Contacts of the strand formed by residues 207 - 211 (chain D) 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 D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206D  HIS*     1.3    82.9    -      -       +      +
    208D  THR*     1.3    72.7    +      -       -      +
    209D  VAL*     4.4     4.0    -      -       +      -
    231D  VAL*     4.9     0.9    -      -       +      -
    232D  GLU      3.5     2.6    +      -       -      +
    233D  CYS*     3.4    27.2    -      -       +      +
    234D  GLU      3.0    23.6    +      -       -      -
    256D  THR*     3.5    12.4    -      -       -      +
    258D  HIS*     3.7    12.8    -      -       +      +
    260D  VAL*     3.8    25.8    -      -       +      -
    323D  ILE*     4.0    25.1    -      -       +      -
    326D  THR*     3.8    23.3    -      -       +      -
    327D  LEU*     4.2    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 208 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207D  ILE*     1.3    73.4    -      -       -      +
    209D  VAL*     1.3    62.9    +      -       -      +
    210D  VAL*     3.9    13.0    -      -       +      -
    234D  GLU      3.6     4.9    -      -       -      +
    236D  ILE*     3.6    24.9    -      -       +      -
    249D  ILE      4.7     4.7    -      -       -      +
    252D  SER*     2.6    34.9    +      -       -      +
    253D  VAL*     3.6     7.3    +      -       -      -
    256D  THR*     2.7    20.5    +      -       -      +
    258D  HIS      3.0    14.7    +      -       -      -
    259D  LEU*     3.4     5.1    -      -       +      +
    260D  VAL      2.9    26.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 209 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207D  ILE*     4.4     6.3    -      -       +      -
    208D  THR*     1.3    75.5    -      -       -      +
    210D  VAL*     1.3    60.7    +      -       -      +
    211D  SER*     4.8     0.3    -      -       -      -
    219D  CYS*     3.6    32.1    -      -       +      +
    233D  CYS*     3.8    21.1    -      -       +      -
    234D  GLU      2.9    11.6    +      -       -      +
    235D  VAL*     3.4    11.7    -      -       +      +
    236D  ILE      2.9    24.6    +      -       -      +
    260D  VAL*     3.3    11.2    -      -       +      +
    262D  VAL*     4.4    10.8    -      -       +      -
    319D  ILE*     4.8     1.6    -      -       +      -
    323D  ILE*     3.6    32.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 210 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208D  THR*     4.1     7.6    -      -       +      -
    209D  VAL*     1.3    70.9    -      -       -      +
    211D  SER*     1.3    66.6    +      -       -      +
    236D  ILE*     3.7    13.0    -      -       +      +
    238D  MET*     3.9    26.3    -      -       +      +
    249D  ILE*     3.7    43.3    -      -       +      -
    259D  LEU*     3.4    26.2    -      -       +      -
    260D  VAL      3.1     3.8    +      -       -      -
    261D  THR*     3.2    13.7    -      -       +      -
    262D  VAL*     2.9    25.1    +      -       -      +
    275D  ILE*     4.3     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 211 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209D  VAL      4.8     0.7    -      -       -      -
    210D  VAL*     1.3    79.6    -      -       -      +
    212D  HIS*     1.3    66.9    +      -       -      +
    215D  PRO*     4.0     2.8    -      -       -      +
    216D  VAL*     3.6    24.7    +      -       -      -
    219D  CYS*     3.7    23.3    -      -       -      -
    235D  VAL*     5.8     0.7    -      -       -      -
    236D  ILE      3.0    11.3    +      -       -      +
    237D  ASN*     3.5     2.8    -      -       -      -
    238D  MET*     3.0    32.1    +      -       -      +
    262D  VAL*     2.7    24.7    +      -       -      +
----------------------------------------------------------
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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