Contacts of the strand formed by residues 249 - 255 (chain 1) in PDB entry 6Q8O


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 MET 249 (chain 1).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     131  PHE*     4.3     6.7    -      -       +      -
     161  THR*     5.5     0.9    -      -       -      -
     171  LEU*     3.8    21.8    -      -       +      -
     651  ARG*     2.4    35.6    +      -       -      -
    2221  GLU*     3.6     0.7    -      -       -      +
    2261  SER*     3.3    32.9    +      -       -      +
    2291  PRO*     4.0    21.1    -      -       +      -
    2371  TRP*     5.1     4.3    -      -       +      -
    2381  PHE*     3.3    24.2    -      -       +      -
    2411  MET*     3.9    24.8    -      -       -      +
    2481  GLY*     1.3    74.9    -      -       -      -
    2501  LYS*     1.3    59.6    +      -       -      +
    2651  GLU*     4.5    13.5    -      -       +      +
    2661  LEU      3.7    16.6    -      -       -      +
    2671  PRO*     4.1     2.7    -      -       -      -
    2681  MET*     4.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 250 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     651  ARG*     3.9    18.4    -      -       -      +
    1021  LYS*     3.8     9.3    -      -       -      +
    2221  GLU*     3.1    38.7    +      -       -      +
    2491  MET*     1.3    76.3    -      -       -      +
    2511  LEU*     1.3    94.1    +      -       -      +
    2521  TYR*     3.4    20.1    +      -       +      -
    2651  GLU*     3.7     0.2    -      -       -      -
    2661  LEU      2.8    32.1    +      -       -      +
    2681  MET*     3.6    29.8    -      -       +      -
    3131  TYR*     5.6     2.9    -      -       -      +
    3231  LEU*     6.0     1.1    -      -       +      -
    3241  GLY      5.3     1.8    -      -       -      -
    3251  THR*     2.6    35.4    +      -       -      +
    3261  GLY*     4.2     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 251 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     171  LEU*     3.5    30.3    -      -       +      -
     181  TYR*     3.5    35.9    -      -       +      -
    1021  LYS*     3.4    28.8    -      -       +      +
    1031  ASP*     4.8     0.2    -      -       -      +
    1061  ILE*     3.5    21.8    -      -       +      -
    2221  GLU*     4.0    11.3    +      -       +      +
    2501  LYS*     1.3   102.6    +      -       -      +
    2521  TYR*     1.3    54.6    +      -       -      +
    2531  GLN*     2.7    16.3    -      -       -      +
    2631  VAL*     4.5     4.5    -      -       +      -
    2641  TYR      3.7     4.9    -      -       -      -
    2651  GLU*     3.6    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 252 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2501  LYS*     3.6    30.3    -      -       +      +
    2511  LEU*     1.3    71.4    -      -       -      +
    2531  GLN*     1.3    65.6    +      -       -      +
    2631  VAL*     3.4     2.3    -      -       -      +
    2641  TYR*     2.9    38.0    +      -       +      +
    2661  LEU*     3.7    18.6    -      -       +      -
    2671  PRO      3.6    18.6    -      -       -      -
    2681  MET*     3.1    38.0    -      -       -      +
    2691  GLY      3.5     6.9    +      -       -      -
    2701  THR*     4.8     4.7    +      -       -      -
    2751  LEU*     3.7    29.4    -      -       +      -
    3111  MET*     3.6    36.6    +      -       +      +
    3231  LEU*     4.3     8.1    -      -       +      +
    3261  GLY*     3.9    14.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 253 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     991  GLY      3.1    23.6    +      -       -      +
    1001  SER*     3.9    11.3    +      -       -      +
    1011  PHE*     3.6    24.7    -      -       +      +
    1021  LYS*     4.1    16.8    -      -       +      +
    2511  LEU      2.7    22.0    -      -       -      +
    2521  TYR*     1.3    76.0    -      -       -      +
    2541  ILE*     1.3    62.0    +      -       -      +
    2621  GLY      2.9    14.8    -      -       -      +
    2631  VAL*     4.3     5.6    -      -       +      -
    2641  TYR*     5.5     0.7    -      -       -      -
    2751  LEU*     5.9     1.8    -      -       -      -
    3251  THR*     3.1    24.1    +      -       -      +
    3261  GLY      2.7    19.5    +      -       -      +
    3271  GLY*     3.2    15.4    -      -       -      +
    3281  VAL*     2.9    15.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 254 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1011  PHE*     3.2     9.1    -      -       -      -
    2531  GLN*     1.3    75.5    -      -       -      +
    2551  SER*     1.3    66.9    -      -       -      +
    2581  VAL*     4.9     2.0    -      -       +      -
    2611  PRO*     3.5    12.8    -      -       +      +
    2621  GLY      2.9    42.5    +      -       -      +
    2641  TYR*     4.8     5.6    -      -       +      -
    2751  LEU*     4.6    18.2    -      -       +      -
    2761  ILE*     4.3    14.6    -      -       +      -
    2801  ALA*     4.1    26.5    -      -       +      -
    3281  VAL*     3.3    22.2    -      -       +      +
    3301  LEU*     3.6    37.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 255 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     991  GLY*     4.4     0.7    -      -       -      -
    1011  PHE*     3.8    11.1    -      -       -      -
    2541  ILE*     1.3    77.3    -      -       -      +
    2561  GLY*     1.3    59.1    +      -       -      +
    2581  VAL*     5.7     0.9    -      -       -      -
    2611  PRO*     4.4     6.3    -      -       -      -
    3281  VAL      2.9    14.8    +      -       -      -
    3291  ILE*     3.2    21.8    -      -       -      +
    3301  LEU*     3.0    30.7    +      -       -      +
     872  SER*     3.5     7.3    +      -       -      -
    1282  CYS*     3.6    31.7    -      -       -      +
    1292  HIS*     5.1     0.4    -      -       -      +
----------------------------------------------------------
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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