Contacts of the strand formed by residues 303 - 312 (chain N) in PDB entry 4G7H


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 PRO 303 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250N  LEU*     3.9    35.9    -      -       +      -
    251N  PHE      3.8     6.5    -      -       -      +
    252N  ARG*     3.5    24.2    -      -       +      +
    291N  LEU*     4.0    19.9    -      -       +      +
    292N  VAL*     4.0    12.0    -      -       -      +
    302N  GLN*     1.3    92.9    +      -       +      +
    304N  LEU*     1.3    61.7    +      -       -      +
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Residues in contact with LEU 304 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251N  PHE*     2.8    23.4    +      -       +      +
    253N  ALA*     3.7    30.1    -      -       +      +
    259N  VAL*     4.6     0.2    -      -       +      -
    270N  LEU*     4.3    20.6    -      -       +      +
    272N  LEU*     4.4     2.9    -      -       +      -
    282N  TYR*     3.5    38.4    -      -       +      -
    284N  LEU*     5.1     1.2    -      -       +      +
    290N  PRO*     3.6     4.5    -      -       -      +
    291N  LEU*     2.8    21.0    +      -       -      -
    292N  VAL*     3.8    23.0    +      -       +      +
    298N  VAL*     3.8    33.0    -      -       +      -
    302N  GLN      3.2     2.0    +      -       -      +
    303N  PRO*     1.3    73.0    -      -       -      +
    305N  ALA*     1.3    61.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 305 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250N  LEU*     3.3     7.3    -      -       -      +
    251N  PHE*     3.1    30.0    +      -       +      -
    284N  LEU*     4.0    17.9    -      -       +      -
    288N  MET*     3.7    24.7    -      -       +      -
    289N  THR      3.3    14.6    -      -       -      +
    290N  PRO*     4.3     0.9    -      -       +      -
    291N  LEU*     3.6    13.9    -      -       -      +
    303N  PRO*     3.5     1.8    -      -       -      +
    304N  LEU*     1.3    81.9    -      -       -      +
    306N  GLU*     1.3    60.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 306 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248N  PRO*     3.7    31.0    -      -       -      +
    249N  TYR      3.9     2.5    -      -       -      -
    250N  LEU*     4.4    16.6    -      -       +      +
    287N  GLY      3.8     0.5    -      -       -      +
    288N  MET*     3.5     2.5    -      -       -      -
    289N  THR*     2.9    46.9    +      -       -      +
    291N  LEU*     3.9    16.5    -      -       +      +
    305N  ALA*     1.3    72.9    -      -       -      +
    307N  ALA*     1.3    64.8    +      -       -      +
    308N  LYS*     3.4    33.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 307 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225N  LEU*     5.5     0.4    -      -       +      -
    245N  LEU*     3.2    24.7    -      -       +      +
    248N  PRO*     3.4     2.1    -      -       -      +
    249N  TYR*     2.9    48.6    +      -       +      +
    251N  PHE      5.2     0.2    -      -       -      +
    287N  GLY      3.7     4.9    -      -       -      -
    288N  MET*     3.6    33.8    -      -       +      +
    305N  ALA      4.1     0.4    -      -       -      -
    306N  GLU*     1.3    71.6    -      -       -      +
    308N  LYS*     1.3    61.3    -      -       -      +
    311N  LEU*     4.3     4.7    -      -       +      -
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Residues in contact with LYS 308 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245N  LEU*     4.3     1.1    -      -       -      +
    248N  PRO*     4.2    20.6    -      -       +      -
    287N  GLY*     3.1    19.3    +      -       -      +
    289N  THR*     5.9     2.9    -      -       -      -
    306N  GLU*     3.4    31.8    +      -       +      +
    307N  ALA*     1.3    75.8    -      -       -      +
    309N  GLY*     1.3    72.2    +      -       -      +
    310N  LEU      3.3     8.3    +      -       -      +
    311N  LEU*     5.1     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 309 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245N  LEU*     2.7    53.9    +      -       -      +
    247N  GLU*     5.6     0.6    -      -       -      +
    248N  PRO*     5.4     2.6    -      -       -      +
    307N  ALA      4.4     0.2    +      -       -      -
    308N  LYS*     1.3    76.4    -      -       -      +
    310N  LEU*     1.3    57.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 310 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241N  ILE*     3.6    33.0    -      -       +      -
    243N  ALA      3.4    14.1    -      -       -      +
    244N  GLU*     3.9    17.5    -      -       +      +
    286N  VAL*     4.3     2.8    -      -       -      +
    287N  GLY*     4.4     4.5    -      -       -      -
    308N  LYS      3.3     5.6    +      -       -      +
    309N  GLY*     1.3    74.5    -      -       -      -
    311N  LEU*     1.3    61.5    +      -       -      +
    312N  ARG*     4.3    10.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 311 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225N  LEU*     4.4    10.1    -      -       +      -
    241N  ILE*     3.8     3.1    -      -       -      +
    242N  LEU*     2.9    37.7    +      -       +      -
    243N  ALA*     2.9    46.0    +      -       +      +
    245N  LEU*     3.6    36.1    -      -       +      -
    285N  PRO*     4.0    20.6    -      -       +      -
    286N  VAL      3.1    19.7    -      -       -      +
    287N  GLY*     4.1     7.0    -      -       -      -
    288N  MET*     4.1     7.6    -      -       +      -
    307N  ALA*     4.3     9.0    -      -       +      -
    308N  LYS      5.1     1.3    -      -       -      +
    310N  LEU*     1.3    75.5    -      -       -      +
    312N  ARG*     1.3    59.8    +      -       -      +
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Residues in contact with ARG 312 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239N  GLY*     2.4    37.1    +      -       -      +
    240N  GLU*     3.3    17.2    -      -       -      +
    241N  ILE*     3.3    35.2    -      -       +      +
    242N  LEU*     3.8     3.8    -      -       -      +
    266N  GLU*     6.0     0.9    -      -       -      -
    285N  PRO*     3.4     7.4    -      -       -      +
    286N  VAL*     3.0    46.3    +      -       +      +
    310N  LEU*     4.9    12.1    +      -       -      +
    311N  LEU*     1.3    75.6    -      -       -      +
    313N  MET*     1.3    72.4    +      -       -      +
----------------------------------------------------------
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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