Contacts of the strand formed by residues 329 - 340 (chain F) in PDB entry 6Q2J


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 PHE 329 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283F  VAL*     4.7     3.6    -      -       +      -
    293F  VAL*     4.1    18.2    -      -       +      -
    318F  LEU*     4.0    11.7    -      -       +      +
    324F  TRP*     5.2     4.9    -      +       -      -
    325F  ALA*     2.7    21.9    +      -       +      +
    326F  GLN*     4.0    14.8    -      -       -      +
    328F  THR*     1.3   101.6    -      -       -      +
    330F  ARG*     1.3    61.7    +      -       -      +
    356F  LEU*     4.5    22.9    -      -       +      -
    357F  VAL      3.5    11.2    -      -       -      -
    358F  LEU*     3.6    25.4    -      -       +      -
    359F  ASN*     5.0     3.3    +      -       -      -
    362F  LEU*     5.0     1.3    -      -       +      -
    370F  MET*     3.8    34.3    -      -       +      -
    372F  LEU*     4.4    15.3    -      -       +      -
    395F  VAL*     4.0    23.1    -      -       +      -
    397F  VAL*     5.0     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 330 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289F  GLU      4.6     2.8    +      -       -      -
    290F  ASP*     4.0    12.7    +      -       -      +
    318F  LEU*     5.0     1.3    -      -       -      -
    329F  PHE*     1.3    76.1    -      -       -      +
    331F  VAL*     1.3    66.3    -      -       -      +
    332F  GLU*     3.6    17.1    +      -       -      +
    356F  LEU*     3.6     4.5    -      -       -      -
    357F  VAL*     2.9    63.0    +      -       +      +
    358F  LEU      3.5    15.0    +      -       -      -
    359F  ASN*     3.5    29.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 331 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316F  SER*     4.4    15.4    +      -       -      +
    318F  LEU*     3.7    43.7    -      -       +      +
    330F  ARG*     1.3    76.5    -      -       -      +
    332F  GLU*     1.3    60.4    +      -       -      +
    333F  HIS      3.8     1.9    +      -       -      -
    354F  TYR*     4.5    18.2    -      -       +      -
    355F  ARG      3.4    11.2    -      -       -      +
    356F  LEU*     3.8    15.5    -      -       +      -
    374F  VAL*     3.8    29.4    -      -       +      -
    393F  PHE*     5.6     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 332 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330F  ARG*     3.6    20.6    +      -       +      +
    331F  VAL*     1.3    72.3    -      -       -      +
    333F  HIS*     1.3    61.5    +      -       -      +
    334F  TRP*     3.2    35.3    +      -       +      -
    353F  ASP      4.1     0.5    -      -       -      +
    354F  TYR*     3.7     1.4    -      -       -      -
    355F  ARG*     2.9    47.8    +      -       +      +
    357F  VAL*     3.4    25.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 333 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    310F  LEU*     4.4     7.2    -      -       +      +
    314F  TYR*     4.2    26.8    -      -       +      +
    316F  SER*     4.1    12.8    -      -       -      +
    331F  VAL      3.8     2.5    +      -       -      +
    332F  GLU*     1.3    76.3    -      -       -      +
    334F  TRP*     1.3    83.4    +      -       -      +
    335F  PRO*     4.0    10.2    -      -       +      +
    352F  HIS*     3.6    28.6    +      +       +      -
    353F  ASP      3.4     8.5    +      -       -      -
    354F  TYR*     3.2    48.1    +      +       +      -
----------------------------------------------------------
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Residues in contact with TRP 334 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332F  GLU*     3.2    46.7    -      -       +      -
    333F  HIS*     1.3    81.9    -      -       -      +
    335F  PRO*     1.3    80.8    -      -       +      +
    353F  ASP*     2.9    48.4    +      -       +      +
    355F  ARG*     3.3    48.2    -      -       -      +
    702F  NAG      4.5    18.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 335 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    307F  SER*     6.2     0.7    -      -       -      +
    310F  LEU*     3.6    42.2    -      -       +      -
    333F  HIS*     4.0     4.9    -      -       +      +
    334F  TRP*     1.3   102.9    -      -       +      +
    336F  ASN*     1.3    68.2    +      -       -      +
    350F  THR*     5.6     2.0    -      -       +      -
    351F  VAL      3.5     7.4    -      -       -      +
    352F  HIS*     3.5    28.5    -      -       +      +
    353F  ASP*     5.9     0.4    -      -       -      -
    702F  NAG      4.0     8.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 336 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294D  ARG*     4.1     6.4    +      -       -      -
    335F  PRO*     1.3    76.6    -      -       -      +
    337F  GLU*     1.3    75.7    +      -       -      +
    338F  THR*     6.1     1.0    -      -       -      -
    350F  THR*     3.3     9.2    -      -       -      +
    351F  VAL*     2.9    37.7    +      -       +      +
    353F  ASP*     5.7     4.0    -      -       -      +
    702F  NAG      1.4    73.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 337 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294D  ARG*     3.2    31.8    +      -       +      +
    295D  THR*     4.9     2.6    -      -       -      -
    296D  ILE      5.3     1.7    -      -       -      +
    303F  VAL*     3.8    27.1    -      -       -      +
    336F  ASN*     1.3    91.1    +      -       -      +
    338F  THR*     1.3    62.4    +      -       -      +
    348F  ARG*     2.9    38.9    +      -       +      +
    349F  ALA      3.2    14.4    -      -       -      +
    350F  THR*     4.1    13.1    -      -       +      +
    351F  VAL      4.6     0.7    -      -       -      +
    702F  NAG      5.0     2.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 338 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297F  ARG*     6.1     0.2    -      -       -      +
    299F  PHE*     5.6     4.7    -      -       +      -
    336F  ASN*     6.1     0.9    -      -       -      -
    337F  GLU*     1.3    75.2    -      -       -      +
    339F  SER*     1.3    76.1    +      -       -      +
    340F  VAL*     6.3     0.7    -      -       +      -
    348F  ARG*     3.3    10.7    -      -       -      +
    349F  ALA*     2.9    33.6    +      -       +      +
    351F  VAL*     3.9    27.6    -      -       +      -
    702F  NAG      4.6    14.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 339 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338F  THR*     1.3    92.5    +      -       -      +
    340F  VAL*     1.3    60.3    +      -       -      +
    346F  PHE*     3.9    34.8    -      -       -      -
    347F  VAL      3.8     4.0    -      -       -      -
    348F  ARG*     4.4     7.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 340 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299F  PHE*     4.6    28.5    -      -       +      -
    301F  ALA*     6.6     0.2    -      -       +      -
    338F  THR*     4.3     1.2    +      -       +      -
    339F  SER*     1.3    75.1    -      -       -      +
    341F  GLN*     1.3    77.4    +      -       -      +
    346F  PHE*     3.4     4.5    -      -       -      -
    347F  VAL*     2.9    49.6    +      -       +      +
    349F  ALA*     4.7     8.3    -      -       +      -
----------------------------------------------------------
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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