Contacts of the strand formed by residues 41 - 48 (chain A) in PDB entry 5IVH


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 LYS 41 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  VAL*     3.6    24.0    -      -       +      -
     35A  ALA      3.4     6.1    -      -       -      +
     36A  GLU*     3.2    27.6    -      -       -      +
     37A  THR      4.5     0.2    -      -       -      +
     40A  GLY*     1.3    72.9    -      -       -      -
     42A  VAL*     1.3    58.4    +      -       -      +
     82A  TRP*     2.8    20.8    +      -       -      +
     84A  GLY*     3.7    29.2    +      -       -      +
     85A  VAL*     3.5    12.1    -      -       +      +
     86A  ARG      2.9    13.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  VAL      3.7     0.5    -      -       -      +
     34A  VAL*     3.2     5.5    -      -       -      -
     35A  ALA*     3.0    37.1    +      -       +      +
     37A  THR*     3.6    21.5    -      -       +      -
     41A  LYS*     1.3    73.4    -      -       -      +
     43A  LYS*     1.3    59.8    +      -       -      +
     58A  PHE*     3.8    19.9    -      -       +      -
     61A  ILE*     4.5     9.4    -      -       +      -
     82A  TRP*     3.4    32.1    -      -       +      -
     85A  VAL*     3.9     3.8    -      -       -      -
     86A  ARG*     3.5     5.6    -      -       +      -
     88A  CYS*     3.8    24.5    -      -       -      -
    205A  PHE*     4.0    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  THR*     4.2    19.1    -      -       +      +
     33A  VAL      3.3     9.2    -      -       -      +
     34A  VAL*     4.7     4.9    -      -       +      -
     42A  VAL*     1.3    73.7    -      -       -      +
     44A  GLY*     1.3    69.7    +      -       -      +
     58A  PHE*     3.8     3.1    -      -       -      -
     85A  VAL*     4.0    13.9    -      -       +      -
     86A  ARG      2.8    12.4    +      -       -      +
     87A  ASP*     3.2    39.4    -      -       -      +
     88A  CYS*     2.8    34.7    +      -       -      +
     89A  CYS*     3.5    17.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  THR*     3.2     9.9    -      -       -      -
     33A  VAL*     3.0    32.5    +      -       -      -
     43A  LYS*     1.3    75.7    -      -       -      +
     45A  VAL*     1.3    62.7    +      -       -      +
     57A  SER      3.1    14.8    -      -       -      -
     58A  PHE*     3.2    20.2    -      -       -      -
     88A  CYS      4.2     3.4    -      -       -      -
     89A  CYS*     4.0     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  THR*     4.1     9.0    -      -       +      -
     29A  THR      3.3    26.9    -      -       -      +
     31A  GLU      3.4    13.2    -      -       -      +
     32A  THR*     4.3     7.6    -      -       +      -
     33A  VAL*     5.7     0.2    -      -       -      -
     44A  GLY*     1.3    75.5    -      -       -      +
     46A  LYS*     1.3    71.5    +      -       -      +
     47A  ARG*     3.5    36.1    -      -       +      +
     56A  TYR*     4.5     2.6    -      -       -      +
     57A  SER*     2.9    32.2    +      -       -      +
     89A  CYS*     4.0    22.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  THR*     2.6    47.5    +      -       +      +
     31A  GLU*     2.9    40.2    +      -       +      +
     45A  VAL*     1.3    76.1    -      -       -      +
     47A  ARG*     1.3    70.9    +      -       -      +
     48A  LEU*     5.4     1.1    -      -       +      -
     54A  SER*     3.9    22.3    +      -       -      +
     55A  TYR*     3.2    15.9    -      -       -      +
     56A  TYR*     3.2    49.8    +      -       +      +
    119A  ASN      5.4     2.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  ASN*     3.9    11.1    +      -       -      +
     27A  LEU*     3.3    13.2    -      -       +      +
     28A  THR*     3.6    24.3    +      -       -      +
     29A  THR*     4.3     0.2    -      -       -      -
     45A  VAL*     3.5    17.0    -      -       +      +
     46A  LYS*     1.3    79.2    -      -       -      +
     48A  LEU*     1.3    66.5    +      -       -      +
     54A  SER*     3.2     7.1    -      -       -      -
     55A  TYR*     2.7    60.2    +      -       +      +
     57A  SER*     3.1    30.8    +      -       -      -
     59A  GLU*     3.2    13.3    +      -       -      -
     88A  CYS      5.1     0.4    +      -       -      -
     89A  CYS*     2.7    33.1    +      -       -      +
     90A  ASN*     4.5     0.6    -      -       -      +
    145A  ARG*     3.3    28.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  ARG      4.4     6.3    -      -       -      +
     27A  LEU*     2.9    53.3    +      -       +      +
     28A  THR      4.9     1.1    -      -       -      +
     29A  THR*     3.8    22.0    -      -       +      -
     46A  LYS*     5.2     1.1    -      -       +      -
     47A  ARG*     1.3    74.5    -      -       -      +
     49A  THR*     1.3    68.8    +      -       -      +
     52A  ASP*     6.3     0.4    -      -       -      -
     53A  ASP      3.5     7.0    -      -       -      +
     54A  SER*     3.8    21.1    -      -       -      -
     55A  TYR*     4.1     7.2    +      -       -      -
    151A  ASP*     4.1     2.3    -      -       -      +
----------------------------------------------------------
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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