Contacts of the strand formed by residues 52 - 63 (chain B) in PDB entry 1Q41


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 GLN 52 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  VAL*     4.2     4.3    -      -       -      -
     42B  ALA      2.7    39.5    +      -       -      +
     44B  PRO*     3.9    15.3    -      -       +      +
     50B  ARG      4.2     6.5    +      -       -      +
     51B  PRO*     1.3    76.9    -      -       -      +
     53B  GLU*     1.3    67.1    +      -       -      +
     54B  VAL*     3.5     6.0    +      -       +      +
    114B  TYR*     3.7    32.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  THR*     4.6    12.3    -      -       +      -
     40B  VAL      3.3     7.2    -      -       -      +
     41B  VAL*     4.2    19.3    -      -       +      +
     52B  GLN*     1.3    78.4    -      -       -      +
     54B  VAL*     1.3    62.8    +      -       -      +
     55B  SER*     5.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  THR      3.8     0.9    -      -       -      +
     39B  THR*     3.4     1.9    -      -       -      +
     40B  VAL*     2.8    47.8    +      -       +      +
     42B  ALA*     4.3     5.8    -      -       +      -
     52B  GLN*     3.7    13.5    -      -       +      +
     53B  GLU*     1.3    80.6    -      -       -      +
     55B  SER*     1.3    66.7    +      -       -      +
     56B  TYR*     4.3     7.9    +      -       +      -
     75B  LEU*     4.0    25.8    -      -       +      -
     77B  ASP*     4.9     5.6    -      -       -      +
    114B  TYR*     3.9    44.2    -      -       +      +
    131B  VAL*     6.3     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 55 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  VAL*     4.2     5.9    -      -       -      +
     38B  THR      3.2     4.5    -      -       -      -
     39B  THR*     2.5    32.2    +      -       -      +
     53B  GLU      5.6     0.2    -      -       -      -
     54B  VAL*     1.3    74.6    -      -       -      +
     56B  TYR*     1.3    64.3    +      -       -      +
     75B  LEU*     3.7     5.7    -      -       -      +
     76B  CYS*     2.9    41.0    +      -       -      +
     77B  ASP*     3.8     8.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 56 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  VAL*     3.7     0.9    -      -       -      -
     38B  THR*     2.8    72.0    +      -       +      +
     40B  VAL*     4.5     5.8    -      -       +      -
     54B  VAL*     4.7    12.1    -      -       +      -
     55B  SER*     1.3    77.8    -      -       -      +
     57B  THR*     1.3    64.7    +      -       -      +
     59B  THR*     3.8    18.6    -      -       -      -
     73B  ALA*     3.9    17.7    -      -       +      -
     74B  LYS      3.1    17.5    -      -       -      +
     75B  LEU*     4.2    10.3    -      -       +      -
     76B  CYS*     3.8     5.6    -      -       -      -
     82B  VAL*     5.7     0.4    -      -       +      -
     84B  ILE*     3.8    23.9    -      -       +      +
    116B  PHE*     3.7    28.9    -      +       -      -
    129B  ASN*     5.5     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 57 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  SER*     3.2    19.4    +      -       -      +
     36B  LYS      2.8    23.0    +      -       -      -
     37B  VAL*     4.3    10.3    -      -       +      +
     56B  TYR*     1.3    79.6    -      -       -      +
     58B  ASP*     1.3    84.1    +      -       -      +
     59B  THR*     3.4     4.9    -      -       -      -
     73B  ALA*     3.5     2.6    -      -       -      +
     74B  LYS*     2.7    53.1    +      -       +      +
     76B  CYS*     4.4    10.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 58 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  SER*     3.5    21.2    +      -       -      -
     36B  LYS      4.5     1.0    +      -       -      -
     57B  THR*     1.3    93.4    +      -       -      +
     59B  THR*     1.3    65.1    +      -       -      +
     60B  LYS*     3.7    19.9    -      -       -      +
     72B  GLN*     3.5    11.2    +      -       -      +
     73B  ALA*     3.9     3.2    -      -       -      -
     74B  LYS*     3.8    29.9    -      -       +      +
     81B  LEU*     6.1     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 59 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56B  TYR*     3.8    27.0    -      -       -      -
     57B  THR*     4.4     1.6    -      -       -      -
     58B  ASP*     1.3    76.1    -      -       -      +
     60B  LYS*     1.3    70.2    +      -       -      +
     71B  TYR*     3.6    32.8    -      -       +      -
     72B  GLN      3.3     6.3    -      -       -      +
     73B  ALA*     4.2     4.0    -      -       -      +
     84B  ILE*     5.6     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 60 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58B  ASP*     3.7    19.0    +      -       -      +
     59B  THR*     1.3    80.5    -      -       -      +
     61B  VAL*     1.3    67.7    +      -       -      +
     62B  ILE*     4.3     3.6    -      -       +      -
     71B  TYR*     3.3     5.6    -      -       -      -
     72B  GLN*     2.8    63.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 61 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  LYS*     1.3    78.4    -      -       -      +
     62B  ILE*     1.3    69.9    +      -       -      +
     63B  GLY      3.6    23.1    -      -       -      +
     64B  ASN*     4.1    14.6    -      -       -      +
     69B  VAL*     3.9    11.9    -      -       +      -
     70B  VAL      3.8     4.0    -      -       -      -
     71B  TYR*     3.8    24.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 62 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  LYS*     3.8     6.7    -      -       +      +
     61B  VAL*     1.3    81.3    -      -       -      +
     63B  GLY*     1.3    62.4    +      -       -      +
     70B  VAL*     3.0    30.2    +      -       +      +
     71B  TYR      4.1    11.0    -      -       -      +
     72B  GLN*     3.7    23.3    -      -       +      -
     83B  ALA*     4.5     1.1    -      -       +      -
    134B  TYR*     3.9    31.6    -      -       +      +
    452B  IXM      3.7    49.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 63 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61B  VAL*     3.6     4.1    -      -       -      +
     62B  ILE*     1.3    83.6    -      -       -      +
     64B  ASN*     1.3    65.3    +      -       -      -
     69B  VAL*     3.4    11.1    -      -       -      +
     70B  VAL*     3.0    32.0    +      -       -      -
    452B  IXM      4.0    14.6    -      -       -      -
----------------------------------------------------------
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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