Contacts of the helix formed by residues 632 - 644 (chain V) in PDB entry 5IY8
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 632 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469V THR* 3.7 3.6 - - - +
471V VAL 2.6 28.5 + - - -
472V ARG* 4.0 3.8 - - - -
473V GLU* 3.8 17.1 + - - +
629V HIS* 3.7 3.9 + - - -
630V GLY 3.7 1.6 - - - -
631V GLY* 1.3 90.7 - - - +
633V ARG* 1.4 67.6 + - - +
634V ARG* 3.4 7.6 + - - +
635V GLN* 3.1 30.0 + - - +
636V GLU* 3.3 13.7 + - - +
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Residues in contact with ARG 633 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473V GLU* 2.7 40.4 + - - +
628V SER* 2.7 30.8 + - - +
629V HIS* 3.3 29.7 + - - -
630V GLY 4.1 0.6 - - - +
632V SER* 1.4 71.4 - - - +
634V ARG* 1.3 61.0 + - + +
636V GLU* 2.9 53.7 + - - +
637V ALA 3.4 0.9 + - - -
672V TYR* 3.5 21.7 - - - +
675V LYS* 4.3 16.6 - - + +
676V ARG* 3.5 38.2 - - + +
679V PHE* 3.2 31.2 - - + -
680V LEU* 4.9 0.7 - - - +
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Residues in contact with ARG 634 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339V VAL* 4.8 4.9 - - - +
468V ALA 4.1 8.8 + - - +
469V THR* 3.1 30.5 - - - +
470V LEU* 3.6 23.6 - - - +
471V VAL* 4.0 21.1 - - - +
475V ASP* 5.4 3.5 + - - -
490V GLU* 2.7 34.6 + - - -
632V SER* 3.2 5.3 - - - +
633V ARG* 1.3 73.8 - - + +
635V GLN* 1.3 64.7 + - - +
637V ALA* 3.3 4.9 + - - +
638V GLN* 3.1 21.5 + - - +
679V PHE* 3.4 42.4 - - + -
682V ASP* 5.9 0.4 + - - -
683V GLN* 4.5 2.4 + - - +
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Residues in contact with GLN 635 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444V HIS* 5.4 3.4 + - - -
469V THR* 3.1 38.2 + - + +
609V LYS* 6.1 0.9 - - - +
612V ASP* 1.7 54.8 + - - +
613V THR* 5.0 4.6 + - - -
629V HIS* 6.1 0.4 - - + -
631V GLY* 4.4 11.5 + - - +
632V SER* 3.1 17.9 + - - +
634V ARG* 1.3 75.8 - - - +
636V GLU* 1.4 54.9 + - - +
638V GLN* 4.2 4.1 - - - +
639V ARG* 2.9 41.8 + - - +
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Residues in contact with GLU 636 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625V GLN* 2.8 27.8 + - - +
629V HIS* 2.7 38.8 + - + +
632V SER 3.3 7.5 + - - +
633V ARG* 2.9 31.1 + - - +
635V GLN* 1.4 74.2 - - - +
637V ALA* 1.4 57.9 + - - +
639V ARG* 3.6 11.7 - - - +
640V LEU* 2.9 32.2 + - - +
659V PHE* 4.5 10.7 - - + -
676V ARG* 2.8 36.6 + - - +
680V LEU* 5.4 5.1 - - + +
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Residues in contact with ALA 637 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341V PRO* 5.8 1.7 - - - +
633V ARG 3.4 1.0 + - - -
634V ARG 3.3 4.4 + - - +
635V GLN 3.2 0.6 - - - -
636V GLU* 1.4 78.1 - - - +
638V GLN* 1.3 58.9 + - - +
640V LEU* 3.7 10.8 - - - +
641V GLY* 2.9 27.0 + - - -
679V PHE* 3.7 32.5 - - + -
680V LEU* 4.8 13.2 - - + -
683V GLN* 5.5 2.9 - - + +
685V TYR* 5.1 10.6 + - + -
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Residues in contact with GLN 638 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341V PRO* 5.2 8.7 - - - +
342V CYS* 3.4 26.2 - - + +
442V GLU* 5.1 1.7 - - - +
444V HIS* 5.3 1.2 - - - -
468V ALA* 3.4 24.6 + - + +
469V THR* 2.6 34.9 + - - +
612V ASP* 2.8 29.2 + - - -
613V THR 4.3 11.1 - - - +
634V ARG 3.1 12.8 + - - +
635V GLN* 3.4 8.4 + - - +
637V ALA* 1.3 74.1 - - - +
639V ARG* 1.3 59.0 + - - +
641V GLY* 3.6 1.2 + - - -
642V ARG* 2.9 45.7 + - - +
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Residues in contact with ARG 639 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561V PHE* 3.5 51.6 - - - +
612V ASP* 3.0 33.9 + - - +
617V LEU* 4.6 17.7 - - + -
623V LEU* 3.9 15.0 - - + +
625V GLN* 3.0 27.7 + - - -
629V HIS* 3.8 18.0 + - - -
635V GLN* 2.9 28.0 + - - +
636V GLU* 3.6 6.6 - - - +
638V GLN* 1.3 75.8 - - - +
640V LEU* 1.4 62.8 + - - +
642V ARG* 3.3 12.1 - - - +
643V VAL* 3.1 27.4 + - + +
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Residues in contact with LEU 640 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494V MET* 5.0 1.0 - - + +
505V VAL* 4.0 15.0 - - + -
507V CYS* 4.0 11.2 - - - -
623V LEU* 3.8 15.6 - - + +
636V GLU 2.9 19.9 + - - +
637V ALA* 3.7 7.6 - - - +
639V ARG* 1.4 71.1 - - - +
641V GLY* 1.3 59.5 - - - +
643V VAL 3.3 0.3 + - - -
644V LEU* 2.9 50.8 + - + +
659V PHE* 3.5 42.4 - - + -
680V LEU* 4.7 9.4 - - + -
685V TYR* 3.6 36.1 - - + +
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Residues in contact with GLY 641 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341V PRO* 5.2 14.4 - - - -
494V MET* 4.2 19.1 - - - +
502V ILE* 5.2 0.9 - - - +
637V ALA 2.9 21.1 + - - -
638V GLN* 3.8 1.1 - - - -
639V ARG 3.5 0.2 - - - -
640V LEU* 1.3 75.7 - - - +
642V ARG* 1.3 57.5 + - - +
644V LEU 3.9 0.3 - - - +
645V ARG* 2.8 28.9 + - - -
685V TYR* 4.8 2.2 - - - -
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Residues in contact with ARG 642 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341V PRO* 5.2 1.9 - - + +
342V CYS* 2.9 41.2 + - - +
343V GLY* 4.5 7.4 - - - -
611V GLY 3.0 27.3 + - - -
612V ASP* 4.1 8.1 + - - +
614V SER* 4.4 10.9 + - - +
615V PHE 4.1 21.6 + - - +
616V ASP* 4.7 3.6 - - - +
617V LEU* 3.6 28.4 - - + +
618V PRO 4.8 2.8 - - - +
619V GLU* 5.6 0.5 - - - -
638V GLN* 2.9 43.4 + - - +
639V ARG* 3.3 19.5 - - - +
641V GLY* 1.3 73.2 - - - +
643V VAL* 1.3 65.6 + - + +
645V ARG* 4.2 15.0 + - - +
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Residues in contact with VAL 643 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559V ILE* 3.7 34.3 - - + -
617V LEU* 3.9 37.0 - - + -
618V PRO 3.9 8.3 - - - +
619V GLU* 3.6 8.1 - - - +
620V ALA* 3.2 25.9 + - + -
622V VAL 5.2 0.2 - - - +
623V LEU* 4.9 10.1 - - + -
639V ARG* 3.1 25.2 + - + +
640V LEU 4.1 0.7 - - - +
642V ARG* 1.3 78.1 - - - +
644V LEU* 1.3 80.1 + - + +
645V ARG* 3.9 2.1 + - - +
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Residues in contact with LEU 644 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494V MET* 4.7 3.2 - - + +
503V ALA* 4.3 8.0 - - - +
505V VAL* 4.2 14.4 - - + -
620V ALA 3.6 0.7 - - - -
621V ASN* 3.4 8.5 - - - +
622V VAL 3.3 38.8 - - - +
623V LEU* 3.8 13.2 - - + +
640V LEU* 2.9 40.3 + - + +
641V GLY 3.9 1.2 - - - +
642V ARG 3.8 0.2 - - - -
643V VAL* 1.3 87.4 - - + +
645V ARG* 1.4 85.1 + - - +
657V ALA* 4.3 9.0 - - + -
658V PHE 3.7 25.8 - - - +
659V PHE* 4.3 0.9 - - + -
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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