Contacts of the strand formed by residues 45 - 51 (chain H) in PDB entry 1VPO


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 LEU 45 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37H  VAL*     4.3    10.3    -      -       +      -
     38H  ARG      3.6     5.2    -      -       -      +
     39H  GLN*     3.8    33.0    -      -       +      +
     43H  LYS      3.6     0.2    +      -       -      -
     44H  ARG*     1.3    74.8    -      -       -      +
     46H  GLU*     1.3    61.4    -      -       -      +
     94H  TYR*     5.1     1.1    -      -       +      -
    108H  TRP*     4.4    14.6    -      -       +      -
     41L  TYR*     5.6     1.1    -      -       +      -
     49L  PRO*     4.3    16.8    -      -       +      -
     92L  TYR*     3.7    46.0    -      -       +      -
    103L  PHE*     3.4    56.6    +      -       +      +
    104L  GLY      5.2     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 46 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37H  VAL*     4.0     4.4    -      -       -      +
     38H  ARG*     2.8    72.5    +      -       +      +
     40H  THR*     5.8     3.9    -      -       +      +
     44H  ARG*     4.0     1.3    +      -       +      +
     45H  LEU*     1.3    75.4    -      -       -      +
     47H  TRP*     1.3    76.3    +      -       -      +
     48H  VAL*     3.3     3.5    +      -       -      +
     60H  SER*     4.3     7.5    +      -       -      -
     62H  SER*     3.8    13.7    +      -       -      -
    102L  LYS*     6.0     5.9    -      -       +      -
    103L  PHE      6.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 47 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35H  SER*     4.5     4.3    -      -       -      -
     36H  TRP      4.2     8.1    -      -       -      -
     37H  VAL*     4.4    12.8    -      -       +      -
     46H  GLU*     1.3    85.2    -      -       -      +
     48H  VAL*     1.3    61.7    +      -       -      +
     49H  ALA*     3.7     7.1    +      -       -      -
     50H  SER*     2.5    44.7    +      -       -      -
     58H  TYR*     3.6    31.0    -      -       +      -
     59H  TYR      3.3    25.8    -      -       -      -
     60H  SER*     3.6     9.8    -      -       -      -
    105H  LEU*     5.5     0.9    -      -       +      -
   1010H  TES      3.9    30.1    -      -       +      +
     94L  PHE*     5.1     2.5    -      +       +      -
     99L  VAL*     4.2     6.7    -      -       +      -
    100L  PRO*     3.5    31.2    -      -       +      -
    101L  PRO*     3.7    33.9    +      -       +      +
    102L  LYS*     6.2     1.2    -      -       -      +
    103L  PHE*     4.2    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 48 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36H  TRP*     2.8    30.1    +      -       +      +
     37H  VAL      4.2     0.2    -      -       -      -
     38H  ARG*     3.5    48.0    -      -       +      +
     46H  GLU      3.6     3.8    -      -       -      +
     47H  TRP*     1.3    76.8    -      -       -      +
     49H  ALA*     1.3    68.1    +      -       +      +
     59H  TYR*     3.5     1.7    -      -       -      +
     60H  SER*     3.1    31.0    +      -       -      -
     63H  VAL*     3.7    21.8    -      -       +      +
     67H  PHE*     4.0    14.8    -      -       +      -
     80H  LEU*     4.5     7.4    -      -       +      -
     93H  TYR*     4.5     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 49 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35H  SER*     3.3     1.7    -      -       -      -
     36H  TRP*     2.8    28.8    +      -       +      +
     47H  TRP*     3.7     5.2    +      -       -      -
     48H  VAL*     1.3    88.0    -      -       +      +
     50H  SER*     1.3    66.5    +      -       -      +
     58H  TYR      3.1    20.2    -      -       -      +
     59H  TYR*     3.3    23.6    -      -       +      -
     69H  ILE*     4.0    14.9    -      -       +      +
     80H  LEU*     5.3     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 50 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  ALA*     5.7     0.2    -      -       -      -
     34H  LEU      3.2     8.3    -      -       -      -
     35H  SER*     2.6    17.8    +      -       -      -
     47H  TRP*     2.5    38.4    +      -       -      -
     49H  ALA*     1.3    71.8    -      -       -      +
     51H  ILE*     1.3    62.9    +      -       -      +
     52H  VAL*     5.6     0.4    -      -       -      -
     57H  THR*     3.3     4.5    -      -       -      -
     58H  TYR*     3.0    33.1    +      -       -      +
     69H  ILE*     3.8     6.3    -      -       -      +
   1010H  TES      3.6    25.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 51 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32H  TYR      4.3     1.0    -      -       -      +
     33H  ALA*     3.3     2.3    -      -       -      -
     34H  LEU*     2.9    39.0    +      -       +      +
     50H  SER*     1.3    75.8    -      -       -      +
     52H  VAL*     1.3    65.5    +      -       -      +
     55H  GLY*     3.5    24.9    -      -       -      +
     56H  ASN      3.2     4.7    -      -       -      +
     57H  THR*     3.6    18.4    -      -       +      -
     69H  ILE*     4.1     6.7    -      -       +      -
     70H  SER*     4.1    17.7    -      -       -      -
     71H  ARG*     3.9    37.0    -      -       +      +
     78H  LEU*     4.1    20.0    -      -       +      -
----------------------------------------------------------
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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