Contacts of the helix formed by residues 1038 - 1051 (chain B) in PDB entry 4Z4Q


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 LYS1038 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1028B  ARG      3.6    14.1    -      -       -      +
   1029B  ALA*     2.9    28.3    -      -       -      +
   1030B  LEU*     4.1     0.7    -      -       -      +
   1031B  PRO*     4.0    16.4    -      -       +      -
   1037B  LEU*     1.3    75.2    -      -       -      +
   1039B  PRO*     1.3    76.9    -      -       +      +
   1040B  VAL*     3.2    10.1    -      -       +      +
   1041B  GLN*     2.8    43.2    +      -       +      +
   1042B  ARG*     3.1    10.9    +      -       -      +
   1167B  SER*     4.1    12.9    +      -       -      +
   1168B  THR      2.5    35.0    +      -       -      +
   1169B  GLY      3.5     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO1039 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1026B  GLN      4.3     3.6    -      -       -      +
   1027B  ASP*     3.5    41.7    -      -       +      +
   1028B  ARG*     3.8    17.5    -      -       -      +
   1030B  LEU      4.6     6.7    -      -       -      +
   1037B  LEU      4.7     0.7    -      -       -      +
   1038B  LYS*     1.3    87.3    -      -       +      +
   1040B  VAL*     1.3    63.6    +      -       -      +
   1042B  ARG*     3.2    22.9    +      -       -      +
   1043B  ARG*     3.0    49.6    +      -       -      +
   1074B  HIS*     5.3     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1040 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1028B  ARG      5.9     0.4    -      -       -      +
   1038B  LYS*     4.6    10.5    -      -       +      -
   1039B  PRO*     1.3    81.5    -      -       -      +
   1041B  GLN*     1.3    80.4    +      -       +      +
   1043B  ARG*     3.5     2.8    +      -       +      +
   1044B  ILE*     3.1    35.0    +      -       +      +
   1069B  ILE*     5.8     0.2    -      -       +      -
   1074B  HIS*     3.5    42.4    -      -       +      +
   1080B  SER*     5.0     2.0    -      -       -      +
   1081B  ILE*     4.4    15.5    -      -       +      +
   1084B  ALA*     4.0    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN1041 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1036B  GLY      4.1     3.3    -      -       -      +
   1037B  LEU*     3.3    25.9    -      -       +      +
   1038B  LYS*     2.8    51.5    +      -       -      +
   1040B  VAL*     1.3    89.5    -      -       +      +
   1042B  ARG*     1.3    66.3    +      -       -      +
   1044B  ILE*     3.2     4.8    +      -       -      +
   1045B  LEU*     2.9    28.5    +      -       -      +
   1084B  ALA*     5.1     5.5    +      -       +      +
   1087B  ARG*     5.5     8.3    -      -       -      +
   1088B  MET*     3.8    32.1    -      -       +      +
   1167B  SER*     5.6     2.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG1042 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1032B  ASP*     3.3    17.8    -      -       -      +
   1035B  ASP*     2.9    28.2    +      -       -      -
   1037B  LEU*     2.9    39.1    +      -       +      +
   1038B  LYS      3.1     5.8    +      -       -      +
   1039B  PRO*     3.6    26.2    -      -       -      +
   1041B  GLN*     1.3    75.3    -      -       -      +
   1043B  ARG*     1.3    60.5    +      -       +      +
   1045B  LEU*     3.3     3.7    +      -       -      +
   1046B  TYR*     2.8    30.8    +      -       -      +
   1152B  PRO*     3.9    14.6    +      -       +      +
   1153B  THR*     3.5    17.9    +      -       -      +
   1154B  VAL*     3.6    26.8    -      -       -      +
   1155B  LEU*     3.7    22.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG1043 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1023B  TYR*     5.4     3.6    +      -       -      -
   1027B  ASP*     5.8     1.2    +      -       -      -
   1039B  PRO*     3.0    30.1    +      -       -      +
   1040B  VAL*     3.9     3.4    -      -       -      +
   1042B  ARG*     1.3    76.3    -      -       +      +
   1044B  ILE*     1.3    61.3    +      -       -      +
   1046B  TYR*     4.3     5.4    -      -       +      +
   1047B  SER*     2.8    36.2    +      -       -      -
   1069B  ILE*     4.5    10.5    -      -       +      -
   1073B  PHE*     3.4    37.5    +      -       +      -
   1074B  HIS*     2.9    38.4    +      -       +      +
   1075B  PRO*     4.6     6.0    -      -       -      +
   1076B  HIS*     5.3     1.6    +      -       -      -
   1151B  GLU*     2.9    42.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1044 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1040B  VAL*     3.1    23.6    +      -       +      +
   1041B  GLN*     3.6     8.1    -      -       -      +
   1043B  ARG*     1.3    74.7    -      -       -      +
   1045B  LEU*     1.3    62.5    +      -       +      +
   1047B  SER*     4.1     0.3    -      -       -      -
   1048B  MET*     3.1    45.1    +      -       -      +
   1069B  ILE*     3.7    24.4    -      -       +      +
   1081B  ILE*     3.8    14.4    -      -       +      +
   1084B  ALA*     3.7    16.6    -      -       +      -
   1085B  MET*     3.6    34.8    -      -       +      +
   1088B  MET*     3.2    30.1    -      -       +      -
   1099B  VAL*     4.7     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1045 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1037B  LEU*     3.8    18.2    -      -       +      -
   1041B  GLN      2.9    18.2    +      -       -      +
   1042B  ARG      3.7     4.0    -      -       -      +
   1044B  ILE*     1.3    74.9    -      -       -      +
   1046B  TYR*     1.3    66.2    +      -       -      +
   1048B  MET      3.9     0.2    -      -       -      -
   1049B  ASN*     3.0    25.5    +      -       -      +
   1088B  MET*     4.1    20.4    -      -       +      -
   1098B  LEU*     4.3    23.1    -      -       +      +
   1099B  VAL*     4.5     0.2    -      -       +      -
   1123B  LEU*     3.8    26.2    -      -       +      +
   1127B  ALA*     4.7     6.1    -      -       +      -
   1130B  LEU*     3.6    32.8    -      -       +      -
   1131B  LEU*     3.8     9.5    -      -       +      +
   1155B  LEU*     4.2    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR1046 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1042B  ARG      2.8    21.7    +      -       -      +
   1043B  ARG*     4.0     4.5    -      -       -      +
   1045B  LEU*     1.3    73.0    -      -       -      +
   1047B  SER*     1.3    65.2    +      -       -      +
   1049B  ASN*     3.2     4.9    +      -       -      +
   1050B  LYS*     2.9    42.6    +      -       +      +
   1073B  PHE*     3.7    35.7    -      +       -      -
   1131B  LEU*     4.6     9.0    -      -       +      -
   1134B  ILE*     3.9    26.2    -      -       +      -
   1141B  PHE*     3.8    14.4    -      +       -      -
   1149B  GLU*     5.3     1.0    +      -       -      +
   1150B  LYS      3.8    12.0    +      -       -      -
   1151B  GLU*     4.7     0.7    -      -       +      -
   1152B  PRO*     3.6    44.0    -      -       +      -
   1155B  LEU*     5.0     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER1047 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1043B  ARG      2.8    18.3    +      -       -      -
   1046B  TYR*     1.3    78.3    -      -       -      +
   1048B  MET*     1.3    64.6    +      -       -      +
   1049B  ASN      2.9     1.0    +      -       -      -
   1050B  LYS*     3.0    16.1    +      -       -      +
   1051B  ASP*     3.1    24.6    +      -       -      -
   1065B  SER      4.7     1.0    +      -       -      -
   1068B  ASN*     4.1     4.9    -      -       -      +
   1069B  ILE*     3.5    31.8    +      -       -      +
   1072B  ASN*     5.0     1.0    +      -       -      -
   1073B  PHE*     3.9    25.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET1048 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1044B  ILE*     3.1    37.6    +      -       +      +
   1047B  SER*     1.3    79.5    -      -       -      +
   1049B  ASN*     1.3    60.6    +      -       -      +
   1051B  ASP*     3.4     3.9    +      -       -      -
   1052B  SER      3.4     2.1    +      -       -      -
   1053B  ASN*     2.9    60.3    +      -       +      +
   1065B  SER*     4.3    14.4    -      -       -      +
   1069B  ILE*     4.9     4.0    -      -       +      -
   1085B  MET*     4.5    14.8    -      -       -      +
   1099B  VAL*     4.7     6.1    -      -       +      -
   1121B  ALA*     4.2     6.3    -      -       +      -
   1122B  ARG*     3.5    36.1    -      -       -      +
   1123B  LEU*     3.6    21.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN1049 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1045B  LEU      3.0     8.7    +      -       -      +
   1046B  TYR*     3.8     5.0    -      -       +      +
   1047B  SER      3.0     1.0    -      -       -      -
   1048B  MET*     1.3    76.7    -      -       -      +
   1050B  LYS*     1.3    65.1    +      -       -      +
   1052B  SER*     2.9    14.4    +      -       -      -
   1054B  THR*     3.6    24.2    -      -       -      +
   1123B  LEU*     3.6     7.8    -      -       +      +
   1128B  GLY*     5.5     4.9    -      -       -      -
   1131B  LEU*     3.3    46.0    -      -       +      +
   1134B  ILE*     4.5    12.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS1050 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1046B  TYR*     2.9    32.4    +      -       +      +
   1047B  SER*     3.4    11.0    -      -       -      +
   1049B  ASN*     1.3    76.2    +      -       -      +
   1051B  ASP*     1.3    68.2    +      -       -      +
   1052B  SER*     3.3     8.7    +      -       -      -
   1072B  ASN*     6.0     1.3    -      -       -      +
   1073B  PHE*     4.6    11.4    -      -       +      -
   1149B  GLU*     3.0    28.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP1051 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1047B  SER*     3.1    17.8    +      -       -      +
   1048B  MET*     3.9     6.9    -      -       -      +
   1049B  ASN      3.1     0.8    -      -       -      -
   1050B  LYS*     1.3    90.5    -      -       -      +
   1052B  SER*     1.3    72.1    +      -       -      +
   1053B  ASN*     3.0     3.4    +      -       +      -
   1060B  ARG*     3.4    34.4    +      -       -      +
   1065B  SER*     6.0     0.3    -      -       -      -
   1068B  ASN*     3.2    33.8    +      -       -      +
   1072B  ASN*     5.6     1.6    +      -       -      -
----------------------------------------------------------
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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