Contacts of the strand formed by residues 35 - 40 (chain L) 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 VAL 35 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22L  CYS*     4.9     2.7    -      -       -      -
     29L  VAL*     3.9    41.1    -      -       +      +
     32L  TYR      4.6     4.0    -      -       -      +
     33L  ASN      3.6     2.6    -      -       -      -
     34L  TYR*     1.3    78.9    -      -       -      +
     36L  SER*     1.3    68.4    +      -       -      +
     37L  TRP*     4.0    12.6    -      -       +      +
     50L  ILE*     4.4     1.6    -      -       -      +
     51L  TYR*     3.5     1.4    -      -       -      -
     52L  GLY      3.2     5.7    +      -       -      -
     53L  VAL*     2.8    46.0    +      -       +      +
     68L  LYS*     5.1     0.2    -      -       +      -
     73L  ALA*     3.7    23.3    -      -       +      -
     90L  CYS*     4.4     7.6    -      -       +      -
     91L  SER      3.2    11.7    -      -       -      +
     92L  SER*     4.5     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 36 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106H  TYR      4.4     0.2    +      -       -      -
    107H  TYR      2.8    24.7    +      -       -      -
    108H  GLY*     3.6     3.5    -      -       -      -
     34L  TYR      3.9     1.2    +      -       -      -
     35L  VAL*     1.3    72.9    -      -       -      +
     37L  TRP*     1.3    64.5    +      -       -      +
     38L  TYR*     4.0     5.4    -      -       -      -
     48L  LEU*     3.9    11.2    -      -       -      -
     50L  ILE      3.1     9.4    -      -       -      -
     51L  TYR*     3.5    16.1    -      -       -      +
     52L  GLY      4.3     1.4    +      -       -      -
     90L  CYS*     3.0     8.4    -      -       -      +
     91L  SER*     2.8    46.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 37 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6L  GLN*     3.8    10.5    -      -       -      -
     20L  ILE*     3.5    37.5    -      -       +      -
     21L  SER      4.1     0.7    -      -       -      -
     22L  CYS*     3.5    31.9    -      -       +      -
     35L  VAL*     4.0    13.0    -      -       +      +
     36L  SER*     1.3    77.4    -      -       -      +
     38L  TYR*     1.3    58.8    +      -       -      +
     48L  LEU*     3.7     4.3    -      -       -      +
     49L  MET*     2.7    33.0    +      -       +      -
     50L  ILE*     2.8    42.9    +      -       +      +
     53L  VAL      4.8     2.9    +      -       -      -
     66L  GLY*     4.9     1.2    -      -       -      -
     67L  SER      5.2     0.2    +      -       -      -
     73L  ALA*     3.8    12.2    -      -       +      +
     74L  SER*     4.0    10.9    +      -       -      -
     75L  LEU*     3.5    47.3    -      -       +      -
     88L  TYR*     4.7     3.6    -      -       +      -
     89L  TYR      3.3    10.5    -      -       -      -
     90L  CYS*     3.7    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 38 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45H  LEU*     5.0     1.6    -      -       +      -
    108H  GLY*     3.4     4.3    -      -       -      -
    109H  MET*     2.9    46.3    +      -       +      +
    112H  TRP*     3.8    18.4    -      +       -      -
     36L  SER*     4.0     7.0    -      -       -      -
     37L  TRP*     1.3    77.3    -      -       -      +
     39L  GLN*     1.3    59.2    +      -       -      +
     40L  GLN      4.1     0.2    -      -       -      -
     46L  PRO*     4.1    14.6    -      -       +      -
     47L  LYS      3.1    17.5    -      -       -      +
     48L  LEU*     3.6    17.9    -      -       +      -
     49L  MET*     4.1     2.5    -      -       -      -
     87L  ASP      3.8     0.2    -      -       -      +
     88L  TYR*     3.2    11.2    -      -       -      +
     89L  TYR*     2.7    49.8    +      -       +      +
     91L  SER*     3.7    10.8    -      -       -      -
    100L  TYR*     2.9    28.7    +      -       -      -
    102L  PHE*     3.6    24.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLN 39 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38L  TYR*     1.3    73.0    -      -       -      +
     40L  GLN*     1.3    63.3    +      -       -      +
     41L  HIS*     3.2    31.9    +      -       +      +
     45L  ALA      4.3     0.7    -      -       -      +
     46L  PRO*     3.4     0.8    -      -       -      +
     47L  LYS*     2.8    48.1    +      -       +      +
     49L  MET*     3.6    20.9    -      -       +      +
     64L  PHE*     3.9    15.2    -      -       -      -
     83L  GLY      4.9     0.2    +      -       -      -
     84L  ASP*     4.5     4.9    +      -       -      +
     86L  ALA*     3.7    11.0    -      -       +      -
     87L  ASP      3.6     3.4    -      -       -      -
     88L  TYR*     2.7    41.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 40 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39H  GLN*     3.0    41.7    +      -       -      -
     45H  LEU*     3.8     2.3    -      -       -      +
     95H  TYR*     3.6     9.5    +      -       -      -
     39L  GLN*     1.3    75.7    -      -       -      +
     41L  HIS*     1.3    66.2    +      -       -      +
     42L  PRO*     4.0     0.5    -      -       -      +
     43L  GLY      5.9     1.0    -      -       -      +
     44L  LYS      3.0    28.2    +      -       -      +
     45L  ALA      4.2     0.9    -      -       -      -
     46L  PRO*     3.7    30.0    -      -       +      +
     86L  ALA*     3.3     4.1    -      -       -      +
     87L  ASP*     2.8    47.5    +      -       +      +
     89L  TYR*     3.7    20.1    +      -       +      -
----------------------------------------------------------
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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