Contacts of the helix formed by residues 687 - 698 (chain G) in PDB entry 2VKZ
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.
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 SER 687 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653G TYR* 3.9 1.8 + - - -
686G PRO* 1.3 75.4 - - - +
688G LEU* 1.3 66.5 + - - +
689G GLU* 3.0 24.9 + - - -
690G VAL* 2.8 17.4 + - - +
691G ALA* 2.8 31.6 + - - +
715G GLN* 3.4 8.9 + - - +
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Residues in contact with LEU 688 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687G SER* 1.3 80.3 + - - +
689G GLU* 1.3 61.5 + - - +
691G ALA* 3.9 1.0 - - - +
692G SER* 3.0 31.0 + - - -
715G GLN* 3.4 28.5 - - - +
718G ASN* 4.2 32.1 - - + +
719G ILE* 4.2 17.3 - - + +
722G ALA* 5.3 9.0 - - + +
723G HIS* 5.2 1.0 - - - -
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Residues in contact with GLU 689 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687G SER* 3.0 30.2 + - - -
688G LEU* 1.3 79.5 + - - +
690G VAL* 1.3 70.1 + - + +
692G SER* 3.9 5.5 - - - -
693G GLU* 3.2 20.8 + - - +
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Residues in contact with VAL 690 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653G TYR* 3.1 24.7 - - + +
686G PRO* 3.9 1.3 - - + -
687G SER* 2.8 33.0 + - - +
689G GLU* 1.3 82.6 - - + +
691G ALA* 1.3 65.2 + - - +
693G GLU* 3.1 20.9 - - + +
694G TYR* 3.2 34.9 - - + +
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Residues in contact with ALA 691 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686G PRO* 4.0 9.8 - - + +
687G SER 2.8 14.8 + - - +
688G LEU 3.9 2.0 - - - +
690G VAL* 1.3 74.3 - - - +
692G SER* 1.3 58.8 + - - +
693G GLU 3.0 1.6 - - - -
694G TYR* 2.8 34.6 + - - +
695G ILE* 3.0 17.2 + - + +
703G LEU* 4.5 4.9 - - + +
705G LEU* 5.8 2.2 - - + -
719G ILE* 3.3 37.5 - - + -
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Residues in contact with SER 692 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688G LEU 3.0 20.4 + - - -
689G GLU* 3.9 7.0 - - - -
691G ALA* 1.3 75.4 - - - +
693G GLU* 1.3 64.1 + - - +
695G ILE* 3.4 1.1 + - - +
696G GLU* 3.0 49.3 + - - +
722G ALA* 5.7 0.2 - - - -
723G HIS* 3.1 25.6 + - - -
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Residues in contact with GLU 693 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663G ILE* 4.6 11.1 - - + +
689G GLU 3.2 13.5 + - - +
690G VAL* 3.1 17.5 - - + +
691G ALA 3.0 0.2 - - - -
692G SER* 1.3 77.1 - - - +
694G TYR* 1.3 70.5 + - + +
696G GLU* 5.5 0.4 - - - -
697G THR* 2.5 63.1 + - - +
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Residues in contact with TYR 694 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653G TYR* 3.8 10.2 - - - -
659G LEU* 3.6 23.6 - - - +
663G ILE* 3.1 37.7 - - + +
679G LEU* 4.3 3.4 - - + -
681G ILE* 3.3 28.5 - - + -
686G PRO* 3.9 9.2 - - + -
690G VAL* 3.2 35.1 - - + +
691G ALA* 2.8 18.2 + - - +
693G GLU* 1.3 80.9 - - + +
695G ILE* 1.3 62.4 + - - +
698G LEU* 3.1 54.4 + - + +
700G LEU* 5.2 2.6 - - - +
703G LEU* 3.8 18.4 - - + -
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Residues in contact with ILE 695 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691G ALA 3.0 13.9 + - - +
692G SER 3.7 7.0 - - - +
694G TYR* 1.3 75.2 - - - +
696G GLU* 1.3 60.6 + - + +
698G LEU 3.3 16.6 - - - +
700G LEU* 5.0 1.8 + - - +
703G LEU* 3.8 20.0 - - + -
719G ILE* 4.4 18.2 - - + +
723G HIS* 3.5 47.1 - - + +
726G PHE* 3.9 53.9 - - + -
728G ILE* 5.4 5.4 - - + -
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Residues in contact with GLU 696 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692G SER* 3.0 34.5 + - - +
693G GLU* 4.5 0.4 - - - +
695G ILE* 1.3 83.8 - - + +
697G THR* 1.3 64.7 + - - +
698G LEU 4.3 2.0 - - - +
723G HIS* 3.5 15.0 + - + -
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Residues in contact with THR 697 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663G ILE* 6.0 0.4 - - + -
667G LYS* 3.2 49.2 - - + +
693G GLU* 2.5 58.0 + - - +
696G GLU* 1.3 76.0 - - - +
698G LEU* 1.3 66.9 + - + +
699G GLY* 3.8 1.4 + - - -
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Residues in contact with LEU 698 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663G ILE* 3.2 39.3 - - + +
666G ILE* 3.7 13.0 - - + -
667G LYS* 3.6 18.6 - - + -
679G LEU* 3.7 19.1 - - + -
694G TYR* 3.1 47.8 + - + +
695G ILE 3.3 16.8 - - - +
696G GLU 4.3 2.1 - - - +
697G THR* 1.3 79.7 - - + +
699G GLY* 1.3 59.8 + - - +
700G LEU* 2.9 29.1 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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