Contacts of the strand formed by residues 108 - 115 (chain H) in PDB entry 6XXD


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 GLY 108 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21D  ILE*     4.2    21.3    -      -       -      -
     22D  PRO      5.4     0.6    +      -       -      -
     24D  LEU*     6.2     1.6    -      -       -      -
     70G  LYS*     5.5     1.1    -      -       -      -
     44H  VAL*     5.6     2.5    -      -       -      -
    103H  ALA*     3.5     0.3    -      -       -      -
    104H  THR      2.9    35.6    +      -       -      -
    105H  PRO      3.9     4.7    +      -       -      -
    106H  ASP      3.5     2.2    -      -       -      -
    107H  LYS*     1.3    82.3    -      -       -      +
    109H  VAL*     1.3    61.0    +      -       -      -
    110H  TYR*     3.4    10.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 109 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17D  ALA*     4.7     8.9    +      -       +      +
     18D  ALA*     4.6    17.7    -      -       -      +
     21D  ILE*     4.9     8.5    -      -       +      +
     37H  THR*     4.3    25.0    -      -       +      +
     40H  LEU*     3.8    38.1    -      -       +      +
     41H  ASN*     4.0    11.0    -      -       +      +
     44H  VAL*     3.9    27.1    -      -       +      -
    101H  PHE*     4.8     4.5    -      -       +      -
    102H  ALA      3.6    11.9    -      -       -      +
    103H  ALA*     4.1     2.9    -      -       +      -
    107H  LYS      4.0     1.9    +      -       -      +
    108H  GLY*     1.3    70.7    -      -       -      -
    110H  TYR*     1.3    64.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 110 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101H  PHE*     3.4     9.9    -      -       -      +
    102H  ALA*     2.8    52.2    +      -       +      +
    104H  THR*     4.2     9.1    -      -       +      +
    107H  LYS*     3.5    53.4    -      -       +      +
    108H  GLY      3.4    15.7    -      -       -      -
    109H  VAL*     1.3    75.2    -      -       -      +
    111H  LYS*     1.3    69.1    +      -       -      +
    112H  THR*     5.2     0.7    -      -       -      -
    124H  CYS*     3.7     6.8    -      -       -      +
    125H  PRO*     2.7    50.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 111 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30H  ARG*     5.2     2.6    -      -       -      +
     98H  THR*     5.7     0.9    -      -       -      +
     99H  VAL*     4.0    23.8    -      -       +      +
    100H  TRP      3.7     4.3    -      -       -      +
    101H  PHE*     3.7    27.1    -      -       +      -
    110H  TYR*     1.3    86.6    -      -       -      +
    112H  THR*     1.3    59.6    +      -       -      +
    113H  ASN*     5.1     1.2    -      -       -      +
     52J  ILE*     3.7    28.2    +      -       -      +
     53J  ASP*     3.9    24.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 112 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91H  ILE*     6.0     1.8    -      -       +      -
     99H  VAL*     3.4    23.6    -      -       -      +
    100H  TRP*     3.0    41.1    +      -       +      +
    101H  PHE*     5.2     0.7    -      -       -      -
    102H  ALA*     5.3     4.9    -      -       +      +
    110H  TYR*     4.2     3.3    +      -       -      -
    111H  LYS*     1.3    74.3    -      -       -      +
    113H  ASN*     1.3    75.0    +      -       -      +
    114H  THR*     3.8    20.6    +      -       -      +
    121H  PRO*     4.2     8.4    -      -       +      +
    125H  PRO*     3.6    34.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 113 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99H  VAL*     4.2     6.1    -      -       -      +
    111H  LYS      5.1     1.4    -      -       -      +
    112H  THR*     1.3    82.7    +      -       -      +
    114H  THR*     1.3    61.7    +      -       -      +
    115H  ALA*     3.5     2.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 114 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99H  VAL*     3.3     7.0    -      -       -      +
    100H  TRP*     3.2    28.7    +      -       +      -
    112H  THR*     3.3     9.4    +      -       -      +
    113H  ASN*     1.3    76.7    -      -       -      +
    115H  ALA*     1.3    66.8    +      -       -      +
    118H  SER*     4.2     8.7    -      -       -      -
    119H  SER      3.5    25.6    -      -       -      +
    121H  PRO*     3.8    25.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 115 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98H  THR      4.0    11.9    -      -       -      +
     99H  VAL*     4.2     3.4    -      -       +      -
    100H  TRP*     2.9    16.5    +      -       -      -
    113H  ASN      3.5     3.5    +      -       -      +
    114H  THR*     1.3    76.5    -      -       -      +
    116H  VAL*     1.3    64.2    +      -       -      +
    117H  THR*     3.3    18.2    -      -       +      +
    118H  SER*     3.2    24.0    +      -       -      +
----------------------------------------------------------
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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