Contacts of the strand formed by residues 312 - 317 (chain B) in PDB entry 1HDZ


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 ARG 312 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315A  LYS*     3.7    10.8    -      -       -      -
    255B  LYS*     5.1     5.9    -      -       -      +
    279B  LEU*     3.6    27.9    +      -       +      +
    280B  LEU*     3.9    16.6    +      -       -      +
    282B  CYS*     2.9    42.1    +      -       -      -
    283B  HIS      3.8     9.6    -      -       -      +
    284B  GLU*     3.4    28.6    +      -       -      +
    287B  GLY      3.1    17.0    -      -       -      +
    307B  LEU*     2.8    78.8    +      -       -      +
    308B  LEU*     3.3    19.8    +      -       +      +
    311B  GLY*     1.3    78.8    -      -       -      +
    313B  THR*     1.3    61.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 313 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    313A  THR*     3.8    26.7    -      -       +      -
    314A  TRP      3.6     3.8    -      -       -      -
    315A  LYS*     3.4    24.8    +      -       -      +
    279B  LEU*     4.8     1.3    -      -       -      +
    287B  GLY      3.2     4.8    +      -       -      +
    288B  THR*     3.4    29.0    +      -       +      +
    289B  SER*     2.9    27.4    +      -       -      -
    308B  LEU*     4.9     0.4    -      -       -      -
    311B  GLY      4.5     3.6    +      -       -      -
    312B  ARG*     1.3    76.0    -      -       -      +
    314B  TRP*     1.3    60.9    +      -       -      +
    315B  LYS*     4.3    12.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 314 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303A  ILE*     4.1    10.3    -      -       +      -
    305A  PRO*     5.9     0.7    -      -       +      -
    308A  LEU*     3.5    19.5    -      -       +      +
    313A  THR*     3.5     0.5    -      -       -      -
    314A  TRP*     2.7    81.8    +      +       +      +
    275B  MET*     4.7     6.9    +      -       +      -
    279B  LEU*     3.7    37.4    -      -       +      +
    289B  SER*     3.5    33.5    +      -       -      -
    291B  ILE*     3.6    36.3    -      -       +      +
    301B  LEU*     3.9    29.2    -      -       +      -
    303B  ILE*     4.0    14.1    -      -       +      -
    308B  LEU*     3.9    12.1    -      -       +      -
    313B  THR*     1.3    72.2    -      -       -      +
    315B  LYS*     1.3    59.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 315 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    308A  LEU*     4.4     4.3    -      -       -      -
    311A  GLY      5.7     0.2    -      -       -      +
    312A  ARG      3.2    13.9    -      -       -      +
    313A  THR*     3.7    21.1    -      -       -      +
    186B  VAL*     3.0    42.5    +      -       +      +
    187B  ALA*     4.6     4.8    +      -       -      +
    188B  LYS*     5.2     6.9    -      -       -      +
    288B  THR*     3.9    18.5    -      -       +      +
    289B  SER      3.1    10.7    +      -       -      +
    290B  VAL*     3.2    14.6    -      -       +      -
    291B  ILE*     2.9    26.2    +      -       -      +
    313B  THR*     4.3    11.9    -      -       +      +
    314B  TRP*     1.3    75.1    -      -       -      +
    316B  GLY*     1.3    63.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 316 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    308A  LEU      3.0    27.9    +      -       -      -
    309A  LEU*     3.4     7.9    -      -       -      -
    311A  GLY*     3.5    15.9    -      -       -      -
    312A  ARG      3.4     1.4    +      -       -      -
    186B  VAL*     4.2     5.6    -      -       -      +
    290B  VAL*     4.7     0.4    -      -       -      -
    291B  ILE*     3.5    16.4    -      -       -      -
    315B  LYS*     1.3    79.5    -      -       -      +
    317B  ALA*     1.3    63.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 317 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    309A  LEU*     2.9    17.5    +      -       -      +
    311A  GLY*     4.5     4.7    -      -       -      +
    109B  ASN*     5.7     0.9    -      -       -      +
    178B  THR*     5.6     0.5    -      -       -      +
    182B  SER*     5.3     3.9    +      -       -      +
    186B  VAL*     3.4    36.6    -      -       +      -
    290B  VAL*     4.9     2.0    -      -       +      +
    291B  ILE      3.6     8.2    +      -       -      +
    292B  VAL*     4.7     3.3    -      -       +      +
    316B  GLY*     1.3    76.0    -      -       -      +
    318B  VAL*     1.3    65.5    +      -       -      +
    320B  GLY*     4.9     3.0    +      -       -      +
    321B  GLY*     4.3     3.6    -      -       -      +
    377B  NAD      3.1    18.2    +      -       -      -
----------------------------------------------------------
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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