Contacts of the strand formed by residues 251 - 263 (chain T) in PDB entry 6MZL


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 251 (chain T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172T  VAL*     3.4     2.6    -      -       -      +
    173T  ASN*     2.9    49.3    +      -       +      +
    175T  GLY*     4.4    17.0    -      -       -      -
    249T  LYS*     4.1    29.6    -      -       +      -
    250T  PHE*     1.3    79.4    -      -       -      +
    252T  ASP*     1.3    73.0    +      -       +      +
    253T  PHE      3.4     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 252 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171T  THR*     3.7     8.7    +      -       -      +
    172T  VAL*     4.1     2.6    -      -       -      -
    173T  ASN*     5.2     7.6    +      -       +      +
    250T  PHE      4.2     0.8    +      -       -      -
    251T  LEU*     1.3    80.9    -      -       -      +
    253T  PHE*     1.3    67.8    +      -       -      +
    254T  LYS*     3.6     5.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 253 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170T  SER*     3.4    34.1    -      -       -      -
    171T  THR      3.5    13.0    -      -       -      -
    172T  VAL*     4.1     8.7    -      -       +      -
    227T  GLU      5.0     1.6    -      -       -      -
    230T  SER*     4.0     3.6    -      -       -      -
    231T  ARG*     3.3    54.3    -      -       +      +
    234T  ALA*     3.9    16.6    -      -       +      -
    250T  PHE*     3.5    34.9    +      +       +      -
    251T  LEU      3.4     2.4    -      -       -      -
    252T  ASP*     1.3    77.7    -      -       -      +
    254T  LYS*     1.3    62.1    +      -       -      +
    255T  ILE*     4.1    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 254 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170T  SER*     3.4     4.9    -      -       -      -
    171T  THR*     3.1    30.2    +      -       -      +
    252T  ASP      4.3     5.4    -      -       -      +
    253T  PHE*     1.3    83.1    -      -       -      +
    255T  ILE*     1.3    79.3    +      -       -      +
    256T  GLN*     3.4    26.5    +      -       -      +
    316T  LYS*     5.4    10.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 255 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168T  ILE*     3.7    33.0    -      -       +      -
    169T  VAL      3.8     2.7    -      -       -      -
    170T  SER*     4.2     3.8    -      -       -      -
    227T  GLU*     4.0    26.9    -      -       +      -
    230T  SER*     5.4     0.4    -      -       -      +
    253T  PHE*     4.1    22.9    -      -       +      -
    254T  LYS*     1.3    83.6    -      -       -      +
    256T  GLN*     1.3    63.0    +      -       -      +
    257T  ASN      4.1     4.5    -      -       -      +
    258T  MET*     4.0    17.3    -      -       +      -
    316T  LYS*     3.7    34.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 256 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  GLU*     4.0    19.9    -      -       +      +
     81A  LEU*     5.0     8.0    -      -       +      +
    169T  VAL*     2.6    24.5    +      -       +      +
    171T  THR*     3.3    42.7    +      -       +      +
    254T  LYS*     3.4    39.3    +      -       -      +
    255T  ILE*     1.3    74.6    -      -       -      +
    257T  ASN*     1.3    60.2    +      -       +      +
    314T  GLY      5.4     0.5    -      -       -      +
    315T  ALA      4.5     0.4    -      -       -      -
    316T  LYS*     2.5    45.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 257 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  LEU*     3.3    30.6    -      -       -      +
     77A  LEU*     3.3    23.6    -      -       -      +
     81A  LEU*     3.6    20.1    -      -       +      +
    168T  ILE*     3.5     0.3    -      -       -      -
    169T  VAL*     2.8    44.7    +      -       +      +
    255T  ILE*     3.8     2.1    -      -       -      +
    256T  GLN*     1.3    81.2    -      -       -      +
    258T  MET*     1.3    85.3    +      -       -      +
    313T  THR*     3.8     1.1    +      -       -      -
    314T  GLY*     3.3    25.0    +      -       -      -
    315T  ALA      3.5     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 258 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  LEU      5.4     0.2    -      -       -      -
    165T  LEU*     3.8    33.9    -      -       +      -
    167T  ASN      3.5     3.8    -      -       -      +
    168T  ILE*     3.8    15.0    -      -       +      -
    227T  GLU*     3.8    22.0    -      -       -      +
    255T  ILE*     4.0    10.1    -      -       +      -
    257T  ASN*     1.3    85.4    +      -       -      +
    259T  VAL*     1.3    64.8    +      -       -      +
    312T  LEU      3.7     0.7    -      -       -      +
    313T  THR*     3.2     4.3    -      -       -      -
    314T  GLY      3.0    25.3    +      -       -      -
    315T  ALA*     3.1    21.2    +      -       +      +
    316T  LYS      3.9     4.7    -      -       -      +
    317T  VAL*     3.5    33.4    -      -       -      +
    318T  ARG*     3.7    16.2    -      -       -      -
    321T  ILE*     4.3     6.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 259 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  LEU*     3.2    35.9    -      -       +      +
     43A  PHE*     4.3    18.4    -      -       +      +
    165T  LEU*     3.8     6.6    -      -       -      +
    166T  GLN*     2.8    38.8    +      -       +      -
    167T  ASN*     2.9    20.2    +      -       +      +
    257T  ASN*     4.9     0.4    -      -       -      +
    258T  MET*     1.3    73.4    -      -       -      +
    260T  GLY*     1.3    62.7    +      -       -      +
    311T  VAL*     4.0    16.4    -      -       +      -
    312T  LEU      3.2     7.6    -      -       -      +
    313T  THR*     3.3    27.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 260 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163T  PRO*     5.3     1.3    -      -       -      -
    164T  GLN      3.3    13.2    -      -       -      -
    165T  LEU*     3.9     9.8    -      -       -      +
    166T  GLN*     3.8     3.4    -      -       -      -
    258T  MET      4.4     0.2    -      -       -      -
    259T  VAL*     1.3    77.2    -      -       -      +
    261T  SER*     1.3    60.9    +      -       -      -
    311T  VAL*     3.4     6.8    -      -       -      +
    312T  LEU*     2.9    35.9    +      -       -      +
    321T  ILE*     4.6    11.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 261 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  LEU*     5.2     9.7    -      -       -      +
    163T  PRO*     4.4     1.7    -      -       -      +
    164T  GLN*     2.9    35.5    +      -       -      +
    166T  GLN*     3.4    27.6    +      -       -      +
    260T  GLY*     1.3    75.5    -      -       -      -
    262T  CYS*     1.3    62.9    +      -       -      +
    309T  LYS*     6.2     2.7    -      -       -      -
    310T  VAL      3.2    11.4    -      -       -      -
    311T  VAL*     4.1    15.9    -      -       -      -
    312T  LEU*     4.9     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 262 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161T  ILE*     3.9    11.7    -      -       +      -
    162T  VAL      4.2     2.5    -      -       -      +
    163T  PRO*     3.7    17.5    -      -       +      -
    164T  GLN*     6.2     0.4    -      -       -      -
    261T  SER*     1.3    78.7    -      -       -      +
    263T  ASP*     1.3    62.2    +      -       -      +
    309T  LYS*     3.1    11.3    -      -       -      +
    310T  VAL*     2.8    43.3    +      -       -      -
    312T  LEU*     4.1     7.6    -      -       -      -
    325T  PHE*     3.5    41.3    -      -       -      -
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Residues in contact with ASP 263 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161T  ILE*     3.3    30.6    -      -       -      +
    262T  CYS*     1.3    78.6    -      -       -      +
    264T  VAL*     1.3    65.7    +      -       -      +
    265T  LYS*     3.2    45.3    +      -       -      +
    307T  SER      3.3     7.8    -      -       -      +
    308T  GLY*     3.2    18.4    -      -       -      -
    309T  LYS*     3.4    30.0    -      -       +      -
----------------------------------------------------------
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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