Contacts of the strand formed by residues 238 - 244 (chain D) in PDB entry 6PB4


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 238 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27D  PRO*     5.8     3.6    -      -       -      +
    110D  PRO*     3.7    23.3    -      -       +      -
    111D  THR      2.9    28.7    -      -       -      +
    112D  ALA*     3.4    24.7    -      -       +      -
    113D  HIS      4.2     0.2    -      -       -      +
    124D  ILE*     4.5     9.6    -      -       +      -
    182D  ALA*     4.2     9.4    -      -       +      -
    185D  ILE*     6.2     2.2    -      -       +      -
    186D  GLN*     2.9    40.6    +      -       -      +
    189D  LEU*     5.9     0.4    -      -       +      -
    235D  GLU      3.2     4.4    +      -       -      +
    236D  TRP*     3.0     7.1    -      -       -      +
    237D  MET*     1.3   100.6    -      -       +      +
    239D  LEU*     1.3    63.7    +      -       -      +
    240D  THR*     3.9     6.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 239 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1334C  GLY*     5.9     7.4    -      -       -      -
    107D  LEU*     3.0    21.0    -      -       +      +
    110D  PRO*     3.3     4.7    -      -       -      +
    111D  THR*     2.5    34.9    +      -       -      +
    112D  ALA      3.4     6.3    -      -       -      +
    113D  HIS*     3.1    48.7    -      -       +      +
    236D  TRP      6.1     0.4    -      -       -      +
    237D  MET      3.4    10.5    -      -       -      +
    238D  ILE*     1.3    75.0    -      -       -      +
    240D  THR*     1.3    60.6    +      -       -      +
    241D  VAL      4.2    14.1    -      -       -      +
    242D  LEU*     5.3    15.3    -      -       +      -
    243D  PRO*     6.1     1.8    -      -       +      -
    303D  VAL*     5.5     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 240 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27D  PRO*     4.3    18.7    -      -       -      +
     31D  ARG*     5.3     2.1    +      -       -      -
    106D  GLU*     3.8     0.9    -      -       -      +
    107D  LEU*     2.6    45.4    +      -       -      +
    109D  SER      4.8     1.8    -      -       -      -
    110D  PRO*     3.9    23.6    -      -       +      -
    186D  GLN*     6.3     0.9    -      -       -      +
    238D  ILE*     3.9     5.7    +      -       +      +
    239D  LEU*     1.3    80.1    -      -       -      +
    241D  VAL*     1.3    66.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 241 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27D  PRO*     4.9    12.5    -      -       +      +
     30D  ILE*     4.1    27.1    -      -       +      +
     31D  ARG*     4.3    16.4    -      -       +      +
    104D  HIS*     3.8    14.1    -      -       +      -
    105D  ILE      2.9    19.1    -      -       -      +
    106D  GLU*     3.0    41.3    -      -       -      +
    107D  LEU*     4.2     2.2    -      -       -      -
    239D  LEU*     4.2    13.7    -      -       -      +
    240D  THR*     1.3    90.9    +      -       -      +
    242D  LEU*     1.3    62.2    +      -       -      +
    243D  PRO*     4.6     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 242 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1332C  SER      5.2     2.5    -      -       -      +
     30D  ILE*     5.0     1.1    -      -       -      -
    104D  HIS*     3.3     1.4    -      -       -      +
    105D  ILE*     2.9    48.6    +      -       +      +
    107D  LEU*     4.8    16.6    -      -       +      -
    239D  LEU*     5.3    14.6    -      -       +      -
    241D  VAL*     1.3    77.8    -      -       -      +
    243D  PRO*     1.3   101.1    -      -       +      +
    244D  VAL*     5.3     0.4    -      -       +      -
    269D  TYR*     5.0    10.3    -      -       +      +
    272D  VAL*     6.2     3.8    -      -       +      -
    303D  VAL*     5.1    16.4    -      -       +      -
    306D  LEU*     5.0    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 243 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1331C  ARG      3.8     5.8    -      -       -      +
   1332C  SER*     2.9    35.9    -      -       -      +
   1333C  LEU      5.7     0.2    -      -       -      -
   1334C  GLY*     4.6     9.2    -      -       -      +
     30D  ILE*     4.8    18.4    -      -       +      -
     33D  TRP*     6.3     0.2    -      -       +      -
    102D  MET*     3.8    22.2    -      -       +      -
    103D  GLY      3.6     7.2    -      -       -      +
    104D  HIS*     4.2     2.9    -      -       +      -
    239D  LEU*     6.1     2.2    -      -       +      -
    241D  VAL      4.6     2.2    -      -       -      +
    242D  LEU*     1.3   113.0    -      -       +      +
    244D  VAL*     1.3    67.9    +      -       -      +
    269D  TYR*     4.0     5.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 244 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38D  VAL*     4.1    25.4    -      -       +      -
     56D  LEU*     5.6     5.8    -      -       +      +
     62D  PHE*     4.5    10.3    -      -       +      -
    102D  MET*     3.0    11.1    -      -       -      +
    103D  GLY*     2.9    36.2    +      -       -      +
    104D  HIS*     4.2    11.9    -      -       -      -
    105D  ILE*     4.7     6.3    -      -       +      +
    242D  LEU*     4.3     1.3    -      -       +      +
    243D  PRO*     1.3    83.9    -      -       -      +
    245D  LEU*     1.3    71.9    +      -       -      +
    250D  ARG*     4.6     9.0    -      -       -      +
    269D  TYR*     3.8    29.4    -      -       +      -
----------------------------------------------------------
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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