Contacts of the strand formed by residues 207 - 211 (chain N) in PDB entry 3EXG


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 ILE 207 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205N  THR      3.8     0.2    -      -       -      -
    206N  HIS*     1.3    80.6    -      -       +      +
    208N  THR*     1.3    69.2    +      -       -      +
    209N  VAL*     3.8     1.7    +      -       +      -
    231N  VAL*     4.5     1.8    -      -       +      -
    232N  GLU      3.4     2.8    +      -       -      +
    233N  CYS*     3.8    31.0    -      -       -      -
    234N  GLU*     2.7    33.4    +      -       -      +
    256N  THR*     3.6     8.9    -      -       -      -
    258N  HIS*     4.0    16.4    -      -       +      +
    260N  VAL*     3.7    24.7    -      -       +      -
    323N  ILE*     3.4    38.8    -      -       +      +
    326N  THR*     4.4     3.4    -      -       -      -
    327N  LEU*     4.2    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 208 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207N  ILE*     1.3    73.4    -      -       -      +
    209N  VAL*     1.3    64.1    +      -       -      +
    210N  VAL*     4.0    13.5    -      -       +      -
    234N  GLU      3.8     3.1    -      -       -      +
    236N  ILE*     3.6    21.3    -      -       +      -
    249N  ILE*     4.7     1.6    -      -       +      -
    252N  SER*     2.6    39.2    +      -       -      +
    253N  VAL*     3.5    10.1    +      -       +      -
    256N  THR*     2.9    18.2    +      -       -      +
    258N  HIS      2.9    16.6    +      -       -      -
    259N  LEU*     3.3     6.5    -      -       +      +
    260N  VAL      2.8    26.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 209 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207N  ILE*     4.1    10.5    -      -       +      +
    208N  THR*     1.3    79.2    -      -       -      +
    210N  VAL*     1.3    56.5    +      -       -      +
    211N  SER      4.3     0.2    +      -       -      -
    219N  CYS*     3.5    33.4    -      -       +      +
    233N  CYS*     4.1    18.6    -      -       +      -
    234N  GLU      3.1     9.6    +      -       -      +
    235N  VAL*     3.4     9.3    -      -       +      +
    236N  ILE      2.7    32.2    +      -       -      +
    260N  VAL*     3.4     9.9    -      -       +      +
    262N  VAL*     4.3     8.3    -      -       +      -
    319N  ILE*     4.7     3.1    -      -       +      -
    323N  ILE*     3.7    32.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 210 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208N  THR*     4.0     7.4    -      -       +      -
    209N  VAL*     1.3    75.4    -      -       -      +
    211N  SER*     1.3    67.5    +      -       -      +
    236N  ILE*     3.4    13.5    -      -       +      +
    238N  MET*     3.7    27.3    -      -       +      +
    249N  ILE*     3.7    44.6    -      -       +      -
    259N  LEU*     3.8    13.5    -      -       +      -
    260N  VAL      2.8    13.6    +      -       -      +
    261N  THR*     3.3    12.4    -      -       +      -
    262N  VAL*     2.9    26.0    +      -       -      +
    275N  ILE*     4.1     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 211 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210N  VAL*     1.3    82.2    -      -       -      +
    212N  HIS*     1.3    66.6    +      -       -      +
    215N  PRO*     3.5    18.5    -      -       -      +
    216N  VAL*     3.5    15.2    +      -       -      -
    219N  CYS*     4.0    12.1    -      -       -      -
    235N  VAL*     6.2     0.9    -      -       -      -
    236N  ILE      2.9     7.1    +      -       -      -
    237N  ASN*     3.4     7.1    -      -       -      -
    238N  MET*     3.0    32.4    +      -       -      +
    262N  VAL*     2.5    32.4    +      -       -      -
----------------------------------------------------------
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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