Contacts of the helix formed by residues 581 - 602 (chain B) in PDB entry 2VXO
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 581 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B TYR* 6.3 0.4 - - - -
328B ASN* 4.3 11.2 - - + +
579B PHE* 2.8 26.9 + - + +
580B LEU* 1.3 76.7 - - - +
582B THR* 1.3 61.3 + - - +
584B VAL* 3.0 16.8 + - - +
585B LEU* 2.9 29.1 + - - +
1695B SO4 3.2 36.2 + - - +
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Residues in contact with THR 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B HIS* 4.7 11.7 - - + -
304B TYR* 3.8 31.8 - - + +
581B THR* 1.3 72.2 - - - +
583B GLY* 1.3 58.4 + - - +
585B LEU* 3.5 8.6 + - - +
586B SER* 2.8 29.2 + - - -
589B ARG* 4.8 2.9 + - - +
1695B SO4 3.9 4.5 + - - -
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Residues in contact with GLY 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B THR* 1.3 75.4 + - - +
584B VAL* 1.3 64.4 + - - +
586B SER* 3.3 7.5 + - - -
587B THR* 3.0 28.2 + - - -
1695B SO4 3.1 25.5 + - - -
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Residues in contact with VAL 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B VAL* 3.8 28.7 - - + -
578B THR* 4.0 4.7 - - + -
579B PHE 3.5 22.4 - - - +
581B THR* 3.0 20.3 + - - +
583B GLY* 1.3 74.3 - - - +
585B LEU* 1.3 65.9 + - + +
587B THR* 3.3 7.9 + - - -
588B LEU* 3.0 22.2 + - - +
615B LEU* 3.9 13.7 - - + +
633B ARG* 3.7 38.4 - - - +
1695B SO4 3.4 7.3 + - - +
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Residues in contact with LEU 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B GLY 3.6 6.7 - - - +
274B PHE* 3.6 28.0 - - + -
304B TYR* 3.5 42.2 - - + +
443B LEU* 4.4 19.8 - - + +
447B VAL* 4.4 17.5 - - + -
580B LEU* 4.6 8.7 - - + -
581B THR 2.9 24.4 + - - +
582B THR* 3.8 5.8 - - - +
584B VAL* 1.3 77.3 - - + +
586B SER* 1.3 55.4 + - - +
588B LEU* 4.0 2.1 - - - +
589B ARG* 2.8 46.8 + - - +
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Residues in contact with SER 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LYS* 5.0 1.9 + - - -
582B THR 2.8 19.6 + - - -
583B GLY* 3.6 9.9 - - - -
584B VAL 3.2 0.4 - - - -
585B LEU* 1.3 75.7 - - - +
587B THR* 1.3 63.2 + - - +
589B ARG* 3.5 24.6 + - - +
590B GLN* 3.1 22.9 + - - +
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Residues in contact with THR 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B GLY 3.0 13.8 + - - -
584B VAL* 3.5 10.2 - - - -
586B SER* 1.3 73.3 - - - +
588B LEU* 1.3 60.4 + - - +
590B GLN* 3.1 8.2 + - - +
591B ALA* 2.9 25.8 + - + +
615B LEU* 4.3 13.2 - - + -
633B ARG* 5.9 2.7 + - + -
672B ILE* 4.2 15.4 - - + +
673B PRO 4.5 9.5 + - - +
674B GLY 5.8 0.9 - - - -
675B ILE* 3.8 29.2 - - + -
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Residues in contact with LEU 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B LEU* 4.1 22.2 - - + -
446B ARG* 3.5 31.2 - - + +
447B VAL* 3.5 19.5 - - + -
584B VAL 3.0 14.9 + - - +
585B LEU* 4.1 3.4 - - - +
587B THR* 1.3 74.8 - - - +
589B ARG* 1.3 56.9 + - - +
591B ALA* 3.1 7.4 + - + -
592B ASP* 2.7 34.8 + - + +
613B VAL* 3.3 40.2 - - + +
614B ILE 4.0 1.6 - - - -
615B LEU* 3.9 24.5 - - + +
635B VAL* 5.4 0.4 - - + -
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Residues in contact with ARG 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B GLY 4.7 4.6 + - - -
275B MET 3.3 23.3 - - - +
276B ARG* 4.0 2.7 - - - -
277B LYS* 3.7 40.4 + - + +
304B TYR* 4.6 9.9 + - - -
443B LEU* 3.9 14.5 - - + +
582B THR* 4.8 2.4 + - - +
585B LEU* 2.8 38.4 + - - +
586B SER* 3.6 26.0 + - - +
588B LEU* 1.3 76.0 - - - +
590B GLN* 1.3 57.3 + - - +
592B ASP* 3.6 5.1 + - - +
593B PHE* 3.0 29.3 + - - +
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Residues in contact with GLN 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LYS* 2.6 35.8 + - - +
586B SER 3.1 13.3 + - - +
587B THR* 3.1 11.1 + - - +
588B LEU 3.1 0.6 - - - -
589B ARG* 1.3 73.9 - - - +
591B ALA* 1.3 65.3 + - - +
593B PHE* 3.2 13.2 + - - +
594B GLU* 2.9 63.1 + - - +
672B ILE* 3.8 17.0 - - + -
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Residues in contact with ALA 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B THR 2.9 13.3 + - - +
588B LEU* 3.6 10.3 - - + +
590B GLN* 1.3 75.9 - - - +
592B ASP* 1.3 61.8 + - - +
594B GLU* 3.8 1.6 - - - +
595B ALA* 3.0 25.6 + - - +
613B VAL* 4.2 11.0 - - + -
635B VAL* 4.0 17.3 - - + -
669B ILE* 3.8 27.1 - - + +
672B ILE* 3.7 13.1 - - + +
675B ILE* 5.6 1.6 - - + -
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Residues in contact with ASP 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ARG* 3.3 38.6 - - - +
277B LYS 4.9 0.5 + - - -
443B LEU* 4.8 12.7 - - + +
446B ARG* 4.5 7.8 + - - -
588B LEU* 2.7 22.4 + - + +
589B ARG* 3.7 7.5 - - - +
591B ALA* 1.3 73.1 - - - +
593B PHE* 1.3 65.3 + - - +
595B ALA* 3.8 0.3 - - - +
596B HIS* 2.9 60.6 + - - +
613B VAL* 4.0 21.5 - - + +
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Residues in contact with PHE 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LYS* 3.8 46.9 - - + -
589B ARG 3.0 18.8 + - - +
590B GLN* 3.2 21.3 + - - +
592B ASP* 1.3 80.2 + - - +
594B GLU* 1.3 62.1 + - + +
596B HIS* 3.3 3.4 + - - +
597B ASN* 2.9 67.4 + - - -
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Residues in contact with GLU 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B GLN* 2.9 40.7 + - - +
591B ALA 3.8 3.6 - - - +
593B PHE* 1.3 76.4 - - + +
595B ALA* 1.3 68.0 + - - +
597B ASN* 3.2 5.5 + - - +
598B ILE* 3.0 31.6 + - + +
668B GLU* 3.0 44.0 - - + +
669B ILE* 3.5 7.7 + - + -
672B ILE* 3.4 25.5 - - - +
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Residues in contact with ALA 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B ALA 3.0 18.2 + - - +
592B ASP 3.8 0.7 - - - +
594B GLU* 1.3 77.9 - - - +
596B HIS* 1.3 56.5 + - - +
598B ILE* 3.4 0.7 + - - +
599B LEU* 3.1 22.3 + - - +
611B MET* 3.8 9.9 - - + -
613B VAL* 3.7 26.2 - - + -
637B ILE* 5.2 2.0 - - + -
665B MET* 3.4 29.2 - - - +
669B ILE* 4.0 15.1 - - + +
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Residues in contact with HIS 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ARG* 4.2 12.8 + - - -
436B HIS* 4.9 5.3 + - - +
446B ARG* 5.2 2.5 - - - -
592B ASP* 2.9 50.8 + - - +
593B PHE* 3.9 3.4 - - - +
595B ALA* 1.3 74.2 - - - +
597B ASN* 1.3 61.3 + - - +
599B LEU* 3.4 9.9 + - + +
600B ARG* 3.0 30.1 + - - +
611B MET* 3.0 54.6 + - + +
613B VAL* 4.2 3.3 - - + +
1696B SO4 2.8 31.9 + - - +
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Residues in contact with ASN 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B PHE* 2.9 68.4 + - - +
594B GLU* 3.2 6.3 + - - +
596B HIS* 1.3 74.4 - - - +
598B ILE* 1.3 62.9 - - + +
600B ARG* 3.2 5.9 + - - +
601B GLU* 2.9 54.1 + - - +
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Residues in contact with ILE 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594B GLU* 3.0 21.9 + - + +
595B ALA 3.7 3.8 - - - +
597B ASN* 1.3 75.7 - - + +
599B LEU* 1.3 63.1 + - - +
601B GLU* 3.9 5.1 - - - +
602B SER* 3.2 25.0 + - - -
661B VAL* 3.5 33.4 - - + +
664B LYS* 3.6 50.5 - - + +
665B MET* 3.6 17.0 - - + +
668B GLU* 3.8 20.2 - - + -
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Residues in contact with LEU 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B HIS* 4.6 8.3 - - + -
595B ALA 3.1 14.3 + - - +
596B HIS* 3.6 11.9 - - + +
597B ASN 3.2 0.2 - - - -
598B ILE* 1.3 78.1 - - - +
600B ARG* 1.3 58.1 + - - +
602B SER* 3.1 17.2 + - - -
604B TYR* 3.6 18.2 + - + +
605B ALA* 3.4 25.2 + - + -
608B ILE* 3.7 28.7 - - + -
611B MET* 3.7 22.9 - - + -
657B ILE* 3.5 33.2 - - + -
661B VAL* 4.5 2.9 - - + -
665B MET* 3.8 11.2 - - + +
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Residues in contact with ARG 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B GLU* 3.3 36.4 + - - +
434B SER* 3.9 29.5 + - - -
435B ARG* 4.2 5.7 - - - +
436B HIS* 5.1 1.4 - - - -
596B HIS 3.0 17.6 + - - +
597B ASN* 3.8 7.4 - - - +
599B LEU* 1.3 73.9 - - - +
601B GLU* 1.3 61.5 - - + +
602B SER 3.1 8.6 + - - -
603B GLY* 3.4 12.1 + - - -
605B ALA* 4.1 26.2 - - + +
1696B SO4 3.1 40.4 + - - -
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Residues in contact with GLU 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B ASN* 2.9 43.6 + - - +
598B ILE* 3.9 3.8 - - - +
600B ARG* 1.3 77.5 - - + +
602B SER* 1.3 58.7 + - - +
603B GLY 3.5 0.4 - - - -
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Residues in contact with SER 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B ILE* 3.2 13.8 + - - -
599B LEU* 3.1 14.7 + - - -
600B ARG 3.1 0.2 - - - -
601B GLU* 1.3 77.7 - - - +
603B GLY* 1.3 56.0 + - - +
604B TYR* 3.2 27.4 + - - +
661B VAL* 3.7 35.8 - - - +
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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) + - + + + + + -
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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