Contacts of the strand formed by residues 45 - 51 (chain B) in PDB entry 3EYF


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 45 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  TYR*     6.0     2.0    -      -       +      -
     38A  HIS*     4.9     3.4    -      -       +      +
     44A  PRO*     4.8    10.3    -      -       +      -
     87A  TYR*     3.7    40.3    -      -       +      +
     99A  PHE*     3.6    44.7    +      -       +      +
    100A  GLY      4.9     2.3    +      -       -      +
     37B  VAL*     3.9    11.9    -      -       +      -
     38B  ARG      3.5     3.1    -      -       -      +
     39B  GLN*     3.7    33.4    -      -       +      +
     44B  GLY*     1.3    74.6    -      -       -      -
     46B  GLN*     1.3    62.1    +      -       -      +
     95B  TYR*     4.0    15.7    -      -       +      -
    115B  TRP*     4.4    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 46 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  PHE*     4.3     2.5    -      -       -      -
     37B  VAL*     2.9     6.4    -      -       -      +
     38B  ARG*     2.8    71.8    +      -       +      +
     44B  GLY      5.3     0.7    -      -       -      +
     45B  LEU*     1.3    77.7    -      -       -      +
     47B  TRP*     1.3    73.8    +      -       -      +
     48B  LEU*     4.0     4.2    -      -       +      +
     61B  THR*     5.0     4.9    +      -       -      +
     63B  SER*     4.2    17.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 47 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  TRP*     4.1     7.6    -      +       -      -
     95A  PRO*     3.8    30.3    -      -       +      -
     96A  PRO*     4.0    10.2    -      -       +      +
     97A  VAL*     3.5    54.4    +      -       +      +
     99A  PHE*     4.0     7.3    -      -       +      -
     35B  HIS*     2.7    29.5    +      -       -      -
     36B  TRP      4.0     1.6    -      -       -      -
     37B  VAL*     3.8    20.2    -      -       +      -
     46B  GLN*     1.3    87.7    -      -       -      +
     48B  LEU*     1.3    74.2    +      -       -      +
     49B  THR*     3.5    29.0    +      -       -      -
     50B  VAL*     3.7    15.0    -      -       +      -
     59B  ARG*     3.9    15.7    -      -       +      -
     60B  TYR      4.0     0.9    -      -       -      -
     61B  THR*     3.8    23.1    +      -       -      -
    112B  LEU*     5.1     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 48 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  TRP*     3.0    24.3    +      -       +      +
     38B  ARG*     3.6    44.9    -      -       +      +
     46B  GLN*     4.0     8.1    -      -       -      +
     47B  TRP*     1.3    86.5    -      -       -      +
     49B  THR*     1.3    66.2    +      -       +      +
     60B  TYR*     3.5     0.9    -      -       -      -
     61B  THR*     2.8    36.7    +      -       +      +
     64B  VAL*     4.2    10.4    -      -       +      +
     68B  PHE*     3.8    22.4    -      -       +      -
     81B  LEU*     5.1     1.3    -      -       +      -
     94B  TYR*     3.4    36.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 49 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  HIS*     3.2     3.5    -      -       -      -
     36B  TRP*     2.8    39.3    +      -       +      -
     47B  TRP*     3.5    13.3    +      -       -      -
     48B  LEU*     1.3    84.7    -      -       +      +
     50B  VAL*     1.3    66.8    +      -       -      +
     59B  ARG      2.1    29.7    +      -       -      -
     60B  TYR*     3.0    22.4    -      -       +      -
     64B  VAL*     5.5     0.9    -      -       -      -
     68B  PHE*     5.9     1.8    -      -       +      -
     70B  ILE*     3.7    28.2    -      -       +      +
     81B  LEU*     4.2    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  TRP*     4.0    10.3    -      -       +      -
     33B  GLY      4.5     0.9    -      -       -      -
     34B  ILE      3.1    18.4    -      -       -      +
     35B  HIS*     3.5    33.9    -      -       +      +
     47B  TRP*     3.7    14.4    -      -       +      -
     49B  THR*     1.3    79.5    +      -       -      +
     51B  ILE*     1.3    78.5    +      -       -      +
     58B  GLU*     3.4     4.0    -      -       -      +
     59B  ARG*     3.1    39.2    +      -       +      +
     70B  ILE*     3.9     4.6    -      -       -      +
    108B  TYR*     3.6    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  GLY*     3.1     4.0    -      -       -      -
     34B  ILE*     2.9    43.6    +      -       +      +
     50B  VAL*     1.3    78.8    -      -       -      +
     52B  SER*     1.3    66.8    +      -       -      +
     55B  GLY*     4.1    19.3    -      -       -      +
     57B  ASP      3.4    12.3    -      -       -      +
     58B  GLU*     3.9    10.3    -      -       +      +
     70B  ILE*     3.8    26.4    -      -       +      +
     71B  SER*     3.6    33.4    -      -       -      -
     72B  ARG*     3.4    28.3    -      -       +      +
     79B  MET*     4.8     3.1    -      -       +      -
    108B  TYR*     3.4     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