Contacts of the strand formed by residues 249 - 252 (chain B) in PDB entry 4OMD


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 249 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147B  ILE*     4.2     4.7    -      -       +      -
    148B  VAL      3.2     2.6    +      -       -      -
    149B  VAL*     3.4    13.6    -      -       +      +
    150B  SER      2.9    26.0    +      -       -      -
    247B  ILE*     3.4     3.3    -      -       -      +
    248B  HIS*     1.3    88.2    -      -       +      +
    250B  TYR*     1.3    73.8    +      -       -      +
    288B  ILE*     3.5    20.9    -      -       +      +
    290B  VAL*     4.1     9.6    -      -       +      -
    375B  ALA*     3.8    28.0    -      -       +      +
    378B  ILE*     3.7    12.8    -      -       +      +
    379B  ALA*     3.5    41.1    -      -       +      +
    382B  LEU*     4.1     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 250 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150B  SER*     3.5     6.3    -      -       -      +
    152B  LEU*     4.2    22.2    -      -       +      -
    239B  SER      3.7    16.2    -      -       -      -
    240B  LEU      3.3    24.4    +      -       -      -
    242B  LEU      2.7    29.8    +      -       -      -
    243B  ASN      3.7     1.6    +      -       -      -
    244B  PRO*     3.4    19.9    -      -       -      +
    247B  ILE*     3.7    29.2    -      -       +      -
    248B  HIS      4.5     0.7    -      -       -      -
    249B  ILE*     1.3    78.8    -      -       -      +
    251B  SER*     1.3    60.5    +      -       -      +
    252B  ALA*     4.3     0.4    -      -       -      -
    287B  SER*     3.6    25.3    +      -       -      -
    288B  ILE      2.8    12.2    +      -       -      +
    289B  PHE*     3.7    28.3    -      +       +      -
    290B  VAL*     2.9    30.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 251 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149B  VAL*     4.9     1.3    -      -       -      -
    150B  SER      2.9     7.8    +      -       -      -
    151B  ILE*     3.7    28.8    -      -       -      +
    152B  LEU*     3.0    28.0    +      -       -      +
    249B  ILE      4.2     0.2    +      -       -      -
    250B  TYR*     1.3    73.0    -      -       -      +
    252B  ALA*     1.3    61.4    +      -       -      +
    253B  SER*     4.2     2.4    +      -       -      -
    290B  VAL*     3.6     4.4    -      -       -      +
    371B  ALA*     4.1     7.1    -      -       -      +
    372B  PRO*     3.9    27.9    -      -       -      +
    375B  ALA*     4.1    17.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 252 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152B  LEU*     4.8     5.2    -      -       +      -
    250B  TYR      4.3     0.2    -      -       -      -
    251B  SER*     1.3    76.3    +      -       -      +
    253B  SER*     1.3    59.4    +      -       -      +
    254B  TRP*     3.3    29.1    +      -       +      +
    290B  VAL      2.9     9.7    +      -       -      -
    291B  TRP*     3.6    43.8    -      -       +      -
    292B  ALA      3.1    23.7    +      -       -      -
    371B  ALA*     4.8     0.9    -      -       -      -
----------------------------------------------------------
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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