Contacts of the strand formed by residues 392 - 403 (chain G) in PDB entry 2HU4


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 VAL 392 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95G  ASN      5.2     6.1    -      -       -      +
    361G  TRP*     4.6    13.5    -      -       +      -
    376G  MET      4.4     0.4    -      -       -      -
    377G  ILE*     3.4     7.6    -      -       -      +
    378G  TRP*     2.8    44.1    +      -       +      -
    390G  PHE*     3.9     3.1    -      -       -      -
    391G  SER*     1.3    92.3    -      -       -      +
    394G  LYS*     1.3    74.8    +      -       -      +
    395G  GLN*     5.3     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 394 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    364G  ARG*     4.7     4.2    -      -       -      +
    366G  LYS*     4.1     9.4    -      -       -      +
    375G  GLU*     2.8    39.8    +      -       +      +
    376G  MET      3.3     4.9    -      -       -      +
    377G  ILE*     4.3    15.4    -      -       +      +
    390G  PHE*     4.0    26.2    -      -       +      -
    392G  VAL*     1.3    83.8    -      -       -      +
    395G  GLN*     1.3    64.0    +      -       -      +
    396G  ASP*     4.3    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 395 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96G  GLY*     3.7     6.7    -      -       -      -
     97G  TRP*     2.9    67.7    +      -       +      +
    361G  TRP*     4.9     4.3    -      -       +      -
    375G  GLU*     3.3     2.0    -      -       -      -
    376G  MET*     2.8    43.0    +      -       +      +
    392G  VAL*     5.3     3.4    -      -       +      -
    394G  LYS*     1.3    75.5    -      -       -      +
    396G  ASP*     1.3    66.5    +      -       -      +
    397G  ILE*     3.2    13.7    -      -       +      +
    446G  PHE*     5.6     1.4    -      -       -      -
    453G  THR*     3.6     9.7    +      -       -      -
    454G  VAL*     3.5    13.4    -      -       -      +
    455G  GLY*     4.0    16.8    -      -       -      +
    458G  TRP*     5.9     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 396 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366G  LYS*     2.8    29.9    +      -       -      +
    374G  PHE      4.2     3.8    -      -       -      +
    375G  GLU*     4.5     0.4    -      -       -      +
    394G  LYS*     4.3    14.2    -      -       -      +
    395G  GLN*     1.3    74.2    -      -       -      +
    397G  ILE*     1.3    64.3    +      -       -      +
    398G  VAL      5.0     2.0    -      -       -      +
    399G  ALA*     6.5     0.2    -      -       -      -
    454G  VAL      4.6     0.2    -      -       -      +
    455G  GLY*     3.1    12.8    -      -       -      -
    456G  TRP      3.0    39.5    +      -       -      +
    458G  TRP*     4.2     2.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 397 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97G  TRP*     5.3     1.3    -      -       +      -
    374G  PHE*     3.1    29.7    +      -       +      +
    376G  MET*     3.9    17.5    -      -       +      +
    395G  GLN*     3.2    29.6    -      -       +      +
    396G  ASP*     1.3    83.4    -      -       -      +
    398G  VAL*     1.3    81.8    +      -       +      +
    422G  PHE*     3.9    20.6    -      -       +      -
    424G  VAL*     4.5     1.6    -      -       +      -
    444G  ILE*     3.9     7.4    -      -       +      -
    446G  PHE*     3.9    31.2    -      -       +      -
    456G  TRP      3.3     7.2    -      -       -      +
    458G  TRP*     3.2    27.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 398 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366G  LYS*     3.2     7.0    -      -       -      +
    373G  GLY*     4.0     2.2    -      -       -      -
    374G  PHE*     2.9    41.3    +      -       +      +
    396G  ASP*     5.6     2.0    -      -       -      -
    397G  ILE*     1.3    99.7    -      -       +      +
    399G  ALA*     1.3    73.0    +      -       -      +
    402G  ASP*     3.8    26.5    -      -       +      +
    403G  TRP      4.3     7.9    -      -       -      +
    404G  SER*     5.1     1.3    -      -       -      -
    424G  VAL*     5.4     0.2    -      -       +      -
    426G  LEU*     4.6     7.4    -      -       +      -
    444G  ILE*     3.9    16.8    -      -       +      -
    456G  TRP      3.7     1.5    +      -       -      -
    457G  SER*     4.0    10.1    -      -       -      +
    458G  TRP      4.0     7.6    -      -       -      +
    459G  PRO*     4.5     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 399 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366G  LYS*     4.2     6.5    -      -       -      +
    373G  GLY*     3.0    16.0    -      -       -      -
    396G  ASP*     6.5     0.2    -      -       -      -
    398G  VAL*     1.3    74.1    -      -       -      +
    400G  ILE*     1.3    62.8    +      -       -      +
    401G  THR*     3.1    21.1    -      -       +      +
    402G  ASP*     3.1    15.6    +      -       -      +
    457G  SER*     3.2    26.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 400 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366G  LYS*     3.5    43.7    -      -       +      +
    367G  SER*     4.0    22.0    -      -       -      +
    372G  SER*     3.4    18.4    +      -       -      +
    373G  GLY*     4.1     7.4    -      -       -      -
    399G  ALA*     1.3    68.8    -      -       -      +
    401G  THR*     1.3    61.1    +      -       +      +
    402G  ASP      3.1     8.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 401 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    399G  ALA*     3.8    10.6    -      -       +      +
    400G  ILE*     1.3    81.6    -      -       +      +
    402G  ASP*     1.3    73.0    +      -       -      +
    403G  TRP*     4.5     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 402 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372G  SER*     4.5     2.9    -      -       -      -
    373G  GLY*     2.7    32.9    +      -       -      -
    398G  VAL*     3.8    13.7    -      -       +      +
    399G  ALA*     3.1     4.8    +      -       -      +
    400G  ILE      3.1     1.8    -      -       -      -
    401G  THR*     1.3    94.9    +      -       -      +
    403G  TRP*     1.3    61.0    +      -       -      +
    457G  SER*     4.1     7.4    +      -       -      -
    459G  PRO*     3.4    38.9    -      -       +      +
    461G  GLY      5.7     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 403 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    370G  SER*     4.2    12.6    -      -       -      -
    371G  ARG*     3.6    16.2    -      -       +      +
    372G  SER*     3.4    26.9    -      -       -      -
    398G  VAL*     4.3     5.0    -      -       -      +
    401G  THR      5.8     0.4    -      -       -      -
    402G  ASP*     1.3    79.4    +      -       -      +
    404G  SER*     1.3    60.4    -      -       -      +
    426G  LEU*     4.0    16.7    -      -       -      +
    427G  ILE*     3.4    21.8    -      -       +      +
    428G  ARG*     3.7    18.6    -      -       -      -
    432G  LYS*     3.5    48.9    -      -       +      -
    433G  GLU*     3.4    36.8    +      -       +      +
    460G  ASP*     5.1     4.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 404 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365G  THR*     3.7     9.0    -      -       -      +
    371G  ARG*     2.9    27.2    +      -       -      +
    372G  SER      3.6     0.5    +      -       -      -
    373G  GLY*     2.8    34.8    +      -       -      -
    374G  PHE*     4.6     9.6    -      -       -      -
    398G  VAL*     5.1     2.2    -      -       -      -
    402G  ASP      3.5     0.4    +      -       -      -
    403G  TRP*     1.3    73.3    -      -       -      +
    405G  GLY*     1.3    66.2    +      -       -      -
    424G  VAL*     4.6     7.4    -      -       -      -
    425G  GLU      3.0     9.4    -      -       -      -
    426G  LEU*     4.1     7.4    -      -       -      -
    427G  ILE*     3.0    27.5    +      -       -      +
----------------------------------------------------------
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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