Contacts of the strand formed by residues 33 - 43 (chain B) in PDB entry 1TJJ


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 GLY 33 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  VAL*     3.6    10.9    +      -       -      -
     31B  VAL*     4.0     0.2    -      -       -      +
     32B  PRO*     1.3    77.3    -      -       -      +
     34B  ASN*     1.3    69.4    +      -       -      +
    124B  VAL*     4.0     2.6    -      -       -      +
    125B  VAL*     2.9    29.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 34 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  PRO*     3.7    15.1    -      -       -      +
     29B  ILE*     5.1     0.3    -      -       -      +
     30B  VAL      4.8     3.5    +      -       -      +
     33B  GLY*     1.3    77.8    -      -       -      -
     35B  VAL*     1.3    71.5    +      -       -      +
    122B  GLU*     4.7    12.6    -      -       +      +
    123B  PHE      3.2    12.1    -      -       -      +
    124B  VAL*     3.3    32.3    -      -       -      +
    125B  VAL*     4.5     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 35 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  LEU*     4.2    11.4    -      -       +      -
     25B  GLU      3.2    11.9    -      -       -      +
     26B  PRO*     4.4     1.3    -      -       +      -
     29B  ILE*     3.3    44.2    -      -       +      -
     34B  ASN*     1.3    75.8    -      -       -      +
     36B  THR*     1.3    61.6    +      -       -      +
     37B  LEU*     4.1     0.6    +      -       +      -
    121B  SER      3.7     0.5    -      -       -      +
    122B  GLU*     3.4     5.1    -      -       -      +
    123B  PHE*     2.9    50.2    +      -       +      +
    124B  VAL      5.5     0.2    -      -       -      -
    125B  VAL*     3.4    13.7    -      -       +      -
   1364B  DAO      3.9    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 36 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  THR*     3.7     1.4    +      -       -      +
     24B  LEU*     3.4     5.4    +      -       -      +
     25B  GLU*     2.8    58.9    +      -       -      +
     35B  VAL*     1.3    72.3    -      -       -      +
     37B  LEU*     1.3    62.1    +      -       -      +
    120B  LYS*     3.7    30.7    -      -       +      -
    121B  SER      3.3     7.9    -      -       -      +
    122B  GLU*     2.5    33.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 37 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  LEU*     4.4     4.0    -      -       +      -
     23B  THR*     3.2    11.4    -      -       -      +
     24B  LEU*     4.0    17.3    -      -       +      -
     35B  VAL*     4.1     1.5    -      -       +      -
     36B  THR*     1.3    75.3    -      -       -      +
     38B  SER*     1.3    77.8    +      -       -      +
     39B  VAL*     3.9    18.6    -      -       +      -
    118B  LEU*     4.0    12.8    -      -       +      +
    119B  PRO      3.6     2.6    -      -       -      +
    120B  LYS*     3.4     2.4    -      -       -      -
    121B  SER*     2.9    31.6    +      -       -      +
    123B  PHE*     4.2    13.0    -      -       +      -
   1364B  DAO      4.1    15.5    -      -       +      -
   2484B  PFS      3.5    36.1    -      -       +      -
   2485B  LPE      4.2    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 38 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  SER*     5.4     3.3    +      -       -      -
     22B  LEU*     3.4     6.6    +      -       -      +
     23B  THR*     2.5    52.9    +      -       -      +
     37B  LEU*     1.3    76.0    -      -       -      +
     39B  VAL*     1.3    65.6    +      -       -      +
    118B  LEU      3.3    14.1    -      -       -      -
    119B  PRO*     3.9     0.9    -      -       -      -
    120B  LYS*     3.5    24.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 39 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  ILE*     4.1    16.6    -      -       +      -
     21B  SER*     3.3    14.4    -      -       -      +
     22B  LEU*     3.8    17.7    -      -       +      -
     37B  LEU*     3.9     9.2    -      -       +      -
     38B  SER*     1.3    79.1    -      -       -      +
     40B  VAL*     1.3    69.7    +      -       -      +
    118B  LEU*     2.8    37.7    +      -       +      +
   2484B  PFS      3.5    43.2    -      -       +      +
   2485B  LPE      3.9    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 40 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  ILE*     3.6     4.0    -      -       -      +
     20B  ARG*     2.7    45.3    +      -       +      -
     21B  SER*     2.9    31.9    +      -       -      +
     39B  VAL*     1.3    83.7    -      -       -      +
     41B  GLY*     1.3    57.3    +      -       -      +
    115B  THR*     3.9    15.5    -      -       +      -
    116B  TYR      3.3     4.7    -      -       -      +
    117B  SER*     3.7    28.7    -      -       -      +
    118B  LEU      4.8     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 41 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  VAL      3.3    11.4    -      -       -      -
     19B  ILE*     4.2     2.5    -      -       -      -
     20B  ARG*     4.2     1.3    -      -       -      -
     40B  VAL*     1.3    76.2    -      -       -      +
     42B  SER*     1.3    59.0    +      -       -      -
    115B  THR*     3.4     4.2    -      -       -      +
    116B  TYR*     2.7    35.8    +      -       -      +
   2484B  PFS      3.7    10.1    -      -       -      +
   2485B  LPE      3.9    18.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 42 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  PRO      3.7     1.5    +      -       -      +
     17B  ALA*     3.3     2.1    -      -       -      -
     18B  VAL*     2.9    38.3    +      -       -      +
     20B  ARG*     3.0    39.9    +      -       -      +
     41B  GLY*     1.3    73.1    -      -       -      -
     43B  THR*     1.3    62.4    -      -       -      +
    114B  GLY      3.2     8.1    -      -       -      -
    115B  THR*     3.4    22.4    -      -       -      -
   2485B  LPE      3.8     5.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 43 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  PRO      3.2     9.1    +      -       -      -
     17B  ALA*     3.8    13.2    -      -       -      +
     42B  SER*     1.3    79.2    -      -       -      +
     44B  SER*     1.3    61.5    +      -       -      +
     45B  VAL*     2.7    32.0    +      -       -      +
     47B  LEU*     3.8    24.5    -      -       +      +
    111B  PHE*     4.8     0.9    -      -       +      +
    112B  LYS      3.9    19.5    -      -       -      +
    113B  GLU*     3.3     3.7    -      -       -      +
    114B  GLY*     3.0    31.9    +      -       -      +
    116B  TYR*     4.6     4.3    -      -       +      -
   2485B  LPE      4.1     8.1    -      -       +      -
----------------------------------------------------------
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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