Contacts of the strand formed by residues 78 - 86 (chain C) in PDB entry 3SE3


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 ALA 78 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  LEU*     4.6     8.5    -      -       +      -
    145B  ALA*     4.1    20.6    +      -       +      +
    148B  MET*     6.5     0.2    -      -       -      -
    149B  ARG*     5.8     0.8    -      -       -      +
     45C  ILE*     3.3     4.2    -      -       -      -
     46C  MET*     3.2    44.6    +      -       +      +
     47C  SER      5.9     0.2    -      -       -      +
     77C  GLU*     1.3    75.0    +      -       -      +
     79C  TYR*     1.3    62.0    +      -       -      +
     98C  ASN*     6.2     0.7    -      -       +      -
     99C  PHE      3.8     5.2    -      -       -      +
    100C  TRP*     4.0    16.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 79 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43C  TYR*     3.9     9.0    -      +       -      -
     44C  THR      3.6     1.6    -      -       -      -
     45C  ILE*     3.7    23.1    -      -       +      -
     71C  GLU      4.9     0.8    +      -       -      -
     72C  TRP*     3.3    67.9    -      +       +      -
     73C  ARG      3.6     1.0    +      -       -      -
     74C  SER*     3.1    40.3    +      -       -      -
     77C  GLU*     3.5    27.7    -      -       +      +
     78C  ALA*     1.3    72.9    -      -       -      +
     80C  VAL*     1.3    61.6    +      -       -      +
     81C  THR*     4.1     1.2    +      -       -      -
     97C  HIS      3.9     0.2    -      -       -      +
     98C  ASN*     3.3     6.2    -      -       -      +
     99C  PHE*     3.0    40.0    +      -       +      +
    101C  LEU*     3.6    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 80 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  LEU*     3.6    30.7    -      -       +      -
     27B  PHE*     3.8    33.7    -      -       +      +
     30B  LEU*     4.3    14.4    -      -       +      -
     43C  TYR*     3.1     4.2    -      -       -      -
     44C  THR*     3.0    35.1    +      -       +      +
     46C  MET*     3.6    24.2    -      -       +      +
     52C  LEU*     4.1     4.6    -      -       +      +
     78C  ALA      4.4     0.2    -      -       -      +
     79C  TYR*     1.3    77.3    -      -       -      +
     81C  THR*     1.3    67.4    +      -       -      +
     82C  VAL*     5.4     1.6    -      -       +      -
     96C  SER*     5.0     0.7    -      -       -      -
     97C  HIS      3.6     9.9    -      -       -      +
     98C  ASN*     4.9     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 81 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14C  PHE*     4.6     8.4    -      -       -      -
     25C  LEU*     4.5     2.4    -      -       +      +
     41C  LEU*     4.5    16.6    -      -       +      -
     42C  LEU      3.1    12.3    -      -       -      +
     43C  TYR*     3.9     1.3    -      -       +      -
     72C  TRP*     3.2    43.1    -      -       +      -
     80C  VAL*     1.3    77.5    -      -       -      +
     82C  VAL*     1.3    64.6    +      -       -      +
     83C  LEU*     4.3     0.4    -      -       -      -
     96C  SER*     3.1     8.1    -      -       -      -
     97C  HIS*     3.0    31.3    +      -       -      +
     99C  PHE*     3.3    23.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 82 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  PHE*     4.5    23.8    -      -       +      -
     41C  LEU*     3.4     2.9    -      -       -      -
     42C  LEU*     2.9    47.5    +      -       +      +
     52C  LEU*     4.4    24.7    -      -       +      -
     80C  VAL*     5.3     2.2    -      -       +      +
     81C  THR*     1.3    82.3    -      -       -      +
     83C  LEU*     1.3    62.6    +      -       -      +
     84C  GLU*     4.4     9.4    -      -       +      +
     94C  SER*     3.7    25.6    -      -       -      +
     95C  CYS      3.1    11.2    -      -       -      +
     96C  SER*     4.3    11.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 83 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12C  CYS*     4.8     9.9    -      -       +      -
     14C  PHE*     4.0    24.3    -      -       +      -
     27C  TRP*     3.4    64.6    -      -       +      +
     29C  LEU*     5.1     4.7    -      -       +      -
     39C  TYR*     4.3    17.7    -      -       +      -
     40C  THR      3.5    10.8    -      -       -      +
     41C  LEU*     4.2    17.0    -      -       +      -
     82C  VAL*     1.3    73.9    -      -       -      +
     84C  GLU*     1.3    63.6    +      -       -      +
     93C  PHE*     3.7     6.2    -      -       +      +
     94C  SER*     2.9     4.0    -      -       -      -
     95C  CYS*     2.8    34.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 84 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39C  TYR*     3.1     7.3    -      -       -      +
     40C  THR*     2.7    49.4    +      -       -      +
     42C  LEU*     4.0    22.5    -      -       +      +
     82C  VAL*     4.4     6.9    -      -       +      +
     83C  LEU*     1.3    75.4    -      -       -      +
     85C  GLY*     1.3    59.3    +      -       -      +
     86C  PHE*     4.0    22.0    -      -       +      -
     91C  THR*     4.9     7.4    -      -       +      -
     93C  PHE*     3.4     6.5    -      -       -      +
     94C  SER*     3.3    23.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 85 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36C  PRO*     3.8    16.4    -      -       -      -
     38C  HIS      3.4     7.4    -      -       -      -
     39C  TYR*     4.3     4.5    -      -       -      -
     84C  GLU*     1.3    76.7    -      -       -      +
     86C  PHE*     1.3    59.2    +      -       -      -
     91C  THR*     3.8     0.7    -      -       -      +
     92C  LEU*     2.6    40.3    +      -       -      +
     93C  PHE*     3.1    14.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 86 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36C  PRO*     3.9     0.8    -      -       -      +
     37C  THR*     2.7    29.6    +      -       -      -
     38C  HIS*     2.9    42.1    +      -       +      +
     39C  TYR      4.5     0.2    -      -       -      -
     40C  THR*     3.3    35.0    -      -       -      -
     60C  ASN*     4.6     7.4    -      -       +      -
     84C  GLU*     4.0    19.3    -      -       +      -
     85C  GLY*     1.3    78.6    -      -       -      -
     87C  SER*     1.3    56.9    +      -       -      +
     88C  GLY      4.8     4.3    -      -       -      +
     90C  THR      3.4    14.1    -      -       -      +
     91C  THR*     3.2    33.7    -      -       +      -
     92C  LEU*     3.1     5.6    -      -       -      -
----------------------------------------------------------
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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