Contacts of the strand formed by residues 41 - 47 (chain T) 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 41 (chain T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15S  VAL*     3.9     3.5    -      -       -      +
     16S  VAL*     3.1    23.2    +      -       -      +
     39T  GLU*     4.5     1.7    -      -       -      +
     40T  VAL*     1.3    84.2    -      -       -      +
     42T  LYS*     1.3    69.0    +      -       -      +
     56T  PHE*     3.9     9.0    -      -       -      -
     57T  THR      3.6    10.5    -      -       -      -
     59T  ASN*     3.8    14.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 42 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13S  GLU*     3.2    42.9    +      -       +      +
     14S  TYR      3.2    13.7    -      -       -      +
     15S  VAL*     4.2    19.3    -      -       +      -
     16S  VAL*     4.2     0.7    -      -       -      -
     41T  GLY*     1.3    79.3    -      -       -      +
     43T  LEU*     1.3    59.2    +      -       -      +
     44T  ARG*     4.2     0.9    +      -       -      +
     56T  PHE*     3.2     7.5    -      -       -      -
     57T  THR*     2.8    38.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 43 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12S  THR      3.8     0.3    -      -       -      +
     13S  GLU*     3.2     4.5    -      -       -      -
     14S  TYR*     2.9    32.7    +      -       -      +
     16S  VAL*     4.0    13.8    -      -       +      +
    127S  PHE*     4.4    11.0    -      -       +      -
    135S  PHE*     3.4    37.9    -      -       +      -
     19T  TRP*     5.0     7.4    -      -       +      -
     42T  LYS*     1.3    72.7    -      -       -      +
     44T  ARG*     1.3    59.0    +      -       -      +
     45T  ILE*     4.0    19.3    -      -       +      +
     54T  VAL*     4.7     6.3    -      -       +      -
     55T  SER      3.1    21.8    -      -       -      +
     56T  PHE*     3.6    20.4    -      -       +      -
     83T  PHE*     3.7    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 44 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11S  VAL*     4.0    23.7    -      -       +      +
     12S  THR      3.1    15.0    -      -       -      +
     13S  GLU*     4.3    23.4    +      -       +      +
     42T  LYS      4.2     1.0    +      -       -      +
     43T  LEU*     1.3    73.3    -      -       -      +
     45T  ILE*     1.3    65.2    +      -       -      +
     46T  ALA*     4.3     4.9    -      -       +      +
     53T  GLU      4.2     0.5    -      -       -      +
     54T  VAL      3.7     0.5    -      -       -      -
     55T  SER*     2.8    51.9    +      -       -      +
     57T  THR*     3.4    25.1    +      -       -      +
     80T  GLU*     3.2    24.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 45 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10S  ASN*     3.7     4.3    +      -       -      +
     12S  THR*     2.9    45.7    +      -       +      +
     14S  TYR*     5.1     7.2    -      -       +      -
    135S  PHE*     4.9     8.5    -      -       +      -
     19T  TRP*     4.8    14.4    -      -       +      -
     43T  LEU*     4.0    27.1    -      -       +      +
     44T  ARG*     1.3    83.4    -      -       -      +
     46T  ALA*     1.3    63.0    +      -       -      +
     47T  LYS*     4.2     2.4    +      -       +      +
     52T  THR*     4.2    14.8    -      -       +      -
     53T  GLU      3.6     3.4    -      -       -      +
     54T  VAL*     4.0    31.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 46 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10S  ASN      3.6     9.0    -      -       -      +
     11S  VAL*     4.6    15.0    -      -       +      -
     44T  ARG*     4.3     5.6    -      -       +      +
     45T  ILE*     1.3    73.9    -      -       -      +
     47T  LYS*     1.3    57.3    +      -       -      +
     48T  THR*     5.2     3.4    -      -       +      +
     51T  ARG      4.5     0.2    -      -       -      +
     52T  THR*     3.8     1.3    -      -       -      -
     53T  GLU*     2.8    52.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 47 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7S  SER*     3.9    20.0    -      -       -      +
      8S  SER      3.8    17.2    -      -       -      +
      9S  GLN*     4.3     1.2    -      -       -      -
     10S  ASN*     3.6    16.4    +      -       +      +
     45T  ILE*     4.2     3.5    +      -       +      -
     46T  ALA*     1.3    73.6    -      -       -      +
     48T  THR*     1.3    78.8    +      -       -      +
     49T  GLN      5.9     1.3    -      -       -      -
     51T  ARG      3.6     3.8    -      -       -      +
     52T  THR*     3.3    31.0    -      -       +      +
----------------------------------------------------------
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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