Contacts of the strand formed by residues 383 - 390 (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 GLY 383 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213N  VAL*     4.5     1.3    -      -       -      -
    214N  GLU      3.0    15.5    -      -       -      -
    215N  TYR*     3.9     4.7    -      -       -      -
    216N  VAL*     4.1     4.5    -      -       -      -
    360N  ARG*     3.4     4.2    -      -       -      +
    361N  VAL*     2.8    46.8    +      -       -      +
    381N  ALA      3.4     1.6    +      -       -      -
    382N  GLU*     1.3    81.2    -      -       -      +
    384N  VAL*     1.3    62.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 384 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212N  ARG      3.8     0.5    -      -       -      +
    213N  VAL*     3.4     3.9    -      -       -      -
    214N  GLU*     2.9    46.2    +      -       +      +
    216N  VAL*     5.1     6.5    -      -       +      -
    340N  THR*     6.0     2.0    -      -       +      -
    358N  GLY*     4.7     5.8    -      -       -      +
    359N  ALA      3.1    10.5    -      -       -      +
    360N  ARG*     3.5    41.7    -      -       +      +
    383N  GLY*     1.3    80.8    -      -       -      +
    385N  VAL*     1.3    61.9    +      -       -      +
    386N  HIS*     3.4    24.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 385 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211N  VAL*     3.8    26.7    -      -       +      -
    212N  ARG      3.8     2.5    -      -       -      +
    213N  VAL*     4.4     9.9    -      -       +      +
    355N  VAL*     3.8    27.1    -      -       +      -
    356N  PRO      4.3     2.9    -      -       -      +
    357N  GLU*     3.8     0.6    -      -       -      -
    358N  GLY*     2.7    33.6    +      -       -      -
    359N  ALA      2.8    12.4    +      -       -      +
    361N  VAL*     3.5    35.9    -      -       +      -
    367N  ILE*     4.2     7.4    -      -       +      -
    384N  VAL*     1.3    75.8    -      -       -      +
    386N  HIS*     1.3    68.1    +      -       -      +
    387N  LEU*     4.4     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 386 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180N  LYS*     4.6     6.2    +      -       -      -
    211N  VAL*     3.5     4.9    -      -       -      +
    212N  ARG*     2.9    46.6    +      -       +      +
    214N  GLU*     4.1    15.7    -      -       +      +
    357N  GLU*     3.2    22.5    +      -       -      +
    358N  GLY*     5.3     4.7    -      -       -      -
    384N  VAL*     3.4    29.8    -      -       +      +
    385N  VAL*     1.3    80.3    +      -       -      +
    387N  LEU*     1.3    65.4    +      -       -      +
    388N  HIS*     3.8    21.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 387 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180N  LYS*     6.0     0.9    -      -       -      +
    181N  ASP*     5.4     4.5    -      -       -      +
    205N  TYR*     3.4    34.1    +      -       +      -
    208N  PRO*     4.0    23.8    -      -       +      -
    210N  ARG      4.1     0.9    -      -       -      -
    211N  VAL*     3.9    18.6    -      -       +      -
    353N  VAL*     4.0    19.5    -      -       +      -
    355N  VAL      4.0     6.1    -      -       -      +
    356N  PRO*     3.8     5.2    -      -       +      -
    357N  GLU*     3.2    55.4    +      -       +      +
    385N  VAL*     4.4     8.1    -      -       +      -
    386N  HIS*     1.3    79.3    -      -       -      +
    388N  HIS*     1.3    68.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 388 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176N  ASP*     3.2    21.9    +      -       -      +
    180N  LYS*     6.5     1.1    -      -       +      -
    205N  TYR*     5.0     0.4    -      -       -      -
    208N  PRO*     3.5     4.6    -      -       -      +
    209N  ARG      3.3     2.8    +      -       -      -
    210N  ARG*     2.9    69.4    +      -       -      +
    212N  ARG*     3.8    27.2    -      -       +      +
    386N  HIS*     3.8    21.4    +      -       +      +
    387N  LEU*     1.3    80.8    +      -       -      +
    389N  GLU*     1.3    70.7    +      -       -      +
    390N  PRO*     3.5     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 389 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174N  GLY*     3.3    40.3    +      -       -      +
    175N  VAL      4.2     6.7    -      -       -      +
    176N  ASP*     2.8    24.8    +      -       +      +
    209N  ARG*     2.6    45.4    +      -       +      +
    210N  ARG*     3.2    32.4    +      -       -      +
    346N  ARG*     3.4    31.4    +      -       -      -
    388N  HIS*     1.3    73.3    -      -       -      +
    390N  PRO*     1.3    64.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 390 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171N  LEU*     3.5    36.1    -      -       +      +
    175N  VAL      4.8     1.6    -      -       -      +
    176N  ASP*     4.1     6.1    -      -       -      +
    177N  ALA*     4.3     6.5    -      -       +      +
    205N  TYR*     3.9    43.7    -      -       +      -
    206N  ARG      4.2     2.7    -      -       -      +
    207N  PHE      3.3     7.4    -      -       -      +
    208N  PRO*     3.7     4.9    -      -       +      -
    209N  ARG*     4.7     2.5    +      -       -      -
    388N  HIS      3.5     2.7    -      -       -      -
    389N  GLU*     1.3    93.3    -      -       -      +
    391N  ALA*     1.3    65.7    +      -       -      +
    392N  SER      3.8    13.7    -      -       -      +
    393N  ILE*     4.1     4.0    -      -       +      -
----------------------------------------------------------
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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