Contacts of the helix formed by residues 491 - 505 (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 491 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369A LEU 5.6 1.1 - - - +
371A PRO* 6.5 0.2 - - + -
412A LYS* 3.5 28.0 - - + +
413A ASP* 3.4 11.9 - - - +
489B CYS 4.3 0.4 + - - -
490B THR* 1.3 74.9 - - - +
492B GLU* 1.3 66.4 + - - +
493B GLU* 3.7 10.1 + - - +
494B ASP* 3.0 38.3 + - - +
495B GLN* 3.0 21.5 + - - +
552B ARG* 6.0 1.1 - - - +
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Residues in contact with GLU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLN* 3.8 13.5 + - - -
53A GLU* 3.0 32.9 - - - +
229A GLU* 5.6 6.1 - - - +
412A LYS* 4.2 1.6 - - - +
413A ASP* 2.8 26.3 + - - +
490B THR 3.7 1.8 + - - -
491B THR* 1.3 70.6 - - - +
493B GLU* 1.3 64.3 + - - +
495B GLN* 3.3 13.2 + - - +
496B GLU* 3.0 47.4 + - - +
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Residues in contact with GLU 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP* 3.4 19.6 - - - +
52A SER 2.8 24.0 - - - +
53A GLU* 3.8 37.6 - - - +
54A ILE* 4.0 8.3 + - - +
55A PHE* 5.4 0.3 - - - -
413A ASP* 4.6 0.4 + - - -
415A HIS* 5.7 3.3 + - - -
491B THR* 3.1 9.8 + - - +
492B GLU* 1.3 79.3 + - - +
494B ASP* 1.3 64.8 + - - +
496B GLU* 3.3 2.9 + - - +
497B LYS* 2.9 30.7 + - - +
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Residues in contact with ASP 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B THR* 4.6 4.2 - - + -
491B THR* 3.0 33.6 + - - +
493B GLU* 1.3 79.9 - - - +
495B GLN* 1.3 56.7 + - - +
497B LYS* 3.8 3.2 - - - +
498B LEU* 2.9 32.9 + - - +
545B PHE* 3.5 25.4 - - + -
549B LEU* 3.6 19.9 - - + +
552B ARG* 2.8 34.0 + - - -
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Residues in contact with GLN 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LYS* 4.0 5.1 - - - +
472B PHE* 3.6 22.8 - - + -
487B LYS* 3.0 46.2 + - - +
490B THR* 3.0 40.1 + - - +
491B THR 3.0 12.4 + - - +
492B GLU* 3.5 10.8 - - - +
494B ASP* 1.3 74.1 - - - +
496B GLU* 1.3 54.9 + - - +
498B LEU* 3.2 4.8 + - + +
499B MET* 2.7 40.1 + - + +
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Residues in contact with GLU 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLU* 3.0 31.8 - - - +
55A PHE* 3.7 23.8 - - + -
67A GLN* 3.8 21.5 + - - +
69A PHE* 4.7 5.0 - - - -
492B GLU* 3.0 25.0 + - - +
493B GLU 3.5 9.0 - - - +
495B GLN* 1.3 75.2 - - - +
497B LYS* 1.3 63.4 + - - +
499B MET* 2.9 21.1 + - + +
500B GLN* 3.2 15.2 + - - +
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Residues in contact with LYS 497 (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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54A ILE* 3.4 40.0 - - + +
55A PHE* 4.2 12.0 - - - -
56A PRO* 4.1 29.3 - - + +
493B GLU 2.9 16.6 + - - +
494B ASP* 3.8 6.3 - - - +
496B GLU* 1.3 75.9 - - - +
498B LEU* 1.3 56.2 + - - +
500B GLN* 3.7 4.9 + - - +
501B ILE* 3.3 31.2 + - + +
541B GLU 5.5 1.1 + - - -
545B PHE* 3.5 52.2 - - + +
548B ARG* 6.1 0.6 - - - +
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Residues in contact with LEU 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B VAL* 4.0 20.9 - - + +
472B PHE* 3.7 38.5 - - + -
486B VAL* 5.2 5.2 - - + -
490B THR* 5.4 5.6 - - + -
494B ASP 2.9 20.3 + - - +
495B GLN* 3.5 6.3 - - - +
496B GLU 3.1 0.2 - - - -
497B LYS* 1.3 74.1 - - - +
499B MET* 1.3 62.8 + - - +
500B GLN 3.4 0.2 - - - -
501B ILE* 4.1 4.3 - - + -
502B THR* 2.8 33.9 + - + +
545B PHE* 4.3 4.9 - - + -
546B LEU* 3.6 30.7 - - + -
549B LEU* 3.8 23.3 - - + -
553B MET* 5.8 0.4 - - - -
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Residues in contact with MET 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLN* 6.0 0.7 - - - +
472B PHE* 4.0 15.9 - - + -
473B SER* 3.7 38.9 + - - +
476B VAL* 4.3 18.6 - - + -
477B LYS* 6.4 0.7 - - - -
495B GLN* 2.7 23.0 + - + +
496B GLU* 2.9 12.5 + - + +
498B LEU* 1.3 70.9 - - - +
500B GLN* 1.3 73.4 + - - +
502B THR* 4.3 2.0 - - - -
503B SER* 3.2 23.6 + - - -
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Residues in contact with GLN 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PHE* 3.8 33.6 - - + -
56A PRO* 5.1 5.6 - - + -
59A THR* 4.2 11.8 - - + +
60A PRO* 5.0 2.3 - - - +
63A ALA* 3.2 27.0 - - - +
67A GLN* 3.7 29.1 + - - +
496B GLU 3.2 10.6 + - - +
497B LYS* 3.9 6.1 - - - +
498B LEU 3.4 0.2 - - - -
499B MET* 1.3 82.7 - - - +
501B ILE* 1.3 65.2 + - - +
503B SER* 2.9 24.9 + - - -
504B LEU* 3.0 21.8 + - + +
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Residues in contact with ILE 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO* 3.8 18.6 - - + -
497B LYS* 3.3 18.9 + - + +
498B LEU* 4.2 4.5 - - - +
499B MET 3.5 0.2 - - - -
500B GLN* 1.3 78.7 - - - +
502B THR* 1.3 63.3 + - + +
504B LEU* 4.9 3.1 - - - -
505B HIS* 3.2 36.4 + - - +
507B LEU* 3.9 21.8 - - + -
542B SER* 3.4 41.5 - - - +
545B PHE* 3.5 32.5 - - + -
546B LEU* 4.5 11.2 - - + -
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Residues in contact with THR 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B VAL 3.3 17.9 - - - +
470B ALA* 3.2 28.6 - - - +
471B ASP* 4.5 5.1 - - - +
472B PHE* 3.4 6.8 + - + +
473B SER* 3.0 29.2 + - - -
474B ALA* 5.5 1.0 + - - +
498B LEU* 2.8 28.2 + - + +
499B MET 3.7 0.2 + - - -
501B ILE* 1.3 85.1 - - + +
503B SER* 1.3 59.1 + - - +
505B HIS 3.2 15.8 - - - +
506B SER* 5.3 0.3 - - - -
507B LEU* 4.5 6.3 - - + -
546B LEU* 5.4 1.1 - - + -
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Residues in contact with SER 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B SER* 3.3 17.5 - - - -
499B MET* 3.2 10.2 + - - -
500B GLN* 2.9 22.4 + - - -
502B THR* 1.3 79.4 - - - +
504B LEU* 1.3 67.0 + - - +
505B HIS 3.4 2.3 - - - +
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Residues in contact with LEU 504 (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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58A GLU* 4.2 13.5 - - + +
59A THR* 4.5 5.2 - - - +
60A PRO* 3.7 39.7 - - + -
62A PHE* 5.1 7.2 - - + -
500B GLN* 3.0 27.9 + - + +
501B ILE* 3.5 1.8 + - - +
503B SER* 1.3 82.0 - - - +
505B HIS* 1.3 82.5 + - + +
536B ASP* 3.6 9.4 - - - +
539B ASP* 5.8 0.2 - - - +
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Residues in contact with HIS 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU* 4.1 7.7 + - - -
470B ALA 5.3 0.3 - - - +
501B ILE* 3.2 23.2 + - - +
502B THR* 3.2 25.5 - - - +
503B SER 4.2 1.9 - - - -
504B LEU* 1.3 100.5 + - + +
506B SER* 1.3 60.4 + - - +
507B LEU* 3.8 22.6 + - + +
534B SER* 5.3 0.7 - - - -
536B ASP* 3.0 32.5 - - - +
537B GLU 4.1 12.2 + - - -
539B ASP* 3.5 39.0 - - + +
542B SER* 4.6 4.6 - - - -
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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