Contacts of the strand formed by residues 668 - 675 (chain M) in PDB entry 2W4G


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 HIS 668 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121M  LEU*     6.2     0.4    -      -       -      +
    165M  PHE*     4.5    21.7    -      +       -      -
    169M  ASP*     4.7     5.5    +      -       -      -
    171M  GLU*     4.2    16.6    +      -       -      +
    172M  ASN      2.7    15.4    +      -       -      +
    173M  GLN*     2.6    27.8    +      -       -      +
    174M  SER      3.2    16.3    +      -       -      -
    494M  HIS*     3.6    20.5    +      +       -      -
    498M  LEU*     5.3     3.6    -      -       -      +
    667M  THR*     1.3    69.1    -      -       -      +
    669M  PRO*     1.3    85.9    +      -       +      +
    670M  HIS*     3.3    25.2    +      +       -      -
----------------------------------------------------------
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Residues in contact with PRO 669 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121M  LEU*     5.5     2.1    -      -       -      +
    174M  SER*     3.1    11.2    -      -       -      +
    176M  LEU*     4.5     1.6    -      -       +      -
    490M  PHE*     3.5    36.8    -      -       +      -
    494M  HIS*     3.6    37.3    +      -       +      +
    667M  THR      3.1    13.4    -      -       -      +
    668M  HIS*     1.3   105.4    +      -       +      +
    670M  HIS*     1.3    63.4    +      -       -      +
    671M  PHE*     3.7    19.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 670 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121M  LEU*     6.2     2.2    -      -       -      +
    158M  ILE*     4.5    17.0    +      -       +      +
    161M  ASN*     5.2     3.6    -      -       +      -
    162M  ALA*     4.1    13.8    -      -       +      -
    165M  PHE*     3.9    22.7    -      +       -      -
    173M  GLN*     3.2    34.6    +      -       +      +
    174M  SER*     2.7    18.1    +      -       -      +
    175M  ILE*     2.9    18.7    -      -       +      -
    176M  LEU*     2.7    33.5    +      -       -      +
    668M  HIS*     3.3    41.4    +      +       -      -
    669M  PRO*     1.3    71.3    +      -       -      +
    671M  PHE*     1.3    55.2    +      -       -      +
    672M  VAL*     5.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 671 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121M  LEU*     3.7    19.6    +      -       +      +
    122M  PHE*     3.7    22.0    -      +       +      -
    123M  CYS*     3.5    18.4    +      -       -      +
    158M  ILE*     4.4     4.3    -      -       -      +
    176M  LEU*     3.9    24.7    -      -       +      -
    487M  LEU      4.8     3.1    -      -       -      -
    490M  PHE*     4.1     8.3    -      +       -      -
    491M  PHE*     3.2    57.7    -      +       +      -
    494M  HIS*     4.2    15.5    -      +       -      -
    669M  PRO*     3.7    29.4    -      -       +      -
    670M  HIS*     1.3    71.6    -      -       -      +
    672M  VAL*     1.3    68.5    +      -       -      +
    673M  ARG*     3.9    25.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 672 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123M  CYS*     3.8    16.6    -      -       +      +
    125M  THR*     4.9     2.0    -      -       -      +
    155M  ILE*     4.5    24.2    -      -       +      -
    158M  ILE*     4.2    20.6    -      -       +      -
    175M  ILE*     3.8    22.7    -      -       +      -
    176M  LEU      2.8    21.5    +      -       -      +
    177M  ILE*     3.7    20.6    -      -       +      -
    178M  THR      3.3    13.5    +      -       -      -
    671M  PHE*     1.3    79.1    -      -       -      +
    673M  ARG*     1.3    67.5    +      -       -      +
    674M  CYS*     4.5    13.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 673 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122M  PHE*     3.9    29.5    -      -       +      -
    123M  CYS      3.3    11.6    +      -       -      +
    124M  VAL*     3.4     5.5    -      -       -      -
    125M  THR      3.0    23.7    +      -       -      -
    176M  LEU*     3.0    36.2    +      -       -      +
    178M  THR*     3.6    29.1    +      -       -      +
    484M  ASN*     5.4     2.6    +      -       -      -
    487M  LEU*     5.1    15.8    -      -       -      +
    488M  GLN*     4.6     8.9    +      -       -      +
    491M  PHE*     5.9     1.2    -      -       -      +
    671M  PHE*     3.9    22.0    -      -       -      -
    672M  VAL*     1.3    77.5    +      -       -      +
    674M  CYS*     1.3    63.4    +      -       -      +
    675M  ILE*     3.9     5.3    +      -       +      +
    698M  ASN*     3.2    51.3    +      -       +      +
    700M  VAL*     4.7     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 674 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125M  THR*     3.6     8.5    -      -       +      +
    177M  ILE*     3.5    28.0    -      -       -      -
    178M  THR      2.9    13.5    +      -       -      +
    179M  GLY*     3.7    10.7    -      -       -      -
    183M  ALA*     3.4    31.7    -      -       +      +
    185M  LYS*     4.2     6.7    -      -       +      -
    188M  ASN*     2.9    33.4    -      -       -      +
    672M  VAL*     4.5     7.0    -      -       -      -
    673M  ARG*     1.3    73.9    -      -       -      +
    675M  ILE*     1.3    64.2    +      -       -      +
    694M  GLN*     4.6     2.6    -      -       -      +
    698M  ASN*     4.8     4.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 675 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106M  LEU*     5.4     2.5    -      -       +      -
    124M  VAL*     3.0    34.3    -      -       +      -
    125M  THR      2.5    18.4    +      -       -      +
    126M  VAL*     3.6    22.0    -      -       +      -
    127M  ASN*     3.1    29.3    +      -       -      +
    183M  ALA*     3.9     7.7    +      -       -      +
    673M  ARG*     3.9     9.6    -      -       +      +
    674M  CYS*     1.3    76.5    -      -       -      +
    676M  ILE*     1.3    72.1    +      -       -      +
    677M  PRO*     4.2     0.9    -      -       +      -
    691M  VAL*     4.3    17.5    -      -       +      -
    694M  GLN*     4.1    16.2    -      -       +      +
    695M  LEU*     4.7    11.2    -      -       +      -
    698M  ASN*     3.7    23.6    -      -       -      +
    700M  VAL*     5.7     0.4    -      -       +      -
----------------------------------------------------------
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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