Contacts of the strand formed by residues 62 - 70 (chain B) in PDB entry 4O2C


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 PHE 62 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  THR*     3.6    31.6    -      -       +      -
     94A  THR*     4.1     5.4    -      -       +      -
     96A  GLN*     3.4    29.2    -      -       +      -
     28B  SER*     3.3     3.1    -      -       -      -
     29B  GLY      3.0    24.9    +      -       -      -
     30B  PHE*     2.9    45.0    +      -       +      -
     31B  HIS*     3.4    26.0    -      +       -      -
     32B  PRO      4.1     0.2    -      -       -      -
     33B  SER*     3.5    37.2    -      -       -      -
     54B  LEU*     3.5    17.5    -      -       +      -
     55B  SER      3.4    15.9    -      -       -      +
     56B  PHE*     3.9     5.4    -      +       +      -
     57B  SER*     5.5     0.2    -      -       -      -
     60B  TRP      4.3     0.4    -      -       -      -
     61B  SER*     1.3    73.6    -      -       -      +
     63B  TYR*     1.3    60.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 63 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  PHE*     5.8     1.6    -      -       -      -
     27A  TYR*     3.4    23.6    +      -       -      -
    235A  PRO*     6.5     0.2    -      -       +      -
     26B  TYR*     3.6    33.2    -      +       +      +
     27B  VAL      3.2    12.8    -      -       -      +
     28B  SER*     3.7     7.0    -      -       -      -
     30B  PHE*     4.0     0.7    -      -       -      -
     52B  SER*     4.7     1.5    +      -       -      -
     53B  ASP      4.6     2.6    -      -       -      +
     54B  LEU*     4.6     0.2    -      -       -      +
     55B  SER*     3.1    37.7    +      -       -      +
     56B  PHE*     3.6    30.0    +      -       -      -
     57B  SER*     3.6    20.9    -      -       -      +
     62B  PHE*     1.3    76.3    -      -       -      +
     64B  LEU*     1.3    75.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 64 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  CYS      3.8     0.3    -      -       -      +
     26B  TYR*     3.5     8.3    -      -       -      -
     27B  VAL*     2.8    42.4    +      -       +      +
     30B  PHE*     4.1     8.1    -      -       +      -
     33B  SER      5.0     1.6    -      -       -      +
     35B  ILE*     3.9    28.3    -      -       +      -
     51B  HIS*     4.7     5.8    -      -       +      +
     52B  SER*     3.4    30.5    -      -       -      +
     53B  ASP      4.0     0.2    -      -       -      -
     54B  LEU*     3.7    33.7    -      -       +      +
     63B  TYR*     1.3    82.7    -      -       -      +
     65B  LEU*     1.3    59.1    +      -       -      +
     66B  TYR*     3.9    23.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 65 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235A  PRO*     4.0    27.1    -      -       +      +
    237A  GLY*     4.1    24.9    -      -       -      -
     10B  TYR*     3.7    14.6    -      -       -      +
     24B  ASN*     3.7    32.3    -      -       +      +
     25B  CYS      3.7     9.2    -      -       -      +
     26B  TYR*     4.2     4.2    -      -       +      -
     51B  HIS*     3.0     4.9    -      -       -      +
     52B  SER*     2.9    43.8    +      -       -      +
     64B  LEU*     1.3    73.6    -      -       -      +
     66B  TYR*     1.3    66.4    +      -       -      +
     67B  TYR*     3.7    20.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 66 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  LEU      3.8     0.2    -      -       -      +
     24B  ASN*     3.4     1.6    -      -       -      -
     25B  CYS*     2.7    47.4    +      -       +      +
     27B  VAL*     4.5     3.4    -      -       +      -
     35B  ILE*     4.2    12.0    +      -       -      +
     37B  VAL*     3.4    61.1    +      -       +      +
     39B  LEU*     4.4     5.8    -      -       +      +
     49B  VAL*     4.1    20.6    -      -       +      -
     50B  GLU      3.3     3.4    -      -       -      -
     51B  HIS*     3.6    35.0    +      +       +      -
     64B  LEU*     3.9    35.6    -      -       +      +
     65B  LEU*     1.3    77.0    -      -       -      +
     67B  TYR*     1.3    65.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 67 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  ARG*     6.0     0.2    +      -       -      -
    237A  GLY*     6.3     0.7    -      -       -      -
     12B  ARG*     4.6    11.0    -      -       -      +
     22B  PHE*     4.4    22.4    -      +       +      -
     23B  LEU      3.2     5.8    -      -       -      +
     24B  ASN*     3.3    23.8    -      -       -      +
     39B  LEU*     4.0     4.5    -      -       -      -
     48B  LYS      4.9     0.2    -      -       -      +
     49B  VAL*     3.7     1.9    -      -       -      +
     50B  GLU*     2.9    78.0    +      -       +      +
     51B  HIS*     4.0    14.0    +      -       -      -
     52B  SER*     4.3     3.5    -      -       -      -
     65B  LEU*     3.7    21.3    -      -       +      -
     66B  TYR*     1.3    77.4    -      -       -      +
     68B  THR*     1.3    62.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 68 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  PHE*     3.5     6.7    -      -       -      -
     23B  LEU*     2.8    39.0    +      -       +      -
     39B  LEU*     3.6    21.5    -      -       +      -
     46B  ILE*     4.0    30.0    -      -       +      +
     48B  LYS      3.4    19.8    +      -       -      -
     49B  VAL*     4.2     4.5    -      -       -      -
     67B  TYR*     1.3    77.5    -      -       -      +
     69B  GLU*     1.3    73.0    +      -       -      +
     70B  PHE*     3.6     2.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 69 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  SER*     3.2    20.6    +      -       -      +
     21B  ASN      3.4    14.1    -      -       -      +
     22B  PHE*     3.9    28.5    -      -       +      -
     46B  ILE*     6.0     0.3    -      -       -      +
     68B  THR*     1.3    83.9    +      -       -      +
     70B  PHE*     1.3    64.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 70 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  SER*     4.3     5.4    -      -       -      -
     20B  SER*     4.5     1.1    -      -       -      -
     21B  ASN*     2.7    52.9    +      -       +      -
     22B  PHE      3.3    24.5    -      -       -      -
     23B  LEU*     3.3    28.9    -      -       +      -
     68B  THR*     4.4     5.6    -      -       +      +
     69B  GLU*     1.3    77.3    -      -       -      +
     71B  THR*     1.3    60.3    +      -       -      +
     72B  PRO*     3.5    26.4    -      -       +      +
     78B  TYR*     3.6    44.0    -      +       +      +
     95B  TRP*     3.9    32.8    -      +       -      -
----------------------------------------------------------
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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