Contacts of the helix formed by residues 1384 - 1397 (chain B) in PDB entry 4QY4


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 THR1384 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1383B  LEU*     1.3    78.1    -      -       -      +
   1385B  LYS*     1.3    57.4    +      -       -      +
   1387B  MET*     3.2     6.1    +      -       -      +
   1388B  ASN*     2.9    48.3    +      -       -      +
   1438B  ILE*     4.0    26.0    +      -       +      +
   1439B  ARG*     4.9     4.7    -      -       -      +
   1441B  HIS*     3.2    33.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with LYS1385 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1383B  LEU*     3.2    14.2    -      -       +      +
   1384B  THR*     1.3    76.2    -      -       -      +
   1386B  GLN*     1.3    65.9    +      -       +      +
   1388B  ASN*     3.6     6.5    +      -       +      +
   1389B  ALA*     3.2    23.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN1386 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1383B  LEU*     3.5    28.3    +      -       +      +
   1384B  THR      3.4     0.2    -      -       -      -
   1385B  LYS*     1.3    76.6    -      -       +      +
   1387B  MET*     1.3    63.7    +      -       -      +
   1389B  ALA*     3.1     6.4    +      -       -      +
   1390B  ILE*     3.0    33.4    +      -       +      +
   1446B  LEU*     4.8    11.8    -      -       +      +
   1488B  ILE*     3.5    30.5    -      -       +      +
   1489B  ALA*     4.0    23.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET1387 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1383B  LEU      3.3    20.5    +      -       -      +
   1384B  THR*     3.2     9.9    +      -       -      +
   1386B  GLN*     1.3    78.3    -      -       -      +
   1388B  ASN*     1.3    56.3    +      -       -      +
   1390B  ILE*     3.4     4.5    +      -       -      +
   1391B  ILE*     3.0    33.4    +      -       -      +
   1438B  ILE*     3.9    22.9    -      -       +      -
   1443B  TYR*     3.7    40.6    -      -       +      +
   1444B  ARG      4.9     0.2    -      -       -      -
   1445B  SER*     3.3    37.9    -      -       -      +
   1446B  LEU*     3.6    23.1    -      -       +      +
   1449B  LEU*     4.0    14.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN1388 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1384B  THR*     2.9    34.1    +      -       -      +
   1385B  LYS*     4.1     6.5    -      -       +      +
   1387B  MET*     1.3    75.7    -      -       -      +
   1389B  ALA*     1.3    56.9    +      -       -      +
   1391B  ILE*     4.4     1.5    -      -       -      +
   1392B  ASP*     2.8    43.2    +      -       -      +
   1435B  LYS*     3.7    24.9    +      -       -      +
   1438B  ILE*     3.4    24.5    -      -       -      +
   1439B  ARG*     5.2     2.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA1389 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1385B  LYS      3.2    16.5    +      -       -      +
   1386B  GLN*     3.1     5.9    +      -       -      +
   1388B  ASN*     1.3    77.0    -      -       -      +
   1390B  ILE*     1.3    58.1    +      -       -      +
   1392B  ASP*     3.9     4.4    -      -       -      +
   1393B  THR*     2.7    34.0    +      -       -      -
   1488B  ILE*     3.6    23.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1390 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1386B  GLN*     3.0    21.6    +      -       +      +
   1387B  MET*     3.7     5.6    -      -       -      +
   1389B  ALA*     1.3    78.2    -      -       -      +
   1391B  ILE*     1.3    60.8    +      -       -      +
   1393B  THR*     3.5     4.7    +      -       -      -
   1394B  VAL*     3.4    20.6    +      -       -      +
   1446B  LEU*     4.2    23.6    -      -       +      -
   1449B  LEU*     4.6     3.4    -      -       +      -
   1481B  PHE*     3.5    35.4    -      -       +      -
   1484B  ALA*     3.9    19.6    -      -       +      +
   1485B  ARG*     3.8    33.9    -      -       +      +
   1488B  ILE*     3.7    15.5    -      -       +      -
   1489B  ALA*     4.6     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE1391 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1387B  MET      3.0    20.8    +      -       -      +
   1388B  ASN      4.4     1.6    -      -       -      +
   1390B  ILE*     1.3    73.6    -      -       -      +
   1392B  ASP*     1.3    61.5    +      -       -      +
   1394B  VAL*     3.2     6.7    +      -       +      +
   1395B  ILE*     2.9    48.0    +      -       +      +
   1431B  PHE*     4.2    17.0    -      -       +      -
   1434B  ILE*     4.0     9.2    -      -       +      -
   1435B  LYS*     4.1    17.0    -      -       +      -
   1438B  ILE*     3.7    20.0    -      -       +      -
   1449B  LEU*     4.0    13.9    -      -       +      -
   1453B  VAL*     3.8    29.2    -      -       +      -
   1481B  PHE*     4.2    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP1392 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1388B  ASN*     2.8    33.0    +      -       -      +
   1389B  ALA*     4.0     4.8    -      -       -      +
   1391B  ILE*     1.3    77.0    -      -       -      +
   1393B  THR*     1.3    55.3    +      -       -      +
   1395B  ILE*     3.8     7.7    -      -       -      +
   1396B  ASN*     2.8    50.2    +      -       -      +
   1435B  LYS*     2.5    36.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR1393 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1389B  ALA      2.7    21.5    +      -       -      -
   1390B  ILE      3.5     8.7    -      -       -      -
   1391B  ILE      3.3     0.2    -      -       -      -
   1392B  ASP*     1.3    72.2    -      -       -      +
   1394B  VAL*     1.3    62.9    +      -       -      -
   1396B  ASN*     3.9     4.4    -      -       -      +
   1397B  TYR*     3.0    25.8    +      -       +      +
   1480B  VAL*     4.4     7.2    -      -       +      -
   1484B  ALA*     3.9    21.1    -      -       +      -
   1488B  ILE*     3.6    13.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1394 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1390B  ILE      3.4    14.4    -      -       -      +
   1391B  ILE*     3.2    11.3    +      -       +      +
   1393B  THR*     1.3    74.4    -      -       -      +
   1395B  ILE*     1.3    64.5    +      -       -      +
   1397B  TYR*     3.3    15.6    +      -       -      +
   1406B  SER*     4.0     2.1    -      -       -      -
   1431B  PHE*     3.7    32.1    -      -       +      -
   1453B  VAL*     5.6     1.3    -      -       +      -
   1477B  LEU*     3.8    32.3    -      -       +      +
   1480B  VAL*     3.9    10.5    -      -       +      +
   1481B  PHE*     3.6    43.3    -      -       +      +
   1484B  ALA*     4.9     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE1395 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1391B  ILE*     2.9    38.0    +      -       +      +
   1392B  ASP*     3.9     8.1    -      -       -      +
   1394B  VAL*     1.3    76.4    -      -       -      +
   1396B  ASN*     1.3    66.5    +      -       -      +
   1397B  TYR      3.5     0.2    +      -       -      -
   1404B  GLN*     3.1    21.6    -      -       -      +
   1406B  SER*     2.5    29.8    +      -       -      +
   1410B  ILE*     3.9    17.3    -      -       +      -
   1431B  PHE*     4.0    31.0    -      -       +      -
   1435B  LYS*     4.3    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN1396 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1392B  ASP*     2.8    36.3    +      -       -      +
   1393B  THR*     4.2     3.8    -      -       -      +
   1395B  ILE*     1.3    83.0    -      -       -      +
   1397B  TYR*     1.3    66.1    +      -       -      +
   1398B  LYS*     3.3    14.6    +      -       -      +
   1404B  GLN*     4.3    10.5    -      -       -      +
   1469C  GLN*     5.7     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR1397 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1393B  THR*     3.0    19.4    +      -       +      +
   1394B  VAL      3.5    11.1    -      -       -      +
   1395B  ILE      3.3     2.5    -      -       -      +
   1396B  ASN*     1.3    78.9    -      -       -      +
   1398B  LYS*     1.3    81.4    +      -       -      +
   1399B  ASP*     3.9    10.3    -      -       -      +
   1404B  GLN*     3.3    20.1    -      -       -      +
   1405B  LEU*     3.4    38.8    +      -       +      -
   1476B  VAL*     4.0    11.8    -      -       +      +
   1477B  LEU*     4.8     2.5    -      -       +      -
   1480B  VAL*     3.8    35.4    -      -       +      -
----------------------------------------------------------
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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