Contacts of the helix formed by residues 465 - 476 (chain B) in PDB entry 3OY3
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 PRO 465 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341B LEU* 5.9 6.1 - - + -
463B GLY 3.3 8.7 - - - +
464B CYS* 1.3 88.3 - - - +
466B GLU* 1.3 57.2 + - - +
467B LYS* 3.1 4.7 - - + +
468B VAL* 2.6 53.7 + - + +
469B TYR 3.1 9.0 + - - -
496B MET* 6.3 0.2 - - - -
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Residues in contact with GLU 466 (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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460B ARG* 3.5 34.7 + - - +
464B CYS 3.3 5.1 + - - -
465B PRO* 1.3 70.9 - - - +
467B LYS* 1.3 58.0 + - - +
469B TYR* 3.3 15.1 + - - +
470B GLU* 2.8 47.3 + - + +
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Residues in contact with LYS 467 (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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465B PRO* 3.1 4.1 - - + +
466B GLU* 1.3 79.4 - - - +
468B VAL* 1.3 62.6 + - + +
470B GLU* 3.4 14.6 + - - +
471B LEU* 3.2 21.8 + - - +
496B MET* 4.1 22.1 - - - +
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Residues in contact with VAL 468 (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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341B LEU* 4.9 7.2 - - + -
429B LEU* 4.5 9.3 - - + +
433B ALA* 5.9 1.8 - - + -
464B CYS* 3.8 17.3 - - - -
465B PRO* 2.6 39.8 + - + +
467B LYS* 1.3 68.9 - - - +
469B TYR* 1.3 59.3 - - - +
471B LEU* 3.2 6.2 + - - +
472B MET* 3.0 33.9 + - + +
493B PHE* 4.3 19.5 - - + -
496B MET* 3.6 27.6 - - + -
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Residues in contact with TYR 469 (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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457B ARG 4.8 0.9 + - - -
458B MET 2.6 27.0 + - - -
459B GLU* 3.5 5.4 - - - -
460B ARG* 3.3 61.8 + - + -
461B PRO* 4.7 0.4 - - + -
464B CYS* 3.9 4.6 - - - -
465B PRO 3.1 5.6 + - - +
466B GLU* 3.6 20.2 - - - +
468B VAL* 1.3 74.9 - - - +
470B GLU* 1.3 67.1 + - + +
472B MET* 3.2 23.4 + - - +
473B ARG* 2.9 56.5 + - + +
476B TRP* 4.6 2.5 - + - -
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Residues in contact with GLU 470 (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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466B GLU* 2.8 36.7 + - + +
467B LYS* 3.6 14.7 + - - +
468B VAL 3.3 0.2 - - - -
469B TYR* 1.3 77.2 - - + +
471B LEU* 1.3 60.7 + - - +
473B ARG* 3.5 7.1 + - - +
474B ALA* 3.2 22.5 + - - +
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Residues in contact with LEU 471 (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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425B PHE* 4.3 1.3 - - + -
429B LEU* 4.0 8.5 - - + -
467B LYS 3.2 12.4 + - - +
468B VAL* 3.2 11.8 + - - +
469B TYR 3.1 0.6 - - - -
470B GLU* 1.3 75.9 - - - +
472B MET* 1.3 64.1 + - - +
474B ALA* 3.4 6.5 + - + +
475B CYS* 3.0 28.7 + - - -
484B PRO* 5.2 3.3 - - + +
489B ILE* 3.8 29.4 - - + +
492B ALA* 3.5 33.2 - - + -
493B PHE* 3.1 33.7 - - + -
496B MET* 5.3 4.0 - - + -
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Residues in contact with MET 472 (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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426B GLY* 3.9 6.5 - - - +
429B LEU* 3.8 28.9 - - + +
430B TRP* 3.6 35.0 - - + +
433B ALA* 4.3 3.1 - - + -
461B PRO* 4.2 8.1 - - + -
464B CYS* 3.9 27.1 - - - -
468B VAL* 3.0 15.8 + - + +
469B TYR* 3.3 26.2 - - + +
471B LEU* 1.3 76.1 - - - +
473B ARG* 1.3 59.0 + - - +
475B CYS* 2.9 24.8 + - - +
476B TRP* 3.1 42.1 + - + -
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Residues in contact with ARG 473 (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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455B ASP* 4.9 17.4 + - - -
457B ARG* 3.7 37.3 - - - +
469B TYR* 2.9 54.7 + - + +
470B GLU* 3.8 7.0 - - - +
471B LEU 3.3 0.4 - - - -
472B MET* 1.3 76.6 - - - +
474B ALA* 1.3 60.0 + - - +
476B TRP* 3.3 27.3 + - - +
477B GLN* 3.5 10.2 + - - +
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Residues in contact with ALA 474 (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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470B GLU 3.2 16.6 + - - +
471B LEU* 3.7 7.6 - - + +
472B MET 3.1 0.4 - - - -
473B ARG* 1.3 72.6 - - - +
475B CYS* 1.3 66.4 + - - +
476B TRP 3.0 2.3 + - - -
477B GLN* 3.2 31.2 + - + +
482B ASP 5.5 0.4 - - - +
483B ARG* 3.7 1.6 - - - -
484B PRO* 3.4 29.4 - - + +
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Residues in contact with CYS 475 (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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422B VAL* 3.4 42.6 - - - +
423B TRP* 3.4 11.6 - - - -
425B PHE* 4.1 14.4 - - - -
426B GLY* 3.8 14.1 - - - -
429B LEU* 5.0 0.2 - - - -
471B LEU* 3.0 25.4 + - - -
472B MET* 2.9 12.1 + - - +
474B ALA* 1.3 76.7 - - - +
476B TRP* 1.3 57.5 + - - +
477B GLN 3.4 0.4 - - - -
483B ARG* 3.1 23.3 + - - -
484B PRO* 4.4 2.0 - - - -
489B ILE* 3.8 17.3 - - - -
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Residues in contact with TRP 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B TRP* 3.3 39.1 + + + -
426B GLY 3.2 39.1 - - - -
427B VAL* 3.3 16.9 - - + +
430B TRP* 4.3 2.2 - + + -
440B TYR* 5.3 4.5 - - - -
457B ARG* 2.9 52.7 + - + +
458B MET* 3.8 52.7 - - + -
469B TYR* 4.6 1.1 - + - -
472B MET* 3.1 40.8 + - + +
473B ARG* 3.3 19.2 + - - +
474B ALA 3.0 1.2 - - - -
475B CYS* 1.3 83.4 - - + +
477B GLN* 1.3 63.2 + - - +
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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