Contacts of the strand formed by residues 26 - 35 (chain B) in PDB entry 4HXG


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 LEU 26 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  THR*     2.9    23.8    +      -       -      -
     23B  ARG      2.9    18.8    +      -       -      +
     24B  LYS*     5.7     1.1    -      -       +      -
     25B  ASN*     1.3    85.8    -      -       +      +
     27B  VAL*     1.3    62.3    +      -       -      +
     47B  ILE*     4.4    12.8    -      -       +      -
     48B  GLU      3.6    10.3    -      -       -      +
     49B  ASN*     4.2    18.2    -      -       +      +
     56B  LYS*     6.5     0.4    -      -       +      -
     66B  ILE*     4.4    13.2    -      -       +      -
     70B  GLY*     4.4     8.1    -      -       -      +
     92B  LEU*     3.6    42.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 27 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  ARG      3.4     8.3    -      -       -      +
     22B  THR*     4.1     3.6    -      -       -      +
     26B  LEU*     1.3    79.4    -      -       -      +
     28B  ALA*     1.3    67.1    +      -       -      +
     29B  TYR*     4.2     7.0    -      -       +      -
     46B  VAL      3.8     0.7    -      -       -      +
     47B  ILE*     3.3     5.3    -      -       -      +
     48B  GLU*     2.8    41.3    +      -       +      +
     50B  LEU*     3.8    24.7    -      -       +      -
     66B  ILE*     4.8     0.2    -      -       -      -
    313B  ILE*     3.7    39.7    -      -       +      -
    325B  LEU*     3.5    29.8    -      -       +      -
    335B  LEU*     4.9     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 28 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  ASP      3.8     1.3    -      -       -      +
     20B  PRO*     3.4     0.7    -      -       -      +
     21B  ARG*     2.7    43.6    +      -       +      +
     27B  VAL*     1.3    76.8    -      -       -      +
     29B  TYR*     1.3    65.6    +      -       -      +
     45B  ILE*     4.8     0.4    -      -       +      -
     46B  VAL      3.3     7.9    -      -       -      +
     47B  ILE*     4.1    15.0    -      -       +      -
     64B  PRO*     4.4    19.5    -      -       +      -
     66B  ILE*     4.0    22.6    -      -       +      +
     73B  ILE*     4.6     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 29 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  LEU*     4.0    22.2    -      -       +      -
     18B  SER      3.7    13.2    -      -       -      +
     19B  ASP      3.8     5.2    -      -       -      -
     20B  PRO*     4.2    11.4    -      -       +      -
     27B  VAL*     4.2     3.8    -      -       +      -
     28B  ALA*     1.3    79.1    -      -       -      +
     30B  VAL*     1.3    74.7    +      -       -      +
     31B  LEU*     4.9     0.7    -      -       +      -
     45B  ILE*     3.4     8.8    -      -       -      +
     46B  VAL*     3.0    56.0    +      -       +      +
     48B  GLU*     2.7    31.4    +      -       +      -
     64B  PRO*     4.5     2.2    -      -       -      +
    315B  LEU*     5.6     3.1    -      -       +      -
    325B  LEU*     3.9    26.2    -      -       +      -
    336B  THR*     4.0     4.0    -      -       +      +
    338B  TYR*     2.7    42.9    +      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 30 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  TYR      3.3     2.4    -      -       -      +
     17B  LEU*     3.2     6.8    -      -       -      -
     18B  SER*     2.9    47.7    +      -       -      +
     19B  ASP*     4.1     7.9    -      -       +      -
     29B  TYR*     1.3    82.8    -      -       -      +
     31B  LEU*     1.3    61.0    +      -       -      +
     32B  THR*     3.8    16.6    -      -       -      +
     43B  ASN*     4.2    18.6    -      -       +      +
     44B  THR      3.7     7.2    -      -       -      +
     45B  ILE*     5.0     1.3    -      -       +      +
     61B  ALA      4.3     3.4    -      -       -      +
     62B  SER*     4.3    12.1    -      -       -      -
     63B  MET      4.5     5.2    -      -       -      +
     64B  PRO*     3.6    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 31 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  ALA*     3.5    33.0    -      -       +      -
     16B  TYR      3.7     1.6    -      -       -      -
     17B  LEU*     3.7    17.3    -      -       +      -
     29B  TYR*     4.1     2.7    +      -       +      -
     30B  VAL*     1.3    72.4    -      -       -      +
     32B  THR*     1.3    67.0    +      -       -      +
     33B  LYS*     4.3    12.0    +      -       +      +
     42B  GLU      3.6     1.2    -      -       -      +
     43B  ASN*     3.6     1.0    -      -       -      -
     44B  THR*     2.7    54.4    +      -       +      +
     46B  VAL*     4.1    18.8    -      -       +      -
     57B  PHE*     5.9     2.9    -      -       +      -
    338B  TYR*     4.2    20.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 32 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  TYR*     2.7    55.1    +      -       +      +
     18B  SER*     4.5     5.2    +      -       -      -
     30B  VAL*     3.8    10.2    +      -       -      +
     31B  LEU*     1.3    75.1    -      -       -      +
     33B  LYS*     1.3    75.5    +      -       -      +
     41B  TYR*     4.2    19.5    -      -       +      -
     42B  GLU      3.2     7.2    -      -       -      +
     43B  ASN*     2.5    27.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 33 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  THR      4.2    15.4    +      -       -      -
     13B  LYS*     4.6     6.6    +      -       -      +
     14B  PHE      3.2    28.0    -      -       -      +
     15B  ALA*     3.7    15.7    -      -       +      +
     16B  TYR*     5.4     0.7    -      -       -      -
     31B  LEU*     4.3    12.3    -      -       +      -
     32B  THR*     1.3    87.6    -      -       -      +
     34B  ALA*     1.3    61.9    +      -       -      +
     35B  ASN*     3.7     1.6    +      -       +      +
     41B  TYR*     3.6     5.0    -      -       -      -
     42B  GLU*     3.0    49.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 34 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  PHE*     4.4    12.6    -      -       +      +
     12B  THR*     3.5    42.7    +      -       +      +
     14B  PHE      5.0     2.6    +      -       -      -
     16B  TYR*     5.2     7.1    -      -       +      -
     33B  LYS*     1.3    77.1    -      -       -      +
     35B  ASN*     1.3    60.5    -      -       -      +
     36B  LEU      3.6     1.0    +      -       -      -
     40B  LYS      4.2     0.2    -      -       -      -
     41B  TYR*     3.7    27.6    -      -       +      -
    586B  PRO*     4.1    10.3    -      -       +      -
    589B  ARG*     5.1     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 35 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  LYS*     3.7     1.8    +      -       +      -
     34B  ALA*     1.3    70.6    -      -       -      +
     36B  LEU*     1.3    58.3    +      -       -      +
     37B  GLU*     2.8    26.7    +      -       -      +
     38B  SER*     2.8    29.4    +      -       -      +
     39B  ASN*     3.0    25.3    +      -       -      -
     40B  LYS      3.0    16.9    +      -       -      +
     42B  GLU*     2.9    33.8    +      -       -      +
    586B  PRO*     3.6     4.4    -      -       -      +
----------------------------------------------------------
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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