Contacts of the strand formed by residues 45 - 51 (chain H) in PDB entry 3KYM


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 LEU 45 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36G  TYR*     6.4     0.9    -      -       +      -
     38G  GLN*     5.3     3.4    -      -       -      +
     44G  PRO*     5.6     4.9    -      -       +      -
     87G  TYR*     3.8    38.0    -      -       +      -
     98G  PHE*     3.7    55.2    +      -       +      +
     99G  GLY      4.9     2.6    +      -       -      -
     37H  VAL*     4.2    11.4    -      -       +      -
     38H  ARG      3.7     7.2    -      -       -      +
     39H  GLN*     3.7    31.5    -      -       +      +
     43H  LYS      3.9     1.0    +      -       -      -
     44H  GLY*     1.3    72.1    -      -       -      -
     46H  GLU*     1.3    59.7    +      -       -      +
     95H  TYR*     4.1    21.3    -      -       +      -
    109H  TRP*     4.6    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 46 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98G  PHE*     5.0     1.6    -      -       -      -
     37H  VAL*     3.1     6.1    -      -       -      +
     38H  ARG*     2.8    74.5    +      -       +      +
     44H  GLY      4.1     6.1    -      -       -      +
     45H  LEU*     1.3    77.0    -      -       -      +
     47H  TRP*     1.3    75.2    +      -       -      +
     61H  ALA*     4.7     2.8    -      -       -      +
     63H  SER*     3.5    25.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 47 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94G  TRP*     3.2    35.7    -      +       -      -
     95G  PRO*     3.7    32.8    -      -       +      -
     96G  LEU*     4.1    30.6    +      -       +      +
     98G  PHE*     5.0     6.6    -      -       +      -
     35H  PHE*     4.0    21.2    -      +       -      -
     36H  TRP      3.7     5.2    -      -       -      -
     37H  VAL*     3.9    12.3    -      -       +      +
     38H  ARG*     5.7     0.2    +      -       -      -
     46H  GLU*     1.3    85.7    -      -       -      +
     48H  VAL*     1.3    72.1    +      -       -      +
     49H  SER      3.1    29.1    -      -       -      +
     50H  TRP*     3.8     5.0    -      -       +      +
     59H  LYS*     4.5     4.3    -      -       +      -
     60H  TYR*     3.5    12.8    -      -       -      -
     61H  ALA*     3.3    52.8    -      -       +      +
     62H  ASP*     6.0     0.4    -      -       -      -
    104H  TRP*     6.3     0.2    -      -       -      -
    106H  PHE*     5.7     0.4    -      +       +      -
----------------------------------------------------------
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Residues in contact with VAL 48 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36H  TRP*     2.7    23.5    +      -       +      +
     37H  VAL      3.8     2.5    -      -       -      -
     38H  ARG*     3.6    48.0    -      -       +      +
     47H  TRP*     1.3    78.5    -      -       -      +
     49H  SER*     1.3    70.5    +      -       -      +
     60H  TYR*     3.7     1.7    -      -       -      -
     61H  ALA*     3.0    28.1    +      -       -      +
     64H  VAL*     4.1    10.1    -      -       +      +
     68H  PHE*     3.8    32.1    -      -       +      -
     81H  LEU*     4.1    10.3    -      -       +      -
     94H  TYR*     4.3     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 49 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35H  PHE*     3.2     8.8    -      -       -      -
     36H  TRP*     2.7    30.2    +      -       -      -
     47H  TRP*     3.1     9.2    -      -       -      +
     48H  VAL*     1.3    93.8    -      -       -      +
     50H  TRP*     1.3    58.6    +      -       -      +
     59H  LYS      3.2    11.3    +      -       -      -
     60H  TYR*     3.3    12.5    -      -       -      -
     70H  ILE*     3.1    40.8    -      -       -      +
     81H  LEU*     4.4     5.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 50 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  PRO*     3.6    12.3    -      -       +      +
     34H  MET      3.5    11.2    -      -       -      -
     35H  PHE*     3.1    39.5    -      +       +      -
     47H  TRP*     3.8     6.5    -      -       +      +
     49H  SER*     1.3    75.0    +      -       -      +
     51H  ILE*     1.3    75.4    +      -       -      +
     52H  GLY*     4.1    11.4    -      -       -      -
     53H  PRO*     5.5     0.4    -      -       +      -
     57H  ILE*     3.6    35.2    -      -       +      -
     58H  THR*     3.4     3.3    -      -       -      -
     59H  LYS*     2.9    56.6    +      -       +      +
     70H  ILE*     3.9     5.1    -      -       -      +
     99H  GLU*     3.0    20.9    +      -       -      -
    104H  TRP*     3.4    35.7    -      +       +      -
----------------------------------------------------------
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Residues in contact with ILE 51 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  PRO*     3.4     0.3    -      -       -      +
     34H  MET*     2.9    28.5    +      -       +      +
     50H  TRP*     1.3    95.5    +      -       -      +
     52H  GLY*     1.3    66.1    +      -       -      +
     55H  GLY*     3.8    28.0    -      -       -      +
     57H  ILE*     3.6    12.1    -      -       +      -
     58H  THR*     3.8    12.3    -      -       +      -
     70H  ILE*     3.7    31.8    -      -       +      +
     71H  SER*     3.8    16.4    -      -       -      +
     72H  ARG*     3.7    24.2    -      -       +      +
     79H  LEU*     3.7    24.9    -      -       +      -
----------------------------------------------------------
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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