Contacts of the strand formed by residues 251 - 258 (chain N) in PDB entry 3H1I


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 ALA 251 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250N  VAL*     1.3    76.2    -      -       -      +
    252N  HIS*     1.3    61.6    +      -       -      +
    253N  VAL*     4.9     2.8    -      -       +      +
    324N  PHE*     4.2     1.2    -      -       -      +
    325N  VAL*     3.4     4.7    -      -       -      +
    326N  ALA      3.2    31.5    +      -       -      +
    328N  PRO*     5.1     0.2    -      -       +      -
    331N  ILE*     3.7    23.4    -      -       +      +
    425N  VAL      3.1    13.0    -      -       -      +
    427N  PRO*     3.7    16.4    -      -       +      +
    428N  ILE*     3.5    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 252 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145N  MET*     2.9    45.0    -      -       +      +
    146N  THR*     3.6    18.2    +      -       -      -
    149N  THR*     3.4    18.7    +      -       -      +
    250N  VAL*     3.8    13.8    -      -       -      +
    251N  ALA*     1.3    73.9    -      -       -      +
    253N  VAL*     1.3    66.6    +      -       -      +
    323N  HIS*     3.1    21.4    +      -       -      +
    324N  PHE      3.7     3.8    -      -       -      -
    325N  VAL*     3.3    33.7    -      -       +      +
    423N  ALA      3.5     1.1    -      -       -      +
    424N  ALA*     3.5     2.1    -      -       -      +
    425N  VAL*     2.8    37.4    +      -       +      +
    428N  ILE*     4.7     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 253 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149N  THR*     4.8     0.2    -      -       -      -
    251N  ALA      4.9     2.5    -      -       -      -
    252N  HIS*     1.3    84.5    -      -       -      +
    254N  ALA*     1.3    65.2    +      -       -      +
    255N  LEU*     5.6     0.2    -      -       +      -
    322N  PHE      3.8     0.6    -      -       -      +
    323N  HIS*     3.0     7.6    -      -       -      -
    324N  PHE*     2.9    49.8    +      -       +      -
    331N  ILE*     3.8    28.7    -      -       +      -
    335N  MET*     3.2    31.9    -      -       +      -
    422N  LEU*     3.9    15.7    -      -       +      -
    423N  ALA      3.2     5.8    -      -       -      +
    424N  ALA*     4.8     7.4    -      -       +      -
    428N  ILE*     5.0     4.5    -      -       +      -
    431N  LEU*     4.8     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 254 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149N  THR*     3.4    26.9    -      -       +      -
    150N  PHE*     5.5     3.1    -      -       +      -
    153N  LEU*     4.3    16.0    -      -       +      +
    253N  VAL*     1.3    76.4    -      -       -      +
    255N  LEU*     1.3    60.4    +      -       -      +
    310N  PHE*     5.4     3.1    -      -       +      -
    322N  PHE      3.2     7.4    -      -       -      +
    323N  HIS*     4.3     8.3    -      -       +      -
    421N  ALA      3.6     0.7    -      -       -      +
    422N  LEU*     3.4     5.9    -      -       -      +
    423N  ALA*     2.7    43.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 255 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153N  LEU*     5.1     0.4    -      -       -      -
    254N  ALA*     1.3    74.9    -      -       -      +
    256N  ALA*     1.3    64.5    +      -       -      +
    310N  PHE*     4.0     1.5    -      -       -      -
    321N  GLY*     2.9     2.1    -      -       -      -
    322N  PHE*     2.7    59.2    +      -       +      +
    335N  MET*     4.4     4.7    -      -       +      -
    339N  GLN*     4.2    13.0    -      -       -      +
    342N  TRP*     3.8    23.5    -      -       +      -
    420N  PRO*     4.0    21.5    -      -       +      -
    421N  ALA      3.1    16.4    -      -       -      +
    422N  LEU*     3.1    35.4    -      -       +      -
    434N  TYR*     5.8     0.2    -      -       +      -
    437N  ILE*     4.2    20.2    -      -       +      -
    441N  MET*     4.9     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 256 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153N  LEU*     4.4    14.1    -      -       +      -
    236N  PHE*     3.8     2.6    -      -       -      -
    255N  LEU*     1.3    79.1    -      -       -      +
    257N  VAL*     1.3    62.0    +      -       -      +
    310N  PHE*     4.0    12.6    -      -       +      -
    319N  LEU*     4.3     9.6    -      -       +      -
    320N  PHE      3.0    27.1    -      -       -      +
    321N  GLY*     3.6     2.7    -      -       -      +
    342N  TRP*     4.2     2.7    -      -       -      -
    420N  PRO*     3.3     5.0    -      -       -      +
    421N  ALA*     2.7    40.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 257 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236N  PHE*     3.8     8.7    -      -       -      -
    256N  ALA*     1.3    79.0    -      -       -      +
    258N  GLU*     1.3    69.7    +      -       -      +
    259N  GLY      3.3     0.2    +      -       -      -
    319N  LEU*     3.8     2.9    -      -       -      -
    320N  PHE*     2.6    60.7    +      -       +      +
    342N  TRP*     4.9     5.2    -      -       +      -
    414N  TYR*     3.5    31.0    -      -       +      +
    415N  ILE*     4.4     7.9    -      -       +      -
    418N  LYS*     4.1    12.6    -      -       +      -
    419N  CYS      4.8     0.4    -      -       -      +
    420N  PRO*     4.2     4.9    -      -       +      -
    441N  MET*     3.9    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 258 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158N  PHE*     5.3     0.4    -      -       -      -
    233N  ARG*     5.4     4.7    +      -       -      -
    234N  CYS      5.0     3.4    -      -       -      +
    236N  PHE*     2.7    59.4    +      -       +      +
    257N  VAL*     1.3    81.6    -      -       -      +
    259N  GLY*     1.3    69.1    +      -       -      +
    316N  ASP      5.2     2.1    -      -       -      +
    317N  THR*     3.5    24.2    +      -       -      +
    318N  GLY      3.9     5.2    -      -       -      +
    320N  PHE*     4.9     0.5    -      -       -      +
    414N  TYR*     3.9    18.4    -      -       -      +
     24R  SER*     4.5     8.9    +      -       -      -
     25R  SER*     4.6     1.6    +      -       -      -
     26R  GLN*     3.5    36.6    -      -       -      +
----------------------------------------------------------
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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