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


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 H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205H  THR      3.6     0.8    -      -       -      -
    206H  HIS*     1.3    85.9    -      -       +      +
    208H  THR*     1.3    66.8    +      -       -      +
    209H  VAL*     3.7    10.7    +      -       +      -
    231H  VAL*     4.6     0.4    -      -       +      -
    232H  GLU      3.6     0.8    +      -       -      -
    233H  CYS*     3.3    14.9    -      -       -      -
    234H  GLU*     2.5    34.8    +      -       -      +
    256H  THR*     3.9     7.0    -      -       -      -
    258H  HIS*     3.3    27.6    -      -       +      +
    259H  LEU      4.2     0.7    -      -       -      +
    260H  VAL*     3.2    32.1    -      -       +      -
    323H  ILE*     4.0    19.1    -      -       +      -
    326H  THR*     3.6    16.2    -      -       -      +
    327H  LEU*     3.9    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 208 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207H  ILE*     1.3    74.8    -      -       -      +
    209H  VAL*     1.3    58.7    +      -       -      +
    210H  VAL*     3.6    23.6    -      -       +      -
    234H  GLU*     3.7     8.3    -      -       -      +
    236H  ILE*     3.7    13.7    -      -       +      -
    249H  ILE*     4.7     1.3    -      -       +      +
    252H  SER*     3.0    27.5    +      -       -      +
    253H  VAL*     3.5     6.1    +      -       +      -
    256H  THR*     2.4    26.1    +      -       -      -
    258H  HIS      2.9    11.2    +      -       -      -
    259H  LEU*     3.4    14.1    -      -       +      +
    260H  VAL      3.1    23.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 209 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207H  ILE*     4.1    11.9    -      -       +      -
    208H  THR*     1.3    77.9    -      -       -      +
    210H  VAL*     1.3    62.2    +      -       -      +
    211H  SER*     5.5     0.4    -      -       -      -
    219H  CYS*     4.0    24.7    -      -       +      -
    233H  CYS*     4.0    23.3    -      -       +      -
    234H  GLU      3.1     7.1    +      -       -      +
    235H  VAL*     3.4    12.4    -      -       +      +
    236H  ILE*     3.0    25.6    +      -       -      +
    260H  VAL*     3.3    16.2    -      -       +      +
    262H  VAL*     4.1    13.2    -      -       +      -
    319H  ILE*     4.3     8.1    -      -       +      -
    323H  ILE*     3.9    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 210 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208H  THR*     3.6    27.6    -      -       +      -
    209H  VAL*     1.3    73.5    -      -       -      +
    211H  SER*     1.3    65.7    +      -       -      +
    236H  ILE*     3.8    22.9    -      -       +      -
    238H  MET*     4.4    12.2    -      -       +      +
    249H  ILE*     4.0    13.0    -      -       +      -
    259H  LEU*     4.0    13.5    -      -       +      -
    260H  VAL      2.9    11.7    +      -       -      +
    261H  THR*     3.3     6.0    -      -       +      -
    262H  VAL*     2.8    26.9    +      -       -      +
    275H  ILE*     3.5    31.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 211 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209H  VAL      5.5     0.2    -      -       -      -
    210H  VAL*     1.3    75.8    -      -       -      +
    212H  HIS*     1.3    71.2    +      -       -      +
    215H  PRO*     3.7    13.3    -      -       -      +
    216H  VAL*     3.8    13.6    +      -       -      +
    219H  CYS*     4.4    12.6    -      -       -      -
    235H  VAL*     5.9     0.9    -      -       -      -
    236H  ILE      3.4    11.0    +      -       -      +
    237H  ASN*     3.6     2.3    -      -       -      -
    238H  MET*     3.0    36.2    +      -       -      +
    262H  VAL*     2.6    34.7    +      -       -      -
----------------------------------------------------------
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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