Contacts of the strand formed by residues 97 - 104 (chain W) in PDB entry 3SDI


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 97 (chain W).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     -5W  SER*     5.2     1.3    +      -       -      -
     45W  ILE*     3.6    20.4    -      -       +      -
     46W  THR      3.0    10.8    -      -       -      +
     47W  GLY*     4.2     1.1    -      -       -      -
     51W  ASP*     3.6    25.4    -      -       +      -
     52W  VAL*     4.1     7.6    -      -       +      +
     55W  LEU*     3.5    26.5    -      -       +      -
     87W  LEU*     4.1     8.1    -      -       +      -
     95W  TYR*     3.2    16.1    +      -       +      +
     96W  PHE*     1.3    81.7    -      -       -      +
     98W  GLY*     1.3    60.2    +      -       -      +
     99W  PRO*     3.9    11.5    -      -       +      +
    115W  LEU*     3.7    23.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 98 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44W  GLY      3.9     1.0    -      -       -      +
     45W  ILE*     4.6     0.2    -      -       -      -
     46W  THR*     2.8    26.8    +      -       -      -
     97W  VAL*     1.3    74.3    -      -       -      +
     99W  PRO*     1.3    66.6    -      -       -      +
    100W  VAL*     3.9     1.6    +      -       -      +
    113W  PHE      3.9     9.6    -      -       -      -
    114W  ASP*     5.6     0.2    -      -       -      -
    127W  SER*     2.7    32.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 99 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43W  LEU*     3.8    19.3    -      -       +      -
     44W  GLY      3.1     7.6    -      -       -      +
     45W  ILE*     4.3     8.5    -      -       +      -
     55W  LEU*     4.7     6.1    -      -       +      -
     59W  PHE*     6.1     0.7    -      -       +      -
     83W  VAL*     4.4     4.5    -      -       +      -
     87W  LEU*     3.9    24.0    -      -       +      -
     97W  VAL*     3.8    17.9    -      -       +      +
     98W  GLY*     1.3    88.5    -      -       -      +
    100W  VAL*     1.3    61.7    +      -       -      +
    112W  GLY*     3.5     2.6    -      -       -      -
    113W  PHE*     3.0    55.5    +      -       +      +
    114W  ASP      4.7     0.4    -      -       -      +
    127W  SER*     5.3     0.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 100 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3W  VAL*     3.8    27.8    -      -       +      +
      5W  ALA*     3.7    29.4    -      -       +      +
     14W  ILE*     4.0     5.4    -      -       +      +
     42W  PHE      3.7     0.2    -      -       -      +
     43W  LEU*     3.3     6.1    -      -       -      +
     44W  GLY      2.7    39.0    +      -       -      +
     98W  GLY      4.1     1.6    -      -       -      +
     99W  PRO*     1.3    79.2    -      -       -      +
    101W  VAL*     1.3    67.9    +      -       -      +
    111W  ALA      3.3    11.9    -      -       -      +
    113W  PHE*     4.5     0.2    -      -       -      -
    125W  ILE*     3.7    23.3    -      -       +      -
    127W  SER*     3.9    23.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 101 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41W  VAL*     4.3    14.8    -      -       +      -
     42W  PHE      3.4     6.3    -      -       -      +
     43W  LEU*     4.2     4.0    -      -       +      -
     76W  PRO*     4.2    10.1    -      -       +      +
     79W  PHE*     3.9    24.9    -      -       +      -
     80W  THR*     3.6    20.6    -      -       -      +
     83W  VAL*     4.3     0.9    -      -       +      -
    100W  VAL*     1.3    79.7    -      -       -      +
    102W  ALA*     1.3    69.0    +      -       -      +
    109W  PHE*     4.3     9.9    -      -       +      -
    110W  ILE*     3.1     8.2    -      -       -      +
    111W  ALA      2.7    36.7    +      -       -      +
    113W  PHE*     3.6    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 102 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5W  ALA*     4.4     2.5    -      -       +      -
     12W  VAL*     4.3    10.8    -      -       +      -
     13W  ALA      4.7     1.1    -      -       -      +
     14W  ILE*     4.0    35.4    -      -       +      -
     41W  VAL*     3.8     0.9    -      -       -      +
     42W  PHE*     2.7    44.4    +      -       +      +
     76W  PRO*     5.2     0.7    -      -       -      -
    100W  VAL      4.2     0.2    +      -       -      -
    101W  VAL*     1.3    80.7    -      -       -      +
    103W  GLY*     1.3    57.3    +      -       -      +
    109W  PHE      3.4     6.1    -      -       -      -
    110W  ILE*     4.1    14.1    -      -       +      -
    178W  ILE*     4.9     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 103 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12W  VAL*     3.7    13.1    -      -       -      +
     40W  HIS      4.0    12.3    -      -       -      -
     41W  VAL*     5.0     0.2    -      -       -      -
     76W  PRO*     3.9    12.5    -      -       -      +
    102W  ALA*     1.3    75.9    -      -       -      +
    104W  ILE*     1.3    66.1    +      -       -      -
    109W  PHE*     2.9    35.9    +      -       -      +
    178W  ILE*     4.8     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 104 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10W  ASP      3.6    26.7    -      -       -      +
     11W  CYS*     3.8    14.8    -      -       -      +
     12W  VAL*     4.4     4.7    -      -       +      -
     40W  HIS*     3.1    30.4    +      -       -      -
     76W  PRO*     4.0     4.0    -      -       -      +
    103W  GLY*     1.3    77.2    -      -       -      +
    105W  ASN*     1.3    65.2    +      -       -      +
    106W  GLY      3.3    28.5    -      -       -      +
    107W  LYS      4.1     3.4    -      -       -      +
    108W  PRO*     4.4     7.9    -      -       +      -
    178W  ILE*     3.9    20.0    -      -       +      +
    179W  LYS*     3.9     0.2    -      -       -      -
    181W  LYS*     3.7    43.7    -      -       +      +
----------------------------------------------------------
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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