Contacts of the strand formed by residues 95 - 102 (chain F) in PDB entry 2QC8


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 LYS 95 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26F  VAL*     4.8     0.7    -      -       +      -
     27F  GLN      3.0    11.7    +      -       -      +
     28F  ALA*     3.6     5.3    -      -       +      -
     29F  MET*     2.9    30.5    +      -       -      +
     50F  GLU*     2.8    27.0    +      -       -      -
     51F  PRO*     3.4    42.3    +      -       +      -
     84F  MET*     4.0    25.8    -      -       +      +
     85F  PHE      3.4    14.4    -      -       -      +
     86F  ARG*     4.7     8.5    -      -       -      +
     87F  ASP*     3.8     4.8    -      -       -      +
     92F  ASP*     4.3    10.9    +      -       -      -
     93F  PRO      3.4    18.2    +      -       -      +
     94F  ASN*     1.3    81.3    -      -       -      +
     96F  LEU*     1.3    62.2    +      -       -      +
     97F  VAL*     4.2     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 96 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29F  MET*     3.6    24.9    -      -       +      -
     31F  ILE*     4.0    14.4    -      -       +      -
     83F  ALA      3.9     0.4    -      -       -      +
     84F  MET*     3.3     4.3    -      -       -      +
     85F  PHE*     2.7    43.5    +      -       +      +
     86F  ARG      4.2     3.8    -      -       -      +
     87F  ASP*     3.4    35.2    -      -       -      +
     88F  PRO*     3.7    21.3    -      -       +      -
     89F  PHE*     4.3     7.4    -      -       +      -
     95F  LYS*     1.3    71.4    -      -       -      +
     97F  VAL*     1.3    62.8    +      -       -      +
     98F  LEU      4.2     0.7    -      -       -      -
    186F  ALA*     5.1     0.9    -      -       +      -
    220F  VAL*     4.3    11.0    -      -       +      -
    223F  PHE*     4.3     9.2    -      -       +      -
    224F  ILE*     4.0    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 97 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28F  ALA*     4.6     9.9    -      -       +      -
     29F  MET      2.9    15.0    +      -       -      +
     30F  TYR*     3.3    12.5    -      -       +      -
     31F  ILE*     2.7    33.7    +      -       -      +
     54F  VAL*     4.8     0.2    -      -       +      -
     57F  LEU*     3.4    35.9    -      -       +      -
     81F  PRO*     3.9    21.1    -      -       +      -
     83F  ALA      3.3     7.4    -      -       -      +
     84F  MET*     4.3     0.4    -      -       +      -
     95F  LYS*     4.2    13.5    -      -       +      +
     96F  LEU*     1.3    81.9    -      -       -      +
     98F  LEU*     1.3    66.9    +      -       -      +
     99F  CYS*     3.5     6.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 98 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31F  ILE*     3.8    29.4    -      -       +      +
     32F  TRP*     5.1     2.9    -      -       -      +
     33F  ILE*     5.4     5.4    -      -       +      -
     40F  LEU*     5.2     2.9    -      -       +      -
     81F  PRO*     3.8     1.4    -      -       -      +
     82F  ALA*     2.8    31.9    +      -       +      -
     83F  ALA*     2.7    25.3    +      -       +      +
     96F  LEU      4.2     0.2    -      -       -      -
     97F  VAL*     1.3    73.6    -      -       -      +
     99F  CYS*     1.3    67.3    +      -       -      +
    114F  ARG*     5.0     4.7    -      -       -      +
    216F  ASP*     3.7    46.2    -      -       +      +
    219F  TRP*     4.1    22.4    -      -       +      -
    220F  VAL*     3.9    17.8    -      -       +      +
    349F  PHE*     4.5     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 99 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30F  TYR*     3.4    36.8    -      -       -      -
     31F  ILE      2.9    19.0    +      -       -      +
     32F  TRP*     4.4     7.6    -      -       -      +
     33F  ILE*     5.1     5.2    +      -       -      +
     79F  LEU*     4.0    19.3    -      -       +      -
     80F  VAL      3.3    11.4    -      -       -      +
     81F  PRO*     4.1    12.6    -      -       -      -
     82F  ALA*     4.2     3.8    -      -       -      +
     97F  VAL*     3.5    15.0    -      -       -      -
     98F  LEU*     1.3    85.4    -      -       -      +
    100F  GLU*     1.3    67.6    +      -       -      +
    101F  VAL*     4.3     0.7    +      -       -      +
    114F  ARG*     5.6     1.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 100 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78F  TYR      3.6     2.9    -      -       -      +
     79F  LEU*     3.6     2.4    -      -       -      -
     80F  VAL*     3.1    34.9    +      -       +      +
     82F  ALA*     4.3     4.3    -      -       +      +
     99F  CYS*     1.3    73.6    -      -       -      +
    101F  VAL*     1.3    61.0    +      -       -      +
    102F  PHE*     3.2    18.4    -      -       +      -
    112F  ASN*     2.8    38.5    +      -       -      +
    114F  ARG*     3.1    46.0    +      -       +      +
    115F  HIS*     3.2    31.9    +      -       -      -
    118F  LYS*     5.4     2.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 101 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32F  TRP*     3.8    35.2    -      -       +      -
     33F  ILE      3.9    17.3    -      -       -      +
     62F  PHE*     3.8    16.2    -      -       +      -
     69F  GLN*     4.4     3.8    -      -       -      +
     77F  MET*     3.5    29.8    -      -       +      -
     78F  TYR      3.3     9.4    -      -       -      +
     79F  LEU*     4.3     1.3    -      -       +      -
     99F  CYS      5.1     0.4    -      -       -      +
    100F  GLU*     1.3    76.0    -      -       -      +
    102F  PHE*     1.3    64.6    +      -       -      +
    109F  ALA*     3.0    29.7    +      -       +      +
    111F  THR*     5.8     1.1    -      -       -      +
    112F  ASN*     3.1    19.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 102 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77F  MET*     3.4    13.3    -      -       -      +
     78F  TYR*     3.0    38.3    +      -       +      -
     80F  VAL*     3.7    34.1    -      -       +      -
    100F  GLU*     3.2    39.0    -      -       +      -
    101F  VAL*     1.3    75.0    -      -       -      +
    103F  LYS*     1.3    63.8    +      -       -      +
    106F  ARG*     3.6    26.2    -      -       -      +
    107F  ARG      3.4     5.4    -      -       -      +
    108F  PRO*     3.5    26.5    -      -       +      -
    109F  ALA      4.0     0.7    -      -       -      +
    112F  ASN*     4.0     4.3    -      -       -      -
    115F  HIS*     3.9    24.2    -      +       -      -
----------------------------------------------------------
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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