Contacts of the strand formed by residues 86 - 93 (chain A) in PDB entry 3KDM


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 ALA 86 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  GLN*     3.9    15.7    -      -       +      -
     40A  GLN      3.4    18.6    -      -       -      +
     41A  HIS*     3.7    16.2    -      -       +      +
     42A  PRO*     4.6     6.5    -      -       -      -
     84A  ASP      3.1    10.2    +      -       -      +
     85A  GLU*     1.3    75.5    -      -       -      +
     87A  ASP*     1.3    65.4    +      -       -      +
     88A  TYR*     3.7     7.7    -      -       +      -
    107A  LYS*     3.7     5.7    -      -       -      +
    108A  VAL      3.0    28.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  TYR      3.9     0.2    -      -       -      +
     39A  GLN*     3.6     0.7    -      -       -      -
     40A  GLN*     2.7    40.0    +      -       +      +
     42A  PRO*     3.7    16.0    -      -       -      +
     86A  ALA*     1.3    74.4    -      -       -      +
     88A  TYR*     1.3    60.4    +      -       -      +
     89A  TYR*     3.9    27.9    +      -       +      +
    105A  GLY      5.7     0.4    -      -       -      -
    106A  THR      3.3     8.5    -      -       -      +
    107A  LYS*     2.6    52.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  GLN*     2.9     9.6    +      -       -      -
     20A  ILE*     3.8    19.1    -      -       +      -
     37A  TRP*     4.6     4.0    -      -       +      -
     38A  TYR      3.1    15.3    -      -       -      +
     39A  GLN*     3.1    38.3    +      -       +      -
     49A  MET*     5.0     2.0    -      -       +      -
     64A  PHE*     3.8    23.1    -      +       -      -
     75A  LEU*     3.6    21.8    -      -       +      -
     77A  ILE*     4.0     6.4    -      -       +      +
     84A  ASP*     2.6    32.9    +      -       -      +
     86A  ALA*     3.7    12.1    -      -       +      -
     87A  ASP*     1.3    74.8    -      -       -      +
     89A  TYR*     1.3    62.1    +      -       -      +
    105A  GLY*     3.4     0.5    -      -       -      -
    106A  THR      2.9    31.5    +      -       -      +
    108A  VAL*     3.4    33.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  GLN*     3.5     2.9    -      -       -      +
     37A  TRP*     3.4     5.0    -      -       -      -
     38A  TYR*     2.7    44.6    +      -       +      -
     40A  GLN*     3.5    23.1    +      -       +      -
     87A  ASP*     3.9    33.8    +      -       +      +
     88A  TYR*     1.3    74.6    -      -       -      +
     90A  CYS*     1.3    66.9    +      -       -      +
    102A  PHE*     4.3     7.4    -      -       +      -
    103A  GLY      3.6    13.7    -      -       -      +
    104A  THR      3.8     4.0    -      -       -      -
    105A  GLY*     3.5    24.2    -      -       -      -
     39B  GLN*     3.4    16.3    +      -       -      -
     43B  LYS      3.7     2.9    +      -       -      -
     44B  GLY*     3.7    27.8    -      -       -      -
     45B  LEU*     3.6    34.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  LEU*     3.9     4.0    -      -       -      -
      6A  GLN*     3.1    25.8    +      -       -      -
     22A  CYS*     2.1    54.3    -      -       +      -
     35A  VAL*     4.9     1.1    -      -       +      -
     36A  SER      3.1    10.3    -      -       -      +
     37A  TRP*     3.7    18.3    -      -       +      -
     89A  TYR*     1.3    74.8    -      -       -      +
     91A  SER*     1.3    60.0    +      -       -      +
    102A  PHE*     3.5     4.2    -      -       -      -
    103A  GLY*     2.7    36.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  LEU*     3.7     6.6    -      -       -      +
     29A  VAL*     5.5     0.2    -      -       -      +
     35A  VAL*     3.3     8.3    -      -       -      +
     36A  SER*     2.9    42.4    +      -       -      +
     38A  TYR*     3.7     2.6    -      -       -      -
     90A  CYS*     1.3    77.5    -      -       -      +
     92A  SER*     1.3    64.9    +      -       -      +
    100A  TYR*     2.7    35.5    +      -       -      -
    101A  VAL      3.1    15.7    -      -       -      -
    102A  PHE*     4.0    10.3    -      -       -      -
    107B  TYR      4.2     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  LEU*     3.7    13.4    -      -       -      +
     28A  ASP*     3.5    25.0    +      -       -      -
     29A  VAL*     3.6    11.2    +      -       -      -
     32A  TYR*     5.2     0.7    -      -       -      +
     34A  TYR*     3.3    16.1    +      -       -      +
     35A  VAL*     4.2     2.6    -      -       -      +
     91A  SER*     1.3    78.4    +      -       -      +
     93A  TYR*     1.3    81.6    +      -       -      +
    100A  TYR*     3.6     8.9    -      -       -      -
    101A  VAL*     3.0    33.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 93 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  ASP*     3.3    10.7    -      -       -      +
     32A  TYR*     3.4    55.9    -      +       +      -
     34A  TYR*     3.4    33.5    +      +       +      +
     92A  SER*     1.3    93.0    +      -       -      +
     94A  THR*     1.3    81.6    +      -       -      +
     95A  SER*     3.7    13.9    -      -       -      -
     99A  PRO*     3.6    10.8    -      -       +      -
    100A  TYR*     4.6     2.2    -      -       -      +
    107B  TYR*     3.8    38.2    -      +       +      +
----------------------------------------------------------
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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