Contacts of the strand formed by residues 27 - 36 (chain A) in PDB entry 2HA6


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 GLY 27 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  LYS*     4.9     0.9    -      -       -      -
     24A  ALA*     2.9    36.9    +      -       -      +
     25A  PRO      3.4     0.6    +      -       -      -
     26A  GLY*     1.3    79.3    -      -       -      +
     28A  PRO*     1.3    74.2    -      -       -      +
    140A  GLN*     3.5     9.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  ARG*     3.7    44.2    -      -       +      +
     22A  LEU      3.2    11.0    -      -       -      +
     23A  LYS*     4.6     1.8    -      -       -      -
     27A  GLY*     1.3    85.9    -      -       -      +
     29A  VAL*     1.3    66.0    +      -       -      +
    104A  PRO*     5.1     0.2    -      -       -      +
    105A  TYR*     3.6    39.2    +      -       +      +
    140A  GLN*     4.0     5.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 29 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  ARG*     3.5     5.7    -      -       -      +
     22A  LEU*     2.8    48.5    +      -       +      +
     24A  ALA*     4.1     6.5    -      -       +      -
     28A  PRO*     1.3    79.5    -      -       -      +
     30A  SER*     1.3    65.2    +      -       -      +
    102A  TRP*     4.3     7.6    -      -       +      -
    103A  THR      3.5    11.0    -      -       -      +
    104A  PRO*     5.2     1.3    -      -       +      -
    105A  TYR*     3.6    10.3    -      -       -      +
    136A  ARG*     3.5    33.2    -      -       +      +
    139A  ALA*     4.4     3.6    -      -       +      -
    140A  GLN*     3.4    36.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  GLN*     4.8     2.3    +      -       -      +
      8A  LEU*     4.3    10.5    -      -       -      +
     20A  ILE      3.7     4.7    -      -       -      -
     29A  VAL*     1.3    74.0    -      -       -      +
     31A  ALA*     1.3    60.2    +      -       -      +
     32A  PHE*     3.9    18.2    -      -       -      -
    101A  VAL      3.8     0.3    -      -       -      +
    102A  TRP*     3.3     5.0    -      -       -      +
    103A  THR*     2.8    45.9    +      -       -      +
    104A  PRO      3.1    14.6    +      -       -      -
    105A  TYR*     3.4    18.1    -      -       -      -
    107A  ARG*     4.2     8.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  GLY*     3.2     4.0    -      -       -      -
     20A  ILE*     2.8    44.6    +      -       +      +
     22A  LEU*     3.4    32.8    -      -       +      -
     30A  SER*     1.3    73.6    -      -       -      +
     32A  PHE*     1.3    63.7    +      -       -      +
     33A  LEU*     3.9    13.2    -      -       +      -
     62A  ALA      3.7     0.3    -      -       -      +
    101A  VAL      3.3     4.7    -      -       -      -
    102A  TRP*     3.9    11.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  LEU*     3.3    32.1    -      -       +      -
     10A  VAL*     3.7    30.3    -      -       +      -
     17A  LEU*     4.4    12.3    -      -       +      -
     18A  ARG      4.3     2.2    -      -       -      -
     19A  GLY*     3.4    18.4    -      -       -      -
     30A  SER*     3.9    24.7    -      -       -      -
     31A  ALA*     1.3    73.4    -      -       -      +
     33A  LEU*     1.3    60.7    +      -       -      +
     35A  ILE*     3.7    24.3    -      -       +      +
     62A  ALA*     3.5     9.4    -      -       +      -
    100A  ASN*     3.4     3.6    -      -       -      -
    101A  VAL*     2.8    41.4    +      -       +      +
    103A  THR*     4.8     2.0    -      -       +      -
    107A  ARG*     4.3     9.6    -      -       -      -
    190A  PHE*     3.5    28.7    -      +       +      -
----------------------------------------------------------
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Residues in contact with LEU 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  ILE*     4.7     4.3    -      -       +      -
     22A  LEU*     4.9     8.1    -      -       +      -
     31A  ALA*     4.0    19.7    -      -       +      -
     32A  PHE*     1.3    77.0    -      -       -      +
     34A  GLY*     1.3    62.5    +      -       -      +
     35A  ILE      3.5     0.2    -      -       -      -
     61A  ASP      4.5     0.5    -      -       -      +
     62A  ALA*     2.8    35.3    +      -       -      +
     63A  THR      4.0    17.3    -      -       -      +
     64A  THR*     3.3    19.6    -      -       -      +
     65A  PHE*     3.7    44.2    -      -       +      +
    100A  ASN*     3.5    18.6    -      -       +      +
    101A  VAL      4.8     0.4    -      -       -      +
    102A  TRP*     3.9    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  LEU*     1.3    75.1    -      -       -      +
     35A  ILE*     1.3    64.8    +      -       -      +
     36A  PRO*     3.4     9.0    -      -       -      +
     60A  LEU*     4.0     8.2    -      -       -      +
     61A  ASP      4.9     1.2    -      -       -      +
     64A  THR      3.8     3.8    +      -       -      -
     65A  PHE*     4.6     0.6    -      -       -      +
     66A  GLN*     3.7    30.7    -      -       -      +
     98A  TYR*     3.4    14.4    -      -       -      -
     99A  LEU      3.3     2.6    +      -       -      -
    100A  ASN*     3.1    15.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  LEU*     3.8    34.1    -      -       +      -
     32A  PHE*     3.7    39.0    -      -       +      +
     34A  GLY*     1.3    73.3    -      -       -      +
     36A  PRO*     1.3    79.5    -      -       +      +
     37A  PHE      3.4     0.2    +      -       -      -
     56A  TRP*     4.6     6.7    -      -       +      -
     60A  LEU*     4.6     1.6    -      -       -      -
     62A  ALA*     4.4     2.2    -      -       +      -
     98A  TYR*     3.2     1.3    -      -       -      -
     99A  LEU*     2.7    60.2    +      -       +      +
    101A  VAL*     4.2     5.2    -      -       +      -
    182A  TRP*     3.8    32.1    -      -       +      +
    190A  PHE*     4.3     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  GLY      3.4     9.2    -      -       -      +
     35A  ILE*     1.3    93.8    -      -       +      +
     37A  PHE*     1.3    59.8    +      -       -      +
     38A  ALA      3.7     3.6    -      -       -      +
     53A  LYS*     3.9    33.7    -      -       +      +
     56A  TRP*     3.9    23.8    -      -       +      -
     60A  LEU*     3.8    26.7    -      -       +      -
     97A  LEU      3.7     2.2    -      -       -      +
     98A  TYR*     3.3    28.9    -      -       +      -
    182A  TRP*     4.4     4.7    +      -       -      -
----------------------------------------------------------
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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