Contacts of the strand formed by residues 320 - 330 (chain 0) in PDB entry 6FF7


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 320 (chain 0).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3120  GLU*     6.3     1.1    -      -       +      -
    3130  TYR      3.2    11.4    -      -       -      +
    3140  THR*     5.0     3.6    -      -       -      -
    3180  GLY      3.5     6.3    +      -       -      +
    3190  THR*     1.4    73.6    -      -       -      +
    3210  GLY*     1.4    58.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 321 (chain 0). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3120  GLU*     3.2     7.9    -      -       -      +
    3130  TYR*     2.8    35.6    +      -       -      +
    3200  VAL*     1.4    76.2    -      -       -      +
    3220  ARG*     1.4    58.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 322 (chain 0). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3100  LEU*     4.7    15.0    -      -       +      -
    3110  VAL      3.4     8.3    -      -       -      +
    3120  GLU*     4.6     0.9    -      -       -      +
    3210  GLY*     1.4    70.3    -      -       -      -
    3230  ARG*     1.3    58.2    +      -       -      +
    3240  VAL      4.3     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 323 (chain 0). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3090  ARG      3.3     2.9    -      -       -      +
    3100  LEU*     3.5     3.5    -      -       -      -
    3110  VAL*     2.8    39.1    +      -       +      +
    3130  TYR*     4.2    18.4    -      -       +      -
    3210  GLY      3.9     0.2    +      -       -      -
    3220  ARG*     1.3    73.1    -      -       -      +
    3240  VAL*     1.3    66.9    +      -       -      +
    3250  LYS*     3.4     4.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 324 (chain 0). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2540  ILE      5.6     1.3    -      -       -      +
    2550  PRO*     5.2     5.6    -      -       +      -
    2560  LYS*     4.6    25.6    -      -       +      +
    2570  LYS*     5.6     3.6    -      -       +      +
    3080  TYR*     5.9     3.8    -      -       +      -
    3090  ARG      3.4     7.9    -      -       -      +
    3100  LEU*     4.9     1.1    -      -       -      +
    3220  ARG      4.3     0.6    +      -       -      -
    3230  ARG*     1.3    71.4    -      -       -      +
    3250  LYS*     1.3    59.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 325 (chain 0). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3070  GLN      3.8     0.9    -      -       -      +
    3080  TYR*     3.6     2.8    -      -       -      +
    3090  ARG*     2.9    37.7    +      -       +      +
    3110  VAL*     5.6     7.9    -      -       +      -
    3230  ARG*     3.4     6.2    +      -       +      +
    3240  VAL*     1.3    73.6    -      -       -      +
    3260  PRO*     1.3    62.0    -      -       -      +
    3270  TYR*     4.0     1.4    +      -       +      +
    3510  GLU*     6.1     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 326 (chain 0). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3070  GLN      3.4     9.0    -      -       -      +
    3080  TYR*     4.3     5.4    -      -       +      -
    3240  VAL      4.3     0.4    -      -       -      -
    3250  LYS*     1.3    76.1    -      -       -      +
    3270  TYR*     1.3    60.4    +      -       -      +
    3510  GLU*     4.0     4.3    -      -       -      +
    3520  LEU*     3.1    38.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 327 (chain 0). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3050  VAL      3.7     0.5    -      -       -      +
    3060  PHE*     3.6     4.2    -      -       -      +
    3070  GLN*     2.8    42.9    +      -       +      +
    3090  ARG*     6.6     0.4    -      -       +      -
    3250  LYS*     5.2     0.9    -      -       +      +
    3260  PRO*     1.3    75.5    -      -       -      +
    3280  ILE*     1.3    60.6    +      -       -      +
    3490  TYR*     3.7    26.2    -      -       +      +
    3500  TYR      3.1    14.6    -      -       -      +
    3510  GLU*     4.9     1.3    -      -       -      -
    3520  LEU*     4.3     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 328 (chain 0). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3040  ALA*     5.7     5.4    -      -       +      -
    3050  VAL      3.4     8.3    -      -       -      +
    3060  PHE*     5.3     2.0    -      -       -      -
    3270  TYR*     1.3    73.9    -      -       -      +
    3290  ILE*     1.3    60.6    +      -       -      +
    3480  ARG      3.5     1.4    -      -       -      +
    3490  TYR*     4.3     0.7    -      -       -      -
    3500  TYR*     2.7    45.1    +      -       +      +
    3520  LEU*     5.3     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 329 (chain 0). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3040  ALA*     3.5     4.9    -      -       -      +
    3050  VAL*     3.1    33.7    +      -       +      +
    3280  ILE*     1.3    74.9    -      -       -      +
    3300  ASP*     1.4    67.6    +      -       -      +
    3310  LEU*     4.7     0.3    -      -       -      +
    3470  GLN*     5.4     1.1    -      -       -      -
    3480  ARG      3.4    29.2    -      -       -      +
    3490  TYR*     4.0     5.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 330 (chain 0). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3030  HIS      4.1     5.8    -      -       -      +
    3040  ALA*     4.4     4.9    -      -       -      +
    3290  ILE*     1.4    77.4    -      -       -      +
    3310  LEU*     1.3    60.6    +      -       -      +
    3320  GLY*     3.2     6.7    +      -       -      +
    3330  SER      5.6     0.4    -      -       -      +
    3360  GLY*     5.8     3.6    -      -       -      -
    3370  THR*     4.4    21.8    -      -       -      +
    3440  ILE*     5.3     7.3    -      -       +      +
    3450  GLU      4.4     8.7    +      -       -      +
    3460  PRO*     3.9    25.0    -      -       +      +
    3470  GLN*     4.0    14.6    +      -       -      +
    3480  ARG      4.8     0.2    +      -       -      -
----------------------------------------------------------
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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