Contacts of the strand formed by residues 470 - 476 (chain A) in PDB entry 1SL2


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 470 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    457A  ALA*     3.4     8.2    -      -       -      +
    468A  PRO      4.8     4.3    -      -       -      +
    469A  TRP*     1.3    77.0    -      -       -      +
    471A  GLN*     1.3    61.3    -      -       -      +
    660A  CYS*     2.5    46.8    +      -       -      +
    661A  ARG      5.4     0.7    -      -       -      +
    662A  THR*     4.6    10.8    -      -       -      +
    663A  GLU*     4.2    27.4    -      -       +      +
    666A  ALA*     4.4     3.1    -      -       +      -
    696A  MET*     3.6    31.9    -      -       +      -
    697A  GLY*     3.4    15.7    -      -       -      +
    698A  PRO*     5.2     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 471 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  PHE*     4.2     1.8    -      -       -      -
    456A  GLY*     3.2    12.1    -      -       -      -
    457A  ALA*     3.0    28.7    +      -       +      +
    470A  VAL*     1.3    75.8    -      -       -      +
    472A  ALA*     1.3    62.4    +      -       -      +
    649A  MET*     3.5    20.5    -      -       +      +
    657A  GLN*     2.8    33.1    +      -       -      +
    658A  VAL      3.4     3.6    -      -       -      +
    666A  ALA*     4.9     0.4    -      -       -      -
    696A  MET*     3.2     9.1    -      -       -      +
    697A  GLY      2.7    47.9    +      -       -      +
    698A  PRO      4.2     1.1    -      -       -      -
    699A  ASN*     3.3     9.2    +      -       -      -
    700A  TRP*     3.2    28.1    -      -       -      +
    703A  CYS*     3.5     6.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 472 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    470A  VAL      4.2     0.2    +      -       -      -
    471A  GLN*     1.3    72.7    -      -       -      +
    473A  GLY*     1.3    60.9    +      -       -      +
    474A  ILE*     4.1     2.4    +      -       +      +
    656A  ILE      3.6     1.9    -      -       -      +
    657A  GLN*     3.6     3.1    -      -       -      -
    658A  VAL*     2.8    42.8    +      -       +      +
    660A  CYS*     4.0     8.3    -      -       -      -
    666A  ALA*     3.9    24.5    -      -       +      +
    669A  VAL*     3.9    20.6    -      -       +      -
    670A  ILE*     4.0     8.5    -      -       +      -
    695A  LYS      3.5     4.7    -      -       -      -
    696A  MET*     4.7     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 473 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    471A  GLN      4.1     0.4    -      -       -      -
    472A  ALA*     1.3    73.5    -      -       -      +
    474A  ILE*     1.3    61.0    +      -       -      +
    656A  ILE      3.4     3.4    -      -       -      -
    657A  GLN*     3.4    25.4    +      -       -      -
    693A  GLU      3.6     1.2    -      -       -      +
    694A  GLY*     3.2     3.1    -      -       -      -
    695A  LYS*     2.8    44.4    +      -       -      +
    703A  CYS*     3.8    10.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 474 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    472A  ALA      4.8     3.1    -      -       -      +
    473A  GLY*     1.3    80.7    -      -       -      +
    475A  ASP*     1.3    63.6    +      -       -      +
    625A  TRP*     3.6    15.4    -      -       +      -
    655A  GLU*     3.0     5.9    -      -       -      +
    656A  ILE*     2.9    45.9    +      -       +      -
    657A  GLN*     4.7     0.6    -      -       -      +
    658A  VAL*     6.3     0.4    -      -       +      -
    669A  VAL*     4.9     5.8    -      -       +      +
    670A  ILE*     4.2    23.1    -      -       +      +
    673A  ALA*     3.9    19.5    -      -       +      -
    692A  THR*     3.5    31.6    -      -       -      +
    693A  GLU      3.2     7.9    -      -       -      +
    694A  GLY*     4.2     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 475 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    473A  GLY      4.3     0.2    -      -       -      -
    474A  ILE*     1.3    74.9    -      -       -      +
    476A  ALA*     1.3    78.8    +      -       -      +
    477A  SER*     3.4     1.4    +      -       -      -
    625A  TRP*     4.6     0.9    -      -       -      -
    654A  ASP*     2.7    29.2    -      -       -      +
    655A  GLU*     3.4     5.5    -      -       +      +
    692A  THR*     3.3     3.8    -      -       -      -
    693A  GLU*     2.9    37.7    +      -       +      +
    704A  HIS*     3.0    27.3    -      -       +      +
   4002A   MG      2.4    22.7    -      -       -      -
   4004A  DAD      2.9    12.7    +      -       -      +
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Residues in contact with ALA 476 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    475A  ASP*     1.3    82.5    -      -       -      +
    477A  SER*     1.3    56.8    +      -       -      +
    479A  LEU*     4.0    20.6    -      -       +      -
    622A  CYS*     4.7     2.0    -      -       -      -
    625A  TRP*     4.4     2.2    -      -       +      -
    654A  ASP*     2.9    31.1    +      -       +      +
    677A  MET*     3.7    26.5    -      -       +      -
    691A  ASP      3.6     7.4    -      -       -      +
    692A  THR*     4.3     0.4    -      -       -      +
   4001A   MG      2.5    25.6    -      -       -      -
   4004A  DAD      2.8     2.5    +      -       -      -
----------------------------------------------------------
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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