Contacts of the strand formed by residues 43 - 54 (chain G) in PDB entry 5IYB


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 43 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37G  THR      4.0     0.2    -      -       -      +
     38G  CYS*     4.4     0.4    -      -       -      -
     39G  THR*     2.8    43.7    +      -       -      -
     40G  GLY      4.5     0.6    -      -       -      -
     41G  LYS      3.8     0.4    -      -       -      -
     42G  TYR*     1.3    77.7    -      -       -      +
     44G  PHE*     1.3    67.7    +      -       -      -
     45G  VAL*     3.4     3.8    +      -       -      +
     77G  PHE      3.4     8.1    -      -       -      -
     78G  ARG*     4.7     2.0    -      -       -      +
    157G  ILE*     4.2    20.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 44 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60D  VAL*     4.7    15.3    -      -       +      -
     36G  GLY      5.1     2.7    -      -       -      -
     37G  THR      3.7     4.5    -      -       -      +
     38G  CYS*     3.4    39.0    -      -       +      -
     42G  TYR      4.9     0.4    -      -       -      -
     43G  GLY*     1.3    70.9    -      -       -      -
     45G  VAL*     1.3    59.6    +      -       -      +
     46G  ILE*     3.2    23.5    +      -       +      +
     76G  VAL*     3.8     2.1    -      -       -      -
     77G  PHE*     3.3    32.6    +      +       +      -
    103G  PRO*     3.4    31.6    -      -       +      -
    104G  MET*     3.6    36.3    -      -       +      -
    156G  ASP*     5.2     4.0    -      -       +      -
    157G  ILE*     3.8    23.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 45 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60D  VAL*     5.9     0.2    -      -       -      -
      7G  LEU*     5.7     6.5    -      -       +      -
     34G  VAL*     3.9    28.0    -      -       +      +
     35G  GLU*     3.9     6.0    -      -       -      -
     36G  GLY*     2.8    32.7    +      -       -      -
     37G  THR*     3.1    20.6    +      -       -      +
     39G  THR*     4.3    18.8    -      -       +      +
     42G  TYR*     5.6     2.0    -      -       +      -
     43G  GLY      4.1     6.7    -      -       -      +
     44G  PHE*     1.3    69.4    -      -       -      +
     46G  ILE*     1.3    61.9    +      -       -      +
     47G  ALA      4.6     8.3    -      -       -      +
     48G  VAL*     5.2     2.0    -      -       +      -
     72G  TYR*     5.7     4.3    -      -       +      +
     74G  ALA*     5.1    13.2    -      -       +      -
     75G  ILE      4.2     4.9    -      -       -      +
     76G  VAL*     4.8    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 46 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37D  VAL*     5.1     2.0    -      -       +      -
     41D  LEU*     3.7    27.4    -      -       +      -
     60D  VAL*     4.8     6.3    -      -       +      -
     61D  PHE*     4.3    15.5    -      -       +      +
     64D  THR*     4.0    40.2    -      -       +      +
      2G  PHE*     5.2     3.4    -      -       +      -
     35G  GLU*     3.8    12.4    -      -       -      +
     36G  GLY*     4.9     1.5    +      -       -      -
     44G  PHE*     3.5    31.2    -      -       +      +
     45G  VAL*     1.3    74.8    -      -       -      +
     47G  ALA*     1.3    62.7    +      -       -      +
     75G  ILE*     3.0    29.0    +      -       +      +
     76G  VAL      4.6     0.2    -      -       -      -
     77G  PHE*     4.4    16.4    -      -       +      +
    103G  PRO*     4.8     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 47 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41D  LEU*     4.1    20.6    -      -       +      -
     44D  ARG*     4.6    11.2    -      -       +      -
     61D  PHE*     5.4     0.2    -      -       +      -
     35G  GLU*     3.8    17.3    -      -       -      +
     45G  VAL*     3.6     3.6    -      -       -      -
     46G  ILE*     1.3    83.2    -      -       -      +
     48G  VAL*     1.3    67.5    +      -       -      +
     49G  THR*     3.6     1.0    +      -       +      -
     74G  ALA*     3.3     3.4    -      -       -      +
     75G  ILE*     2.7    45.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 48 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44D  ARG*     5.1     6.2    -      -       -      -
     30G  LEU*     3.9    20.0    -      -       +      -
     31G  PHE*     3.5    30.7    -      -       +      -
     34G  VAL*     4.2    13.0    -      -       +      -
     35G  GLU*     4.5     8.4    +      -       +      -
     45G  VAL*     5.2     3.6    -      -       +      -
     47G  ALA*     1.3    75.0    -      -       -      +
     49G  THR*     1.3    64.4    +      -       -      +
     50G  THR      3.7    20.4    -      -       -      +
     51G  ILE*     3.7    21.3    -      -       +      -
     72G  TYR*     3.8    26.0    -      -       +      -
     73G  LYS      3.7     7.2    -      -       -      +
     74G  ALA*     3.9     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 49 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40D  LEU*     5.0    13.5    -      -       +      -
      4G  HIS*     2.9    38.4    +      -       +      +
     31G  PHE*     5.6     1.7    -      -       -      -
     47G  ALA*     3.6     1.3    +      -       +      +
     48G  VAL*     1.3    77.3    -      -       -      +
     50G  THR*     1.3    76.8    +      -       -      +
     73G  LYS      2.6    27.0    +      -       -      +
     75G  ILE*     3.6    25.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 50 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4G  HIS*     5.3     0.2    -      -       -      -
     48G  VAL*     3.6     1.9    -      -       -      +
     49G  THR*     1.3    90.7    +      -       -      +
     51G  ILE*     1.3    69.3    +      -       -      +
     52G  ASP*     5.1     1.1    +      -       -      -
     72G  TYR*     3.4     6.8    -      -       -      +
     73G  LYS*     2.9    52.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 51 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27G  LYS*     4.2    36.1    -      -       +      +
     30G  LEU*     4.5    16.8    -      -       +      -
     31G  PHE*     4.8     9.6    -      -       +      -
     48G  VAL*     3.7    26.2    -      -       +      -
     50G  THR*     1.3    75.0    -      -       -      +
     52G  ASP*     1.3    64.0    +      -       -      +
     53G  ASN*     4.3     3.6    -      -       -      +
     54G  ILE*     4.1    20.6    -      -       +      -
     70G  VAL*     4.0    15.7    -      -       +      -
     71G  LYS      3.9     9.9    -      -       -      +
     72G  TYR*     4.1     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 52 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50G  THR*     3.7     5.8    +      -       -      -
     51G  ILE*     1.3    76.3    -      -       -      +
     53G  ASN*     1.3    74.3    +      -       -      +
     71G  LYS*     2.7    36.0    +      -       +      +
     72G  TYR*     4.2     6.1    -      -       -      +
     73G  LYS*     4.7    16.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 53 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51G  ILE*     3.6     2.4    -      -       -      -
     52G  ASP*     1.3    90.1    -      -       -      +
     54G  ILE*     1.3    91.4    +      -       -      +
     55G  GLY*     4.1     6.9    +      -       -      +
     70G  VAL*     3.4     4.2    -      -       -      +
     71G  LYS*     2.6    57.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 54 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23G  LEU*     4.1    27.8    -      -       +      +
     26G  VAL*     4.4    17.7    -      -       +      -
     27G  LYS*     4.6    18.6    -      -       +      -
     51G  ILE*     4.1    13.7    -      -       +      -
     53G  ASN*     1.3    89.5    +      -       -      +
     55G  GLY*     1.3    74.3    +      -       -      +
     68G  TYR*     3.6    27.1    -      -       +      -
     69G  PRO      3.6     7.6    -      -       -      +
     70G  VAL*     4.0    17.5    -      -       +      -
----------------------------------------------------------
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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