA*     3.5    27.9    -      -       -      +
   1237D  VAL*     4.0     0.8    -      -       -      +
   1239D  GLY      4.0     1.6    +      -       -      -
   1240D  SER*     3.0    23.6    +      -       -      +
   1241D  GLU      3.6     6.7    -      -       -      +
   1242D  THR*     4.7     3.4    -      -       -      +
   1264D  TYR*     3.6     8.9    +      -       -      -
   1502D  ADP      5.2     0.8    +      -       -      -
   2255D  PHE*     3.3    42.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE1228 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1226D  ARG*     3.9     9.4    -      -       +      +
   1227D  ARG*     1.3    78.1    -      -       -      +
   1229D  GLY*     1.3    58.6    +      -       -      +
   1241D  GLU*     2.8    37.3    +      -       +      +
   1242D  THR      4.2     4.5    -      -       -      +
   1243D  ARG*     3.6    55.6    -      -       +      +
   1259D  GLU*     4.0    21.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY1229 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3232A  LYS*     5.3     7.2    -      -       -      -
   1227D  ARG*     3.5    23.0    -      -       -      +
   1228D  ILE*     1.3    78.8    -      -       -      +
   1230D  ALA*     1.3    57.5    +      -       -      -
   1240D  SER*     3.7     0.3    -      -       -      -
   1241D  GLU*     2.8    37.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA1230 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3232A  LYS*     4.3    16.1    +      -       -      +
   1227D  ARG*     3.5    23.7    -      -       -      +
   1229D  GLY*     1.3    72.7    -      -       -      -
   1231D  VAL*     1.3    62.3    +      -       -      +
   1232D  LYS*     3.6    22.5    +      -       +      +
   1237D  VAL*     4.0    17.3    -      -       +      -
   1239D  GLY      3.7     0.2    -      -       -      -
   1241D  GLU*     4.8     2.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1231 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1229D  GLY      4.2     0.2    +      -       -      -
   1230D  ALA*     1.3    69.0    -      -       -      +
   1232D  LYS*     1.3    62.4    +      -       -      +
   1237D  VAL*     3.7     2.3    -      -       -      -
   1238D  VAL*     2.9    42.9    +      -       +      +
   1239D  GLY*     2.7    30.5    +      -       -      +
   1240D  SER      4.0     1.6    -      -       -      -
   1241D  GLU*     3.4    31.9    -      -       -      +
   1261D  GLN*     3.5    30.5    -      -       +      +
   1263D  LEU*     4.0    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS1232 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3228A  ILE      5.5     0.8    +      -       -      -
   3229A  GLY*     4.6    14.8    -      -       -      -
   3230A  ALA      4.5    16.2    +      -       -      +
   3232A  LYS*     6.5     0.7    -      -       -      +
   3241A  GLU*     5.4     7.3    +      -       -      +
   1230D  ALA*     3.6    17.7    +      -       +      +
   1231D  VAL*     1.3    80.0    -      -       -      +
   1233D  GLU*     1.3    64.3    +      -       -      +
   1234D  GLY*     3.5    20.8    +      -       -      +
   1235D  GLU      4.7     3.6    -      -       -      +
   1236D  ASN      3.2    10.8    -      -       -      +
   1237D  VAL*     4.2    18.4    -      -       +      -
   1238D  VAL*     4.7     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU1233 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3291A  TYR*     5.1     2.4    +      -       -      -
   3301A  GLY*     5.4     2.4    -      -       -      -
   3302A  LYS*     4.0    38.4    +      -       -      +
   1231D  VAL      4.2     0.2    +      -       -      -
   1232D  LYS*     1.3    71.4    -      -       -      +
   1234D  GLY*     1.3    52.5    +      -       -      +
   1235D  GLU*     2.7    16.9    +      -       -      +
   1236D  ASN*     2.7    36.1    +      -       +      +
   1238D  VAL*     3.9    27.1    -      -       +      -
----------------------------------------------------------
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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