Contacts of the strand formed by residues 52 - 62 (chain D) in PDB entry 6H25


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 THR 52 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29D  ARG*     4.6     2.0    -      -       -      +
     48D  LEU*     3.5     4.3    -      -       -      +
     49D  GLN*     2.9    54.0    +      -       +      +
     51D  ASP*     1.3    80.7    -      -       -      +
     53D  SER*     1.3    63.2    +      -       -      +
     54D  VAL*     5.1     0.9    -      -       -      +
    124D  SER      2.4    27.3    +      -       -      -
    125D  ASP*     3.7     1.7    -      -       -      -
    126D  ALA*     3.3    25.5    +      -       -      +
    127D  GLY      4.1    14.9    +      -       -      +
    128D  SER      4.8     0.9    -      -       -      +
    129D  LEU*     4.1    10.9    -      -       -      +
    132D  CYS*     4.0    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 53 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46D  SER*     4.6     3.5    +      -       -      -
     47D  PHE      3.5     6.3    -      -       -      -
     48D  LEU*     3.9    26.0    -      -       -      +
     51D  ASP      4.5     1.3    -      -       -      -
     52D  THR*     1.3    79.5    +      -       -      +
     54D  VAL*     1.3    65.3    +      -       -      +
    122D  VAL*     4.4     0.2    -      -       -      -
    123D  VAL*     3.0    29.1    +      -       -      +
    124D  SER*     2.9    45.9    +      -       -      +
    132D  CYS*     4.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 54 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45D  ALA      3.8     1.6    -      -       -      +
     46D  SER*     3.7     1.5    -      -       -      -
     47D  PHE*     3.0    31.4    +      -       -      -
     52D  THR*     5.1     0.4    -      -       -      +
     53D  SER*     1.3    82.1    +      -       -      +
     55D  LEU*     1.3    67.8    +      -       -      +
    120D  LEU*     4.5    10.5    -      -       +      -
    121D  GLN      4.2     7.0    -      -       -      +
    122D  VAL*     5.0     6.5    -      -       +      -
    129D  LEU*     4.6    12.3    -      -       +      +
    132D  CYS*     3.7    27.3    -      -       +      +
    133D  CYS*     3.7    37.0    -      -       -      -
    136D  ALA*     3.8    19.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 55 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  ARG*     4.7     6.1    -      -       -      +
     85A  MET*     4.2    10.2    -      -       +      +
    139A  LEU*     3.6    31.4    -      -       +      -
     37D  LEU*     5.0     5.6    -      -       +      -
     38D  LEU*     3.8    28.9    -      -       +      -
     44D  SER      5.2     0.4    -      -       -      -
     45D  ALA      3.3    26.0    -      -       -      +
     46D  SER*     3.7    16.4    -      -       -      +
     54D  VAL*     1.3    76.5    -      -       -      +
     56D  ALA*     1.3    66.8    +      -       -      +
    119D  VAL      4.0     0.2    -      -       -      +
    120D  LEU*     3.7     2.6    -      -       -      -
    121D  GLN*     3.2    34.2    +      -       +      +
    123D  VAL*     4.2    17.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 56 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38D  LEU*     5.8     0.4    -      -       -      +
     44D  SER*     3.4     3.6    -      -       -      -
     45D  ALA      2.9    33.0    +      -       -      +
     55D  LEU*     1.3    79.8    -      -       -      +
     57D  GLY*     1.3    58.3    +      -       -      +
     58D  VAL*     5.4     1.8    -      -       +      -
    119D  VAL      3.3     9.4    -      -       -      +
    120D  LEU*     4.3    12.8    -      -       +      -
    136D  ALA*     3.7    37.0    -      -       +      +
    137D  ALA*     4.3     2.9    -      -       -      +
    140D  ALA*     3.9     9.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 57 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  MET*     4.3    22.4    -      -       -      +
     38D  LEU*     5.7     1.1    -      -       -      -
     41D  PRO*     4.7     7.6    -      -       -      -
     43D  GLY      3.4     9.0    -      -       -      -
     44D  SER*     4.7     1.8    -      -       -      -
     56D  ALA*     1.3    72.7    -      -       -      +
     58D  VAL*     1.3    62.0    +      -       -      -
     59D  TYR*     4.3     1.3    -      -       -      -
    119D  VAL*     2.9    41.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 58 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41D  PRO*     4.5     0.6    -      -       -      +
     42D  ASP*     3.3     8.3    +      -       -      +
     43D  GLY      3.1    28.5    +      -       -      +
     56D  ALA      4.4     0.4    +      -       -      -
     57D  GLY*     1.3    79.1    -      -       -      +
     59D  TYR*     1.3    78.0    +      -       -      +
    116D  ILE*     4.1    13.0    -      -       +      -
    117D  THR      3.4     7.0    -      -       -      +
    118D  VAL*     3.8    20.6    -      -       +      -
    140D  ALA*     3.7    30.7    -      -       +      +
    141D  LEU*     3.8    24.5    -      -       +      -
    144D  ALA*     4.3    12.8    -      -       +      +
    146D  VAL*     5.1     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 59 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  GLN*     3.3    21.9    +      -       +      -
     85A  MET*     2.8    27.8    +      -       -      -
     86A  ALA      3.8     0.2    -      -       -      -
     87A  ALA*     3.1    21.5    +      -       -      -
     88A  PRO*     3.3    32.4    -      -       +      +
     40D  ARG*     4.5     3.9    -      -       -      +
     41D  PRO*     3.6    33.4    -      -       +      -
     42D  ASP*     3.4     8.7    -      -       -      +
     57D  GLY      4.3     1.3    -      -       -      -
     58D  VAL*     1.3    87.3    -      -       -      +
     60D  GLY*     1.3    69.3    +      -       -      +
     62D  ALA*     5.4     7.4    -      -       +      -
    115D  SER      5.7     0.2    -      -       -      +
    116D  ILE*     3.4    11.4    -      -       -      +
    117D  THR*     3.0    31.3    +      -       +      +
    119D  VAL*     5.7     1.8    -      -       +      +
    108G  ARG*     5.8     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 60 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42D  ASP*     2.5    27.0    +      -       -      +
     58D  VAL*     5.1     0.7    -      -       -      -
     59D  TYR*     1.3    78.5    -      -       -      +
     61D  PRO*     1.3    76.9    -      -       -      +
     62D  ALA*     3.3     3.8    +      -       -      +
    115D  SER      2.9    18.0    -      -       -      +
    116D  ILE*     3.7     6.4    -      -       -      -
    144D  ALA*     5.4     3.4    -      -       -      -
    146D  VAL*     4.6     9.6    -      -       -      -
    108G  ARG*     4.6     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 61 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60D  GLY*     1.3    82.2    -      -       -      +
     62D  ALA*     1.3    59.7    +      -       -      +
    111D  HIS*     4.5    20.6    -      -       +      +
    114D  THR*     3.2    24.9    -      -       +      +
    115D  SER      4.0     2.0    -      -       -      +
    116D  ILE*     4.4     6.7    -      -       +      -
    144D  ALA      6.1     0.9    -      -       -      +
    145D  GLY      6.4     0.2    -      -       -      -
    146D  VAL*     4.6    13.9    -      -       +      -
    108G  ARG*     3.5    37.1    +      -       +      -
    109G  TYR      5.5     0.6    -      -       -      +
    110G  VAL*     4.5    20.4    -      -       +      -
    135G  GLY      4.4     5.0    -      -       -      +
    136G  SER*     4.5     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 62 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59D  TYR*     5.4     8.1    -      -       +      -
     60D  GLY      4.0     5.2    -      -       -      +
     61D  PRO*     1.3    75.3    -      -       -      +
     63D  GLU*     1.3    62.8    +      -       -      +
    113D  ARG      4.6     0.3    -      -       -      +
    114D  THR*     2.7    20.1    +      -       -      -
    115D  SER*     2.9    29.8    +      -       -      +
    108G  ARG*     4.9    13.5    -      -       -      +
    135G  GLY      4.7     3.1    -      -       -      +
    136G  SER*     4.2    11.1    -      -       -      +
----------------------------------------------------------
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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