Contacts of the strand formed by residues 34 - 42 (chain A) in PDB entry 3A9L


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 MET 34 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  ASN*     2.9    14.4    +      -       -      +
     32A  PRO      3.9     0.4    -      -       -      -
     33A  SER*     1.3    78.3    -      -       -      +
     35A  ILE*     1.3    73.6    +      -       -      +
     36A  TYR*     3.6    28.7    -      -       +      +
     61A  GLY*     3.7     4.9    -      -       -      -
     62A  SER      3.0    21.5    +      -       -      -
     96A  HIS*     3.7     9.5    -      -       -      -
     98A  ASP*     3.4    35.4    -      -       +      -
     99A  ALA      4.0     3.6    -      -       -      +
    100A  VAL*     4.0    14.8    -      -       +      -
    122A  LEU*     3.5    27.6    -      -       +      -
    203A  GLU*     3.8    26.9    -      -       +      +
    207A  TYR*     3.9    12.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  MET*     1.3    78.1    -      -       -      +
     36A  TYR*     1.3    72.7    +      -       -      +
     37A  PHE*     4.0     4.9    +      -       +      -
     62A  SER*     3.5    16.6    -      -       -      +
     63A  LEU      4.3     0.4    -      -       -      +
     64A  TYR*     4.2    13.9    -      -       +      -
     92A  MET*     3.6    44.2    -      -       +      -
     93A  LEU*     4.3    18.6    -      -       +      -
     96A  HIS*     3.7    23.6    -      -       +      +
     98A  ASP      3.4    15.2    +      -       -      +
     99A  ALA*     3.8    13.5    -      -       +      +
    100A  VAL      3.1    24.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  MET*     3.6    14.6    -      -       +      +
     35A  ILE*     1.3    72.1    -      -       -      +
     37A  PHE*     1.3    66.6    +      -       -      +
     52A  ILE*     3.9    10.3    -      -       +      +
     55A  VAL*     3.6    23.6    -      -       +      -
     56A  VAL*     4.1    12.1    -      -       +      -
     59A  THR*     3.3    20.8    -      -       -      +
     61A  GLY*     4.2     6.1    -      -       -      -
     62A  SER      2.9    15.1    +      -       -      +
     63A  LEU*     3.3     7.1    -      -       -      -
     64A  TYR      3.3    14.7    +      -       -      -
    100A  VAL*     3.4    37.8    -      -       +      +
    102A  PHE*     3.5    19.3    -      +       +      -
    199A  ILE*     3.9    12.4    -      -       +      +
    203A  GLU*     2.4    51.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  ILE*     4.1    13.7    -      -       +      -
     36A  TYR*     1.3    74.5    -      -       -      +
     38A  SER*     1.3    67.0    +      -       -      +
     39A  PRO*     4.1    12.6    -      -       +      -
     52A  ILE*     3.4    10.3    -      -       -      +
     64A  TYR*     3.0    43.7    -      +       +      +
     84A  PHE*     5.7     1.6    -      +       -      -
     89A  ALA*     5.8     0.4    -      -       +      -
     93A  LEU*     3.8    30.1    -      -       +      -
     99A  ALA*     4.0    11.0    -      -       +      -
    100A  VAL      3.1    12.5    +      -       -      -
    101A  SER*     3.2    25.6    -      -       -      -
    102A  PHE      2.9    23.6    +      -       -      -
    152A  ILE*     3.8    44.2    -      -       +      -
    153A  VAL*     4.1     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  PHE*     1.3    79.3    -      -       -      +
     39A  PRO*     1.3    63.9    -      -       -      +
     40A  HIS*     3.0    26.7    +      -       -      +
     41A  ALA*     4.2     7.6    -      -       -      +
     48A  THR*     3.8     8.4    -      -       -      -
     52A  ILE*     3.5    16.2    -      -       -      +
     64A  TYR*     3.2     7.0    +      -       -      +
     65A  LEU*     3.5     4.4    -      -       -      +
     66A  PHE      3.0    24.6    +      -       -      +
    102A  PHE      2.9    25.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  PHE*     4.1    14.8    -      -       +      +
     38A  SER*     1.3    85.8    -      -       -      +
     40A  HIS*     1.3    74.7    +      -       +      +
     44A  ILE*     4.0     1.0    -      -       -      +
     64A  TYR*     4.9     0.4    -      -       +      -
     66A  PHE*     3.4    30.1    -      -       +      +
     77A  LEU      5.1     0.3    -      -       -      +
     81A  SER*     4.2     5.6    -      -       -      +
     84A  PHE*     3.4    46.7    -      -       +      -
    101A  SER*     5.1     0.7    -      -       -      -
    103A  HIS*     3.7    33.2    -      -       +      +
    152A  ILE*     4.4     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 40 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  SER*     3.0     9.5    +      -       -      +
     39A  PRO*     1.3   108.3    -      -       +      +
     41A  ALA*     1.3    60.5    +      -       -      +
     44A  ILE*     3.9    14.6    -      -       +      -
     45A  GLU*     2.9    51.6    +      -       -      +
     48A  THR*     3.3     3.5    +      -       -      -
     77A  LEU      5.2     0.4    -      -       -      -
     78A  HIS*     3.2    22.6    -      +       -      -
     79A  VAL      2.6    35.7    +      -       -      -
     81A  SER*     4.0     0.7    -      -       -      -
     84A  PHE*     5.0     0.4    -      +       -      -
    103A  HIS*     3.2     8.7    +      +       -      -
    251A   ZN      2.2    31.4    -      -       -      -
    261A  PO4      3.1    24.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  SER*     4.2     5.8    -      -       -      +
     40A  HIS*     1.3    76.4    -      -       -      +
     42A  GLY*     1.3    68.3    +      -       -      +
     44A  ILE*     3.3    10.0    +      -       -      +
     48A  THR*     3.3    12.8    -      -       -      +
     49A  THR*     3.4    12.3    -      -       -      +
     65A  LEU*     3.8    22.7    -      -       +      -
     66A  PHE      2.9    14.9    +      -       -      +
     67A  GLN*     3.6    14.6    -      -       +      -
     68A  GLY      2.9    17.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  ALA*     1.3    73.2    -      -       -      +
     43A  GLY*     1.3    61.1    +      -       -      -
     44A  ILE      3.6     0.2    +      -       -      -
     45A  GLU      3.9     2.4    -      -       -      +
     46A  VAL*     3.7    19.9    -      -       -      +
     47A  GLY      4.5     2.4    +      -       -      -
     48A  THR*     4.4     0.6    +      -       -      -
     49A  THR*     2.8    23.8    +      -       -      -
     50A  GLU*     5.7     0.6    -      -       -      +
     67A  GLN*     3.7    13.1    +      -       -      +
     68A  GLY      3.5     9.6    -      -       -      -
     69A  LEU*     5.9     0.4    -      -       -      -
    182A  LYS*     6.3     0.9    -      -       -      -
    185A  ARG*     4.6     8.3    +      -       -      -
----------------------------------------------------------
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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