Contacts of the strand formed by residues 3444 - 3449 (chain C) in PDB entry 2H7C


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 THR3444 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3346C  TYR*     3.3    11.9    -      -       +      +
   3348C  VAL*     5.1     2.2    -      -       +      -
   3434C  ALA*     3.7    36.8    -      -       +      +
   3437C  HIS*     3.3    17.9    -      -       +      -
   3438C  ARG*     3.3    11.3    +      -       -      -
   3442C  ALA      3.1    15.2    +      -       -      -
   3443C  PRO*     1.3    71.7    -      -       -      +
   3445C  TYR*     1.3    71.2    +      -       -      +
   3519C  GLU*     2.8    11.3    +      -       -      +
   3520C  TYR*     2.8    46.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR3445 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3346C  TYR      3.0     8.9    +      -       -      +
   3347C  MET*     3.3    10.0    -      -       +      -
   3348C  VAL      2.8    26.8    +      -       -      -
   3443C  PRO*     4.6    10.2    -      -       +      +
   3444C  THR*     1.3    82.4    -      -       -      +
   3446C  MET*     1.3    67.3    +      -       -      +
   3503C  PHE*     3.7    18.8    -      +       -      -
   3507C  GLY      3.4    21.3    +      -       -      -
   3508C  ASN*     3.1    28.2    +      -       -      +
   3509C  PRO*     3.6    24.7    -      -       +      -
   3510C  ASN*     4.6     2.2    +      -       -      -
   3517C  TRP*     4.0    27.6    -      +       +      +
   3518C  PRO      3.6    15.3    -      -       -      -
   3519C  GLU*     3.5    34.5    -      -       +      +
   3520C  TYR*     4.0     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET3446 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3348C  VAL*     3.1    20.4    -      -       +      +
   3349C  GLY*     5.1     1.8    -      -       -      +
   3350C  ILE*     5.4     1.1    -      -       +      -
   3430C  SER*     3.9    26.9    -      -       -      +
   3431C  VAL*     3.8    21.1    -      -       +      -
   3434C  ALA*     3.5    26.0    -      -       +      -
   3445C  TYR*     1.3    79.2    -      -       -      +
   3447C  TYR*     1.3    61.7    +      -       -      +
   3517C  TRP*     3.1    12.4    +      -       -      +
   3520C  TYR*     3.6    35.5    -      -       +      +
   3525C  GLY      4.8     1.2    +      -       -      -
   3526C  TYR*     3.2    19.1    -      -       +      +
   3527C  LEU      2.9    20.4    +      -       -      -
   3539C  LEU*     3.8    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR3447 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3244C  ILE*     5.1     0.4    -      -       +      -
   3245C  SER      4.9     0.4    -      -       -      -
   3246C  GLU*     3.1    38.6    -      -       +      +
   3247C  SER      4.5     0.3    +      -       -      -
   3347C  MET*     4.1    12.1    -      -       +      -
   3348C  VAL      3.4     3.7    +      -       -      +
   3349C  GLY*     3.3    28.2    -      -       -      -
   3350C  ILE*     3.1    38.0    +      -       -      +
   3351C  ASN*     4.4     2.2    +      -       -      -
   3446C  MET*     1.3    77.0    -      -       -      +
   3448C  GLU*     1.3    62.9    +      -       -      +
   3449C  PHE*     3.7    22.2    -      +       +      -
   3471C  GLU*     4.2     9.6    -      -       +      +
   3500C  TRP*     3.6    32.5    -      +       -      -
   3517C  TRP*     3.6    21.3    -      +       +      -
   3526C  TYR*     4.6     3.8    -      -       -      -
   3527C  LEU      3.1    14.6    -      -       -      +
   3529C  ILE*     3.9    13.9    -      -       +      -
   3539C  LEU*     4.4     5.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU3448 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3350C  ILE*     3.2    19.2    -      -       +      +
   3352C  LYS*     3.6    48.3    +      -       +      +
   3447C  TYR*     1.3    75.9    -      -       -      +
   3449C  PHE*     1.3    62.1    +      -       -      +
   3450C  GLN*     3.6     4.2    +      -       +      +
   3526C  TYR*     4.0    25.0    +      -       +      -
   3527C  LEU      3.0     7.2    +      -       -      +
   3528C  GLN*     3.5    12.3    +      -       -      +
   3529C  ILE      3.0    22.4    +      -       -      -
   3539C  LEU*     3.9    21.9    -      -       +      +
   3540C  LYS*     4.2    16.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE3449 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3350C  ILE      2.8     9.6    +      -       -      +
   3351C  ASN*     3.2    24.1    -      -       -      +
   3352C  LYS*     2.7    30.3    +      -       -      +
   3447C  TYR*     3.7    11.2    -      +       +      -
   3448C  GLU*     1.3    70.3    -      -       -      +
   3450C  GLN*     1.3    56.8    +      -       -      +
   3451C  TYR*     3.6    38.6    -      +       +      -
   3453C  PRO*     5.2     0.2    -      -       +      -
   3466C  GLY*     3.9     1.7    -      -       -      -
   3470C  ASP*     3.6    11.2    -      -       +      -
   3471C  GLU*     3.5    42.2    -      -       +      -
   3474C  SER*     4.0    22.7    -      -       -      -
   3492C  LEU*     4.2     9.0    -      -       +      -
   3496C  VAL*     4.8     3.4    -      -       +      -
   3529C  ILE*     3.6    35.7    -      -       +      -
----------------------------------------------------------
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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