Contacts of the strand formed by residues 192 - 199 (chain D) in PDB entry 4CQM


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 192 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200C  LEU*     5.5     0.8    -      -       -      +
    139D  ALA*     4.1     7.2    -      -       -      +
    142D  LEU*     3.7    35.4    -      -       +      -
    143D  VAL*     4.0    22.2    -      -       +      -
    147D  CYS      4.4     6.1    -      -       -      +
    149D  GLY      3.3    13.0    -      -       -      +
    151D  ILE*     3.8    33.9    -      -       +      -
    184D  ALA      4.7     1.2    -      -       -      +
    187D  LEU*     2.8    44.6    +      -       +      +
    188D  GLY*     3.9     4.2    +      -       -      -
    190D  HIS*     3.9    12.6    -      -       +      +
    191D  GLY*     1.3    82.8    -      -       -      +
    193D  ARG*     1.3    65.1    +      -       -      +
    194D  CYS*     3.9     2.2    +      -       -      -
    249D  THR*     4.4     2.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 193 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200C  LEU*     4.5    10.8    -      -       +      -
    149D  GLY      2.9    13.6    +      -       -      +
    150D  SER*     3.4    16.0    +      -       -      +
    151D  ILE*     2.5    35.5    +      -       -      +
    191D  GLY      5.3     2.7    -      -       -      +
    192D  ILE*     1.3    74.7    -      -       -      +
    194D  CYS*     1.3    56.7    +      -       -      +
    195D  ASN*     4.2     6.0    -      -       -      +
    240D  LEU      3.1    16.5    +      -       -      -
    241D  ALA      4.2     1.4    +      -       -      -
    242D  SER      2.8    26.7    +      -       -      -
    243D  GLU*     4.6     2.8    -      -       -      +
    245D  SER*     2.7    35.5    +      -       -      -
    246D  GLY*     3.3    30.6    +      -       -      +
    248D  ILE      3.4    25.7    +      -       -      +
    249D  THR*     3.5    12.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 194 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135D  THR*     5.2     0.2    -      -       -      -
    151D  ILE*     3.3    21.3    -      -       +      +
    153D  ASN*     5.6     0.4    -      -       -      +
    180D  THR*     3.6    26.6    -      -       +      +
    183D  ALA*     3.8    14.4    -      -       +      -
    184D  ALA*     3.6    10.8    -      -       -      +
    187D  LEU*     3.6    31.6    -      -       -      -
    192D  ILE*     3.9     3.6    +      -       -      -
    193D  ARG*     1.3    76.9    -      -       -      +
    195D  ASN*     1.3    57.6    +      -       -      +
    249D  THR*     3.0     7.7    +      -       -      -
    250D  GLY*     2.6    35.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 195 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150D  SER*     5.1     1.8    +      -       -      -
    151D  ILE      2.9    10.8    +      -       -      +
    152D  ILE*     3.5     3.0    -      -       -      +
    153D  ASN      3.0    24.1    +      -       -      -
    180D  THR*     3.5    10.1    -      -       -      +
    193D  ARG*     4.2     9.7    +      -       -      +
    194D  CYS*     1.3    78.9    -      -       -      +
    196D  SER*     1.3    61.4    +      -       -      +
    197D  VAL      4.3     0.2    +      -       -      -
    240D  LEU*     3.9    30.3    -      -       +      +
    248D  ILE*     2.8    30.0    +      -       -      +
    249D  THR*     3.2    13.0    +      -       -      +
    251D  THR*     2.8    40.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 196 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153D  ASN*     3.2     6.3    +      -       -      +
    155D  SER*     3.8    17.5    +      -       -      -
    177D  ILE*     3.8    11.8    -      -       -      +
    180D  THR*     3.1    31.1    +      -       -      +
    195D  ASN*     1.3    74.8    -      -       -      +
    197D  VAL*     1.3    62.5    +      -       -      +
    198D  LEU*     4.0     4.0    -      -       -      -
    251D  THR      3.1     6.8    +      -       -      +
    252D  SER*     3.2    19.0    -      -       -      -
    253D  VAL*     2.9    27.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 197 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152D  ILE*     3.8    17.0    -      -       +      -
    153D  ASN      2.8     9.3    +      -       -      -
    154D  ILE*     3.6    15.2    -      -       +      -
    155D  SER*     2.6    31.9    +      -       -      +
    196D  SER*     1.3    72.6    -      -       -      +
    198D  LEU*     1.3    62.5    +      -       -      +
    199D  PRO*     3.1    21.3    -      -       +      +
    233D  VAL*     4.0    12.8    -      -       +      -
    236D  VAL*     3.9    14.8    -      -       +      -
    237D  VAL*     4.4     5.2    -      -       +      -
    240D  LEU*     3.7    28.3    -      -       +      -
    253D  VAL      3.7     9.2    -      -       -      +
    255D  VAL*     4.0    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 198 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155D  SER*     3.8    14.1    -      -       -      +
    156D  OAS      3.5    26.0    -      -       -      +
    157D  ILE*     4.3     4.7    -      -       -      +
    160D  LYS*     4.3    18.8    -      -       +      -
    177D  ILE*     4.0    16.8    -      -       +      -
    196D  SER*     4.0     8.7    -      -       -      +
    197D  VAL*     1.3    80.5    -      -       -      +
    199D  PRO*     1.3    65.3    -      -       -      +
    252D  SER*     3.6    31.2    -      -       -      +
    253D  VAL      3.0     9.1    +      -       -      -
    254D  GLU*     3.3    29.3    -      -       +      +
    255D  VAL*     3.0    21.5    +      -       -      -
    256D  THR*     3.4     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 199 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23D  ILE*     4.4     6.7    -      -       +      -
    154D  ILE*     3.9    18.8    -      -       +      -
    155D  SER      3.2    17.9    -      -       -      -
    156D  OAS      3.5     7.0    -      -       -      +
    157D  ILE      3.2    20.6    +      -       -      -
    197D  VAL*     3.1    21.8    -      -       +      +
    198D  LEU*     1.3    85.3    -      -       -      +
    200D  GLY*     1.3    69.0    +      -       -      +
    202D  ILE*     4.0     4.7    -      -       +      -
    233D  VAL*     3.9    27.1    -      -       +      -
    255D  VAL*     3.2     9.9    -      -       +      +
    256D  THR*     3.9     0.7    -      -       -      -
----------------------------------------------------------
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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