Contacts of the strand formed by residues 420 - 430 (chain B) in PDB entry 5EMV


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 420 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227B  ARG*     5.1     0.9    +      -       -      -
    288B  LEU*     4.7    10.5    -      -       +      +
    292B  GLY      3.7    21.9    +      -       -      +
    293B  PRO*     3.7    21.1    -      -       +      +
    296B  ALA*     4.4     4.3    -      -       +      -
    297B  PHE*     3.4    40.8    -      -       +      -
    411B  VAL*     3.6    26.2    -      -       +      -
    412B  VAL      3.5    15.9    -      -       -      +
    413B  THR*     3.9     7.6    -      -       +      -
    418B  GLN      3.7     2.2    +      -       -      -
    419B  GLU*     1.3    76.8    -      -       -      +
    421B  LEU*     1.3    64.6    +      -       -      +
    422B  LEU      3.7    15.3    -      -       -      +
    423B  CYS*     4.2     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 421 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225B  THR*     3.8    12.7    +      -       -      +
    227B  ARG*     3.3    49.1    -      -       +      +
    228B  LEU*     4.0    19.2    -      -       +      +
    296B  ALA*     3.4    17.6    -      -       -      +
    339B  MET*     3.9    20.4    -      -       +      -
    341B  LEU*     3.6    30.7    -      -       +      -
    412B  VAL*     2.8    10.7    +      -       +      +
    413B  THR*     4.0     1.6    -      -       -      -
    414B  ASN*     3.8    14.8    -      -       +      +
    419B  GLU*     3.9    11.0    -      -       +      +
    420B  LEU*     1.3    79.7    -      -       -      +
    422B  LEU*     1.3    67.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 422 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223B  LEU*     3.9    20.6    -      -       +      -
    224B  GLY*     3.8    22.0    -      -       -      -
    225B  THR*     4.3     2.5    -      -       +      +
    228B  LEU*     4.4    12.1    -      -       +      +
    230B  LEU*     4.6     5.2    -      -       +      +
    296B  ALA*     3.6     7.4    -      -       -      +
    298B  PHE*     3.6    32.5    -      -       +      -
    333B  TYR*     4.2    28.0    -      -       +      -
    410B  GLN      3.8     0.9    -      -       -      +
    411B  VAL*     3.7     0.9    -      -       -      -
    412B  VAL*     2.7    49.2    +      -       +      +
    420B  LEU*     3.7     3.9    -      -       -      +
    421B  LEU*     1.3    84.8    -      -       -      +
    423B  CYS*     1.3    59.1    +      -       -      +
    424B  THR*     4.3     7.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 423 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285B  LEU*     4.3     4.9    -      -       -      -
    288B  LEU*     4.5     4.5    -      -       +      -
    296B  ALA      2.9    11.3    +      -       -      +
    297B  PHE*     3.4    39.8    -      -       +      -
    298B  PHE*     2.8    27.4    +      -       -      +
    409B  LEU*     3.7    26.0    -      -       -      -
    410B  GLN      3.3     7.2    -      -       -      +
    411B  VAL*     4.2    10.3    -      -       +      -
    420B  LEU*     4.2    14.3    -      -       +      +
    422B  LEU*     1.3    73.9    -      -       -      +
    424B  THR*     1.3    66.4    +      -       -      +
    425B  ALA      5.1     0.2    -      -       -      -
    444B  LEU*     6.0     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 424 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223B  LEU*     3.7    25.3    -      -       +      +
    298B  PHE*     3.4     7.6    -      -       +      +
    300B  VAL*     3.6    26.9    -      -       +      -
    408B  ILE      3.8     1.0    -      -       -      +
    409B  LEU*     3.5     6.8    -      -       -      +
    410B  GLN*     2.8    44.1    +      -       -      +
    422B  LEU*     4.3     7.3    -      -       -      +
    423B  CYS*     1.3    76.8    +      -       -      +
    425B  ALA*     1.3    62.3    +      -       -      +
    426B  TYR*     3.5    36.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 425 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274B  ILE*     4.1    10.1    -      -       +      -
    278B  PHE*     3.5    27.8    -      -       +      -
    285B  LEU*     5.0     1.8    -      -       +      -
    298B  PHE      2.8    15.4    +      -       -      +
    299B  LEU*     3.4    14.8    -      -       +      +
    300B  VAL*     2.7    32.6    +      -       -      +
    408B  ILE      3.7     3.6    -      -       -      -
    409B  LEU*     4.1     9.6    -      -       +      +
    423B  CYS*     4.2     0.6    -      -       -      -
    424B  THR*     1.3    73.7    -      -       -      +
    426B  TYR*     1.3    57.6    +      -       -      +
    444B  LEU*     4.4     4.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 426 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223B  LEU*     5.2     3.3    -      -       -      +
    230B  LEU*     5.4     3.3    -      -       -      +
    233B  PHE*     4.3    21.6    -      +       -      +
    254B  ILE*     4.8     3.4    -      -       +      +
    278B  PHE*     4.2     0.4    -      -       -      -
    300B  VAL*     3.4    19.7    -      -       +      +
    302B  PHE*     3.3    35.0    -      +       +      -
    380B  P1L      5.8     0.9    -      -       +      -
    407B  THR*     3.5    12.1    -      -       -      -
    408B  ILE*     2.7    54.0    +      -       +      +
    410B  GLN*     2.7    47.0    +      -       +      -
    424B  THR*     3.5    29.4    +      -       +      +
    425B  ALA*     1.3    72.5    -      -       -      +
    427B  VAL*     1.3    62.4    +      -       -      +
    428B  PHE*     3.7    22.2    -      +       +      -
----------------------------------------------------------
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Residues in contact with VAL 427 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274B  ILE*     5.5     4.5    -      -       +      -
    277B  LYS*     5.1    13.7    -      -       +      -
    278B  PHE*     4.9     7.9    -      -       +      -
    299B  LEU*     4.0    23.8    -      -       +      -
    300B  VAL      2.9    15.9    +      -       -      +
    301B  LYS*     3.7    27.1    -      -       +      -
    302B  PHE*     3.0    25.3    +      -       -      +
    406B  PHE      4.8     2.7    -      -       -      -
    407B  THR*     4.3    14.1    -      -       +      -
    425B  ALA      4.1     0.2    +      -       -      -
    426B  TYR*     1.3    79.4    -      -       -      +
    428B  PHE*     1.3    67.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 428 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252B  VAL*     4.4     2.2    -      -       +      -
    301B  LYS*     4.7     2.0    -      -       -      -
    302B  PHE*     3.6    37.5    -      +       +      -
    304B  ALA*     4.8     0.9    -      -       +      -
    380B  P1L      3.9    40.6    -      -       +      -
    400B  ASN      5.1     0.7    -      -       -      +
    403B  LEU*     3.6    39.6    +      -       +      +
    404B  GLU*     4.8     1.7    +      -       -      -
    406B  PHE*     3.7    37.9    +      +       -      +
    408B  ILE*     4.0    22.4    -      -       +      -
    426B  TYR*     3.7    34.8    -      +       +      -
    427B  VAL*     1.3    76.9    -      -       -      +
    429B  GLU*     1.3    69.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 429 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301B  LYS*     2.6    37.7    +      -       -      +
    302B  PHE      2.9     6.6    +      -       -      +
    303B  TRP*     3.4    23.4    +      -       +      -
    304B  ALA*     2.9    27.6    +      -       -      +
    400B  ASN*     3.5    24.9    +      -       +      +
    403B  LEU*     3.8     9.6    -      -       -      +
    428B  PHE*     1.3    77.4    -      -       -      +
    430B  VAL*     1.3    62.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 430 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303B  TRP*     4.1     9.2    -      -       -      -
    304B  ALA      3.7     7.6    -      -       -      +
    306B  LEU*     3.7    30.1    -      -       +      +
    380B  P1L      5.2     0.7    -      -       +      -
    396B  ARG*     5.1     7.4    -      -       +      +
    399B  MET*     3.7    33.4    -      -       +      -
    400B  ASN*     2.8    21.3    +      -       -      +
    403B  LEU*     3.3    24.9    -      -       +      -
    429B  GLU*     1.3    75.5    -      -       -      +
    431B  SER*     1.3    75.1    +      -       -      +
----------------------------------------------------------
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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