Contacts of the strand formed by residues 252 - 256 (chain A) in PDB entry 1SID


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 VAL 252 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161A  GLN*     3.2    13.3    +      -       -      +
    163A  HIS*     5.0     2.4    +      -       -      -
    244A  THR*     6.3     2.5    -      -       +      -
    250A  PRO*     4.0     9.6    -      -       +      +
    251A  PRO*     1.3    79.1    -      -       +      +
    253A  LEU*     1.3    73.9    +      -       -      +
    254A  GLN*     4.8     8.5    -      -       -      +
    286A  MET*     4.8     1.0    -      -       -      +
    242B  ASN*     4.5     4.9    -      -       -      +
    243B  TYR*     3.0    21.1    -      -       -      +
    244B  THR*     3.5    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 253 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  VAL*     3.0    49.8    -      -       +      +
    132A  SER*     3.3    33.0    -      -       -      +
    163A  HIS*     4.0    15.7    -      -       +      +
    252A  VAL*     1.3    82.4    -      -       -      +
    254A  GLN*     1.3    81.1    +      -       -      +
    255A  PHE*     5.9     0.2    -      -       -      -
    286A  MET*     3.9    29.4    -      -       +      -
    302A  LEU*     5.3     0.4    -      -       +      -
    242B  ASN*     3.0    26.7    -      -       -      +
    243B  TYR*     3.0    14.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 254 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  GLU*     4.0    12.1    -      -       -      +
    129A  VAL      5.2     0.9    +      -       -      -
    252A  VAL*     4.8     7.7    -      -       -      +
    253A  LEU*     1.3   102.2    +      -       -      +
    255A  PHE*     1.3    62.5    +      -       -      +
    256A  THR*     3.0     9.0    +      -       +      -
    241B  GLY      3.6     4.7    -      -       -      +
    242B  ASN*     3.3    20.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  GLU*     3.8    13.9    -      -       -      -
    129A  VAL      4.0    10.3    -      -       -      -
    130A  VAL*     4.1     8.5    -      -       +      -
    131A  GLY      3.6    15.9    -      -       -      -
    132A  SER*     3.0    40.6    -      -       -      -
    253A  LEU      4.0     0.6    +      -       -      -
    254A  GLN*     1.3    70.8    -      -       -      +
    256A  THR*     1.3    64.9    -      -       -      +
    162B  TYR*     3.3    33.0    -      +       -      -
    164B  VAL*     3.6    20.9    -      -       +      -
    228B  HIS*     3.7    12.8    -      -       +      -
    229B  PRO*     4.2    13.5    -      -       +      -
    239B  TYR*     4.2     7.0    -      -       +      -
    240B  PHE*     3.0     5.7    -      -       -      +
    241B  GLY*     2.7    42.6    +      -       -      +
    242B  ASN*     4.3     6.5    -      -       -      -
    243B  TYR      4.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 256 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  LYS*     5.7     2.1    -      -       -      +
    127A  THR      4.7     5.0    -      -       -      +
    128A  GLU*     3.2    26.7    -      -       -      +
    254A  GLN*     3.0    10.4    +      -       +      +
    255A  PHE*     1.3    73.9    -      -       -      +
    257A  ASN*     1.3    67.2    +      -       -      +
    258A  THR*     2.8    26.2    +      -       -      +
    259A  LEU*     3.6    23.2    +      -       +      +
    239B  TYR*     2.6    20.2    +      -       -      -
    240B  PHE*     3.2     9.0    -      -       +      -
----------------------------------------------------------
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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