Contacts of the strand formed by residues 303 - 312 (chain D) in PDB entry 4OIO


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 PRO 303 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250D  LEU*     4.2    27.8    -      -       +      -
    251D  PHE      3.3    12.1    -      -       -      +
    252D  ARG*     3.7    23.6    -      -       +      +
    291D  LEU*     4.3    22.2    -      -       +      +
    292D  VAL*     4.5     5.0    -      -       -      +
    301D  GLY      3.7     0.4    -      -       -      -
    302D  GLN*     1.3    94.7    +      -       +      +
    304D  LEU*     1.3    65.4    +      -       -      +
    305D  ALA      4.7     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 304 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251D  PHE*     2.8    24.4    +      -       +      +
    253D  ALA*     4.0    19.1    -      -       +      +
    259D  VAL*     4.9     2.0    -      -       +      -
    270D  LEU*     3.8    25.5    -      -       +      +
    272D  LEU*     4.5     4.9    -      -       +      -
    282D  TYR*     3.5    38.8    -      -       +      -
    290D  PRO*     3.6     1.6    -      -       -      +
    291D  LEU*     2.6    32.6    +      -       -      +
    292D  VAL*     3.5    26.5    +      -       +      +
    298D  VAL*     4.2    21.1    -      -       +      -
    302D  GLN      3.8    13.5    -      -       -      +
    303D  PRO*     1.3    74.1    -      -       -      +
    305D  ALA*     1.3    52.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 305 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250D  LEU*     3.7     7.8    -      -       -      +
    251D  PHE*     3.3    25.8    +      -       +      +
    284D  LEU*     3.9    16.6    -      -       +      -
    288D  MET*     3.7    26.2    -      -       +      -
    289D  THR      3.4    15.9    -      -       -      +
    290D  PRO*     3.8     8.7    -      -       +      -
    291D  LEU*     3.8     8.6    -      -       -      +
    303D  PRO*     3.7     0.7    -      -       -      +
    304D  LEU*     1.3    80.2    +      -       +      +
    306D  GLU*     1.3    62.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 306 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248D  PRO*     3.9    19.2    -      -       -      +
    249D  TYR      3.6     8.5    -      -       -      +
    250D  LEU*     3.8    22.5    -      -       +      +
    287D  GLY      4.1     0.5    -      -       -      +
    288D  MET*     3.3     4.6    -      -       -      -
    289D  THR*     2.8    42.5    +      -       -      +
    291D  LEU*     4.4    14.9    -      -       +      +
    305D  ALA*     1.3    76.4    -      -       -      +
    307D  ALA*     1.3    69.1    +      -       -      +
    308D  LYS*     3.8    16.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 307 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225D  LEU*     5.9     1.3    -      -       +      -
    245D  LEU*     3.3    22.1    -      -       +      +
    248D  PRO*     3.9     0.5    -      -       -      +
    249D  TYR*     3.1    38.8    +      -       +      +
    287D  GLY      3.7     6.1    -      -       -      +
    288D  MET*     3.8    22.7    -      -       +      +
    305D  ALA      4.3     0.2    -      -       -      -
    306D  GLU*     1.3    73.1    -      -       -      +
    308D  LYS*     1.3    59.9    +      -       -      +
    311D  LEU*     3.9    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 308 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245D  LEU*     4.7     0.7    -      -       -      -
    248D  PRO*     4.6    25.8    -      -       +      -
    287D  GLY*     3.2    19.3    +      -       -      +
    306D  GLU*     3.8    21.2    +      -       +      +
    307D  ALA*     1.3    75.2    -      -       -      +
    309D  GLY*     1.3    70.2    +      -       -      +
    310D  LEU      3.8     4.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 309 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245D  LEU*     3.2    43.2    +      -       -      +
    247D  GLU      5.8     1.0    +      -       -      -
    248D  PRO*     5.8     0.4    -      -       -      +
    308D  LYS*     1.3    82.9    -      -       -      +
    310D  LEU*     1.3    62.7    +      -       -      -
    311D  LEU*     3.4     6.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 310 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241D  ILE*     3.6    42.0    -      -       +      -
    243D  ALA      3.6    13.9    -      -       -      +
    244D  GLU*     4.4    17.9    -      -       +      +
    245D  LEU      4.4     0.2    -      -       -      +
    286D  VAL      4.3     2.4    -      -       -      +
    287D  GLY*     4.4     5.2    -      -       -      -
    308D  LYS      4.1     4.5    -      -       -      +
    309D  GLY*     1.3    72.4    -      -       -      -
    311D  LEU*     1.3    68.9    +      -       -      +
    312D  ARG*     3.3    33.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 311 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223D  LEU*     4.9     0.9    -      -       +      -
    225D  LEU*     3.9    22.9    -      -       +      -
    241D  ILE      4.3     0.2    -      -       -      -
    242D  LEU*     3.2     7.7    +      -       +      +
    243D  ALA*     3.1    46.8    +      -       +      +
    245D  LEU*     4.1    13.7    -      -       +      -
    285D  PRO*     3.8    24.9    -      -       +      -
    286D  VAL      3.2    17.3    -      -       -      +
    287D  GLY      4.3     8.5    -      -       -      +
    288D  MET*     4.6     6.5    -      -       -      -
    307D  ALA*     3.9    29.8    -      -       +      -
    309D  GLY      3.4    15.9    -      -       -      +
    310D  LEU*     1.3    73.9    -      -       -      +
    312D  ARG*     1.3    60.2    +      -       -      +
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Residues in contact with ARG 312 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239D  GLY*     3.3    20.4    -      -       -      +
    240D  GLU      3.4    11.9    -      -       -      +
    241D  ILE*     3.6    18.1    -      -       -      +
    242D  LEU*     3.7     6.1    -      -       -      +
    285D  PRO*     4.1     5.8    -      -       -      -
    286D  VAL*     3.0    41.9    +      -       +      +
    310D  LEU*     3.3    31.5    +      -       +      +
    311D  LEU*     1.3    74.4    -      -       -      +
    313D  MET*     1.3    69.5    +      -       -      +
    315D  ARG*     6.0     4.0    -      -       -      +
----------------------------------------------------------
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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