Contacts of the strand formed by residues 59 - 63 (chain A) in PDB entry 3HPD


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 ALA 59 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  LEU      3.6     2.0    +      -       -      -
     18A  VAL*     4.6     6.7    -      -       +      -
     19A  HIS*     2.9    29.2    +      -       -      +
     57A  ALA*     3.5     2.8    -      -       -      +
     58A  ASP*     1.3    82.8    -      -       -      +
     60A  VAL*     1.3    65.7    +      -       -      +
     87A  LYS*     4.9     1.1    -      -       -      +
     88A  PRO*     3.5    22.7    -      -       +      +
     90A  VAL*     5.9     0.2    -      -       +      -
    202A  GLY*     3.2    33.4    -      -       -      +
    205A  VAL*     4.0     3.6    -      -       +      -
    206A  ALA*     4.2     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  HIS*     3.3    16.4    -      -       +      +
     21A  ILE*     4.5    15.0    -      -       +      -
     54A  ILE*     3.9    33.7    -      -       +      -
     57A  ALA*     5.0     1.6    -      -       +      -
     59A  ALA*     1.3    79.8    -      -       -      +
     61A  VAL*     1.3    66.6    +      -       -      +
     62A  ILE*     4.2    23.1    -      -       +      -
     78A  ALA*     4.8     6.1    -      -       +      +
     82A  ALA*     4.1    11.2    -      -       +      -
     87A  LYS*     4.6     3.4    -      -       +      -
     88A  PRO      2.9    12.2    +      -       -      +
     89A  ILE*     3.3    11.3    -      -       +      +
     90A  VAL*     2.8    27.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  VAL*     3.6    25.4    -      -       +      -
     19A  HIS      2.7    10.2    +      -       -      +
     20A  ASN*     3.4    20.7    -      -       +      +
     21A  ILE*     2.9    27.5    +      -       -      +
     22A  THR*     5.3     1.1    -      -       -      -
     60A  VAL*     1.3    76.8    -      -       -      +
     62A  ILE*     1.3    69.7    +      -       -      +
     63A  ASN*     5.0     6.7    -      -       +      +
     90A  VAL*     3.4    10.8    -      -       +      +
    195A  CYS      5.6     0.2    -      -       -      +
    198A  ALA*     3.8    36.1    -      -       +      +
    199A  ALA*     4.1     9.4    -      -       +      -
    202A  GLY*     3.8    11.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  ILE*     3.5    11.4    -      -       +      -
     60A  VAL*     4.2    14.6    -      -       +      -
     61A  VAL*     1.3    77.0    -      -       -      +
     63A  ASN*     1.3    63.9    +      -       -      +
     64A  ILE*     4.2     1.3    -      -       +      -
     75A  MET*     3.7    43.3    -      -       +      +
     78A  ALA*     4.8     1.3    -      -       +      -
     79A  THR*     3.1    31.9    -      -       -      +
     89A  ILE*     4.0    18.8    -      -       +      -
     90A  VAL      2.8    12.9    +      -       -      +
     91A  LEU*     3.5    19.5    -      -       +      +
     92A  ASP*     2.9    27.7    +      -       -      +
    109A  ILE*     4.0    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  ILE      3.0     6.3    +      -       -      -
     22A  THR*     3.2    34.0    +      -       -      +
     23A  ASN*     2.8    25.2    +      -       -      +
     30A  THR*     5.8     0.2    -      -       -      +
     61A  VAL*     4.1     6.7    -      -       +      +
     62A  ILE*     1.3    74.9    -      -       -      +
     64A  ILE*     1.3    58.9    +      -       -      +
     65A  GLY      2.9    11.6    +      -       -      -
     66A  THR      5.0     0.2    +      -       -      -
     75A  MET*     3.3    15.6    -      -       -      +
     92A  ASP*     3.7    11.8    -      -       +      +
     94A  VAL*     3.3    11.1    -      -       -      +
    195A  CYS*     3.0    42.8    +      -       -      +
    198A  ALA*     5.4     1.0    -      -       -      +
----------------------------------------------------------
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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