Contacts of the helix formed by residues 654 - 669 (chain A) in PDB entry 2VWV
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 THR 654 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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655A GLU* 1.3 59.5 - - - +
656A ARG* 3.4 20.8 - - + +
657A GLN* 3.2 42.7 + - - +
658A ARG* 3.1 24.1 + - - +
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Residues in contact with GLU 655 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654A THR* 1.3 71.5 - - - +
656A ARG* 1.3 67.0 + - - +
658A ARG* 3.2 12.3 + - + +
659A ARG* 2.8 28.2 + - - +
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Residues in contact with ARG 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654A THR* 3.1 19.2 - - + +
655A GLU* 1.3 77.5 - - - +
657A GLN* 1.3 58.8 + - + +
659A ARG* 3.3 5.7 + - - +
660A GLU* 3.0 28.9 + - - +
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Residues in contact with GLN 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626A PHE* 4.1 27.8 - - + -
649A LEU* 4.6 7.6 - - + -
654A THR* 3.2 35.6 + - - +
656A ARG* 1.3 76.4 - - + +
658A ARG* 1.3 60.9 + - - +
660A GLU* 3.6 6.8 - - - +
661A PHE* 2.8 32.7 + - - +
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Residues in contact with ARG 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A PHE* 4.8 5.9 - - - -
649A LEU* 3.6 26.1 - - + +
654A THR 3.1 13.5 + - - +
655A GLU* 3.6 15.0 - - - +
657A GLN* 1.3 78.6 - - - +
659A ARG* 1.3 62.9 + - - +
661A PHE* 3.6 2.1 - - - +
662A LEU* 3.1 46.5 + - + +
684A THR* 3.1 32.5 + - - +
689A VAL* 3.7 25.0 - - + +
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Residues in contact with ARG 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A GLU 2.8 19.8 + - - +
656A ARG* 3.6 6.1 - - - +
658A ARG* 1.3 74.0 - - - +
660A GLU* 1.3 57.6 + - - +
662A LEU* 3.6 6.4 + - - +
663A SER* 3.0 27.7 + - - -
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Residues in contact with GLU 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626A PHE* 4.5 13.0 - - + -
656A ARG 3.0 16.3 + - - +
657A GLN* 3.6 8.7 - - - +
659A ARG* 1.3 75.6 - - - +
661A PHE* 1.3 69.0 + - - +
663A SER* 2.9 26.2 + - - -
664A GLU* 3.9 1.0 + - - +
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Residues in contact with PHE 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626A PHE* 3.7 45.6 - + + -
647A LYS* 3.7 46.0 - - + -
648A THR 4.4 4.3 - - - -
649A LEU* 3.8 24.5 - - + -
657A GLN 2.8 21.5 + - - +
658A ARG 3.6 2.9 - - - +
660A GLU* 1.3 73.7 - - - +
662A LEU* 1.3 61.4 + - + +
663A SER 3.4 0.2 + - - -
664A GLU* 3.6 12.9 - - - +
689A VAL* 3.8 37.0 - - + -
691A ILE* 3.2 39.7 - - + +
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Residues in contact with LEU 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A PHE* 3.7 33.1 - - + -
658A ARG* 3.1 47.5 + - - +
659A ARG* 4.0 5.2 - - - +
661A PHE* 1.3 75.6 - - + +
663A SER* 1.3 66.2 + - - +
664A GLU 3.2 2.7 - - - -
665A ALA* 3.1 14.7 + - - +
666A SER 3.2 8.7 + - - -
682A VAL* 4.6 5.2 - - + -
684A THR* 3.7 26.9 - - + -
689A VAL* 3.7 26.2 - - + -
690A MET 4.6 3.8 - - - +
691A ILE* 4.3 18.6 - - + -
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Residues in contact with SER 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659A ARG 3.0 13.6 + - - -
660A GLU* 2.9 21.9 + - - -
662A LEU* 1.3 76.1 - - - +
664A GLU* 1.3 60.2 + - - +
666A SER* 2.4 34.9 + - - -
667A ILE* 2.9 22.9 + - - +
759A PHE 5.0 0.7 + - - -
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Residues in contact with GLU 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647A LYS* 2.6 42.0 + - - +
660A GLU 5.2 0.7 - - - +
661A PHE* 3.6 17.2 + - - +
662A LEU 3.2 0.6 - - - -
663A SER* 1.3 83.3 + - - +
665A ALA* 1.3 58.6 + - - +
667A ILE* 3.9 0.9 - - - +
668A MET* 2.8 57.4 + - + +
691A ILE* 3.7 13.4 - - + +
758A ASP* 4.8 3.3 + - - -
759A PHE* 3.3 40.4 + - - +
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Residues in contact with ALA 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A PHE* 4.8 6.1 - - + -
662A LEU* 3.1 12.6 + - - +
664A GLU* 1.3 79.3 - - - +
666A SER* 1.3 61.5 + - - +
668A MET* 4.4 2.2 - - - -
669A GLY* 2.8 24.3 + - - -
679A LEU* 3.4 20.0 - - + +
682A VAL* 3.3 33.9 - - + -
691A ILE* 4.2 15.0 - - + -
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Residues in contact with SER 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A PHE* 4.4 15.7 - - - -
662A LEU 3.2 5.6 + - - -
663A SER* 2.4 36.6 + - - -
665A ALA* 1.3 79.0 - - - +
667A ILE* 1.3 65.3 + - - +
669A GLY* 3.6 4.9 + - - -
670A GLN* 3.5 15.2 + - - +
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Residues in contact with ILE 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663A SER* 2.9 30.2 + - - +
664A GLU 3.9 3.4 - - - +
666A SER* 1.3 77.3 - - - +
668A MET* 1.3 65.1 + - - +
670A GLN* 3.1 37.7 + - - +
671A PHE* 3.5 11.9 - - + -
736A TYR* 3.6 37.9 - - + +
759A PHE* 3.5 28.3 - - + +
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Residues in contact with MET 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664A GLU* 2.8 55.3 + - + +
665A ALA* 4.2 2.7 - - - +
667A ILE* 1.3 75.5 - - - +
669A GLY* 1.3 61.5 + - - +
670A GLN 3.2 1.0 + - - -
671A PHE* 3.2 29.4 + - + +
677A ILE* 3.6 29.6 - - + +
678A ARG* 5.9 0.2 - - - -
679A LEU* 4.0 26.7 + - + +
691A ILE* 5.1 3.1 - - + -
693A THR* 3.6 32.5 - - + -
757A SER* 5.5 2.7 - - - +
759A PHE* 4.1 25.8 - - + +
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Residues in contact with GLY 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A ALA 6.0 0.2 - - - -
608A LYS* 5.8 3.3 - - - -
665A ALA 2.8 20.1 + - - -
666A SER 4.0 3.8 - - - -
667A ILE 3.2 0.6 - - - -
668A MET* 1.3 77.2 - - - +
670A GLN* 1.3 58.1 + - - +
671A PHE 3.3 3.6 + - - +
679A LEU* 4.0 16.3 - - - +
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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