Contacts of the strand formed by residues 308 - 313 (chain D) in PDB entry 1NJI


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 308 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22D  GLU*     4.7     3.9    +      -       +      +
     23D  THR*     3.6    25.8    -      -       +      +
     24D  PRO*     4.0    17.8    -      -       +      +
     42D  ALA*     3.8    19.7    -      -       +      -
     43D  GLY      3.1    22.2    -      -       -      +
     44D  TYR*     4.0    21.9    -      -       +      -
    146D  THR*     4.2     4.9    -      -       +      -
    156D  LYS*     5.2     3.0    -      -       -      +
    160D  ASP*     3.7    23.1    -      -       +      +
    162D  MET*     3.2    30.7    -      -       +      -
    204D  GLY*     4.5     1.2    -      -       -      -
    306D  LYS      3.7     1.6    +      -       -      -
    307D  ARG*     1.3    86.9    -      -       +      +
    309D  VAL*     1.3    66.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 309 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42D  ALA*     3.3     6.2    -      -       -      +
     43D  GLY      2.8    47.5    +      -       -      +
     45D  LYS*     4.3    11.9    -      -       +      +
     74D  ILE*     3.5    30.3    -      -       +      -
    202D  VAL*     4.1     7.4    -      -       +      -
    203D  ALA      3.6    12.6    -      -       -      +
    204D  GLY*     4.7     2.9    -      -       -      -
    301D  VAL*     3.6    24.9    -      -       +      -
    302D  PRO      3.9    10.8    -      -       -      +
    307D  ARG*     4.3     8.5    -      -       +      +
    308D  LEU*     1.3    80.1    -      -       -      +
    310D  ARG*     1.3    62.4    +      -       -      +
    311D  PHE*     4.4     3.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 310 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2672A    C      4.4     4.4    +      -       -      -
     24D  PRO*     3.4    34.3    +      -       +      +
     25D  ARG*     3.7     3.4    -      -       -      +
     26D  PHE*     3.4    52.8    -      -       +      +
     29D  TRP*     4.0     4.2    -      -       -      -
     40D  GLY*     6.0     0.8    -      -       -      -
     41D  PHE      3.5    11.4    -      -       -      +
     42D  ALA*     4.2     2.0    -      -       +      -
    162D  MET*     3.1    55.5    -      -       +      +
    163D  GLU      3.4    16.0    +      -       -      -
    164D  THR*     3.3    20.0    +      -       -      +
    201D  ASP      3.4     1.4    -      -       -      +
    202D  VAL*     3.2     8.2    -      -       -      +
    203D  ALA*     2.9    37.8    +      -       +      +
    309D  VAL*     1.3    77.8    -      -       -      +
    311D  PHE*     1.3    61.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 311 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26D  PHE*     3.7     6.5    -      -       -      -
     40D  GLY*     3.1     4.9    -      -       -      -
     41D  PHE      2.7    44.8    +      -       -      +
     42D  ALA*     4.2     1.6    -      -       -      -
     43D  GLY      4.2     7.6    -      -       -      -
     74D  ILE*     3.5    35.0    -      -       +      -
     76D  THR*     3.7    24.2    -      -       +      -
    190D  MET*     4.2    10.5    -      -       +      -
    194D  PHE*     3.8    19.7    -      -       +      -
    200D  ALA*     4.5     3.1    -      -       +      -
    201D  ASP      3.6     2.7    -      -       -      -
    202D  VAL*     4.0    20.2    -      -       +      -
    269D  LEU*     4.3    17.0    -      -       +      -
    295D  THR*     4.5     6.1    -      -       +      -
    297D  VAL*     3.7    24.9    -      -       +      -
    309D  VAL*     4.4     5.4    -      -       +      -
    310D  ARG*     1.3    76.1    -      -       -      +
    312D  ARG*     1.3    63.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 312 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2807A    U      2.6    30.1    +      -       -      -
     26D  PHE*     3.4    39.6    -      -       +      +
     27D  ASN      4.4     0.8    -      -       -      +
     28D  SER*     2.7    35.3    +      -       -      +
     29D  TRP*     4.8     2.2    -      -       +      -
     30D  PRO*     4.1    11.7    -      -       +      -
     39D  GLN      3.9     6.3    -      -       -      +
    194D  PHE*     3.7     5.2    -      -       -      -
    200D  ALA*     3.1     4.7    -      -       -      -
    201D  ASP*     2.6    85.8    +      -       -      +
    263D  THR*     3.8     7.9    +      -       -      +
    265D  LEU*     4.5     2.4    -      -       -      +
    311D  PHE*     1.3    77.6    -      -       -      +
    313D  PRO*     1.3    80.7    -      -       +      +
    315D  VAL*     3.5    18.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 313 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30D  PRO*     3.1    31.0    -      -       +      +
     38D  VAL      5.4     0.2    -      -       -      +
     39D  GLN*     3.4    29.8    -      -       +      +
    193D  ILE*     4.8     8.5    -      -       +      +
    194D  PHE*     3.8    22.4    -      -       +      -
    199D  TYR      4.0     3.8    -      -       -      +
    312D  ARG*     1.3    88.5    -      -       +      +
    314D  ALA*     1.3    71.4    +      -       -      +
    315D  VAL      3.2     1.7    +      -       -      -
----------------------------------------------------------
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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