Contacts of the strand formed by residues 987 - 996 (chain C) in PDB entry 5X22


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 ILE 987 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    675C  ALA*     4.2     0.9    -      -       +      -
    676C  ILE      3.3    21.8    -      -       -      +
    677C  MET*     3.9    26.7    -      -       +      -
    971C  LYS*     4.0     2.2    -      -       -      -
    972C  VAL      3.0    30.1    +      -       -      +
    974C  LEU*     4.1    23.6    -      -       +      -
    983C  ILE*     3.8    23.1    -      -       +      -
    985C  GLY      3.7     6.7    -      -       -      +
    986C  PRO*     1.3    76.6    -      -       -      +
    988C  VAL*     1.3    74.3    +      -       -      +
    989C  VAL*     3.3     5.9    +      -       -      +
    946D  GLY*     3.7    38.6    -      -       -      +
    947D  ILE      4.2     2.2    -      -       -      +
    948D  THR*     4.1     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 988 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    675C  ALA*     3.4     2.6    -      -       -      -
    676C  ILE*     2.9    49.5    +      -       +      +
    885C  ILE*     5.5     0.7    -      -       +      -
    888C  THR*     4.0    14.6    -      -       +      -
    889C  HIS*     3.9    21.1    -      -       +      -
    970C  GLY      3.5     8.1    -      -       -      +
    971C  LYS*     3.7    17.0    -      -       +      -
    987C  ILE*     1.3    69.7    -      -       -      +
    989C  VAL*     1.3    60.6    +      -       -      +
    948D  THR*     3.0    20.9    +      -       +      +
    949D  ILE      3.3    27.4    -      -       -      +
    950D  GLY*     3.6    11.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 989 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    673C  LEU*     3.9    13.5    -      -       +      -
    674C  VAL      3.2    12.6    -      -       -      +
    675C  ALA*     3.9    13.0    -      -       +      -
    861C  LEU*     4.5    11.2    -      -       +      -
    867C  VAL*     3.9    19.7    -      -       +      -
    888C  THR*     3.8     8.8    -      -       -      +
    889C  HIS*     5.5     0.5    +      -       -      -
    892C  LEU*     3.5    28.5    -      -       +      +
    970C  GLY      3.5     6.2    +      -       -      +
    972C  VAL*     3.6    21.5    -      -       +      -
    974C  LEU*     4.1    16.4    -      -       +      -
    987C  ILE      3.3    13.3    +      -       -      +
    988C  VAL*     1.3    81.5    -      -       -      +
    990C  GLY*     1.3    61.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 990 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    673C  LEU*     3.6    13.9    -      -       -      -
    674C  VAL*     2.9    36.2    +      -       -      +
    888C  THR*     3.6    18.4    -      -       -      +
    892C  LEU*     4.0    10.3    -      -       -      -
    989C  VAL*     1.3    78.6    -      -       -      +
    991C  GLN*     1.3    63.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 991 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    578C  VAL*     3.6    31.8    -      -       +      +
    579C  VAL*     6.0     0.2    -      -       -      +
    671C  ASN*     4.6    13.6    +      -       +      +
    672C  VAL      3.3    14.8    -      -       -      +
    673C  LEU*     4.1     3.3    -      -       +      +
    887C  GLU*     3.5    21.8    -      -       -      +
    888C  THR*     3.8     2.6    -      -       -      -
    891C  GLY*     3.6    30.2    -      -       -      +
    892C  LEU*     3.9     0.6    -      -       -      +
    894C  GLY      3.8     4.3    -      -       -      +
    895C  TYR*     3.6    45.4    +      -       +      +
    990C  GLY*     1.3    72.9    -      -       -      -
    992C  MET*     1.3    60.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 992 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    578C  VAL*     6.4     0.2    -      -       -      -
    671C  ASN*     3.5     5.0    -      -       -      -
    672C  VAL*     2.9    34.1    +      -       -      +
    674C  VAL*     3.9    22.0    -      -       +      -
    676C  ILE*     5.3     6.5    -      -       +      -
    841C  ASN*     3.5    22.2    -      -       +      +
    871C  LEU*     3.7    30.5    -      -       +      -
    884C  GLN*     3.6    24.0    -      -       +      +
    887C  GLU*     3.6    15.5    -      -       -      +
    888C  THR*     3.2    25.8    -      -       -      +
    990C  GLY      3.6     0.8    +      -       -      -
    991C  GLN*     1.3    75.6    -      -       -      +
    993C  PHE*     1.3    66.6    +      -       -      +
    994C  ILE*     3.9    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 993 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    575C  GLN      3.3    21.3    -      -       -      -
    577C  PRO*     3.6    26.9    -      -       +      -
    578C  VAL      5.0     0.7    -      -       -      +
    668C  LEU*     3.5    20.0    -      -       +      -
    669C  GLY*     3.2    35.7    -      -       -      -
    670C  GLN      3.4    11.9    -      -       -      -
    671C  ASN*     3.4    19.7    +      -       -      +
    841C  ASN*     3.6    23.0    -      -       -      +
    842C  ARG*     3.3    40.0    +      -       +      +
    887C  GLU*     2.8    20.3    +      -       -      +
    992C  MET*     1.3    70.7    -      -       -      +
    994C  ILE*     1.3    59.7    +      -       -      +
    995C  MET*     3.9    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 994 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    669C  GLY*     4.3     0.4    -      -       -      -
    670C  GLN      2.9    31.8    +      -       -      -
    672C  VAL*     3.8    20.9    -      -       +      -
    674C  VAL*     4.1    14.8    -      -       +      -
    688C  ILE*     5.9     3.1    -      -       +      -
    700C  TYR*     3.0    25.6    +      -       +      +
    839C  LEU*     3.8    29.4    -      -       +      -
    840C  ALA      3.7    13.0    -      -       -      +
    841C  ASN*     4.5     4.0    -      -       +      -
    869C  VAL*     4.5    15.3    -      -       +      -
    871C  LEU*     4.8     7.6    -      -       +      -
    992C  MET*     3.7    21.1    +      -       +      -
    993C  PHE*     1.3    79.3    -      -       -      +
    995C  MET*     1.3    65.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 995 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    564C  MET*     4.5     7.2    -      -       +      +
    565C  GLN*     3.9    33.0    -      -       +      +
    568C  ALA*     3.9    16.2    -      -       +      -
    668C  LEU*     3.4    45.3    -      -       -      +
    669C  GLY*     4.1     0.9    -      -       -      -
    700C  TYR*     4.2     0.2    -      -       -      -
    839C  LEU*     3.3     9.1    -      -       -      +
    840C  ALA*     2.9    54.7    +      -       +      +
    841C  ASN*     3.6    22.7    -      -       -      +
    842C  ARG*     4.2     3.4    -      -       +      +
    993C  PHE*     3.9    15.3    -      -       +      -
    994C  ILE*     1.3    77.5    -      -       -      +
    996C  LYS*     1.3    60.3    -      -       -      +
    997C  LEU*     3.8     4.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 996 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    568C  ALA*     3.7     0.9    -      -       -      -
    569C  VAL*     2.9    31.7    +      -       +      +
    571C  LEU*     4.5    12.2    -      -       +      +
    668C  LEU      4.6     2.4    +      -       -      -
    700C  TYR*     3.4    40.8    +      -       +      -
    702C  SER*     3.1    25.5    +      -       -      +
    831C  ARG*     3.8    10.7    +      -       -      +
    832C  LYS      3.9     9.0    +      -       -      -
    833C  LEU*     4.1    16.6    -      -       +      -
    837C  ASP*     4.0     8.9    +      -       +      +
    838C  LYS      3.8     9.2    -      -       -      +
    839C  LEU*     3.7    18.4    -      -       +      +
    995C  MET*     1.3    72.7    -      -       -      +
    997C  LEU*     1.3    76.1    +      -       -      +
   1000C  MET*     4.2    21.9    -      -       +      -
----------------------------------------------------------
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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