Contacts of the helix formed by residues 465 - 477 (chain B) in PDB entry 2O8C
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 ALA 465 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461B PHE* 4.1 2.9 - - + -
462B PRO* 2.9 18.6 + - + +
464B ILE* 1.3 78.6 - - - +
466B PHE* 1.3 64.6 + - - +
467B GLY 3.2 3.4 - - - -
468B ARG* 3.1 36.2 + - - +
469B TYR* 3.3 32.9 + - + -
25F C 4.0 15.3 - - - -
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Residues in contact with PHE 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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426B CYS* 3.7 29.8 - - + -
433B TYR* 3.8 28.3 - + + +
461B PHE* 3.5 23.1 - + - -
462B PRO 3.7 3.8 + - - -
463B GLU 3.2 13.7 + - - +
465B ALA* 1.3 76.4 - - - +
467B GLY* 1.3 57.3 + - - +
470B SER* 2.8 59.3 + - - -
480B VAL* 4.3 4.7 - - + -
482B ARG* 3.7 34.5 - - + -
517B ILE* 4.2 19.1 - - + -
527B LEU* 3.5 30.1 - - + -
528B GLU* 5.1 0.4 - - + -
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Residues in contact with GLY 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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463B GLU 5.0 0.4 + - - -
464B ILE 4.9 2.2 + - - -
465B ALA 3.1 1.6 + - - -
466B PHE* 1.3 79.4 - - - +
468B ARG* 1.3 61.2 + - - +
470B SER* 3.6 2.3 + - - -
471B ASP* 3.1 23.2 + - - +
527B LEU 3.3 23.6 + - - -
528B GLU* 4.5 6.5 - - - -
529B GLY* 4.1 8.4 + - - -
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Residues in contact with ARG 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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3A VAL* 3.4 28.1 - - + +
4A GLN* 3.0 38.6 + - + +
5A PRO* 4.1 12.5 - - - +
6A LYS* 3.7 20.2 - - - +
464B ILE 5.4 1.6 + - - -
465B ALA* 3.1 27.6 + - - +
467B GLY* 1.3 72.9 - - - +
469B TYR* 1.3 68.1 + - - +
471B ASP* 3.2 16.0 + - - +
472B SER* 3.3 11.8 + - - -
25F C 2.5 41.8 + - - -
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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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3A VAL* 3.5 35.2 - - + -
83A MET* 5.9 2.3 - - + +
447B LEU* 3.6 35.5 + - + +
448B GLY 6.1 0.3 - - - -
449B LEU* 3.7 19.9 - - + +
461B PHE* 3.7 45.3 - + + -
465B ALA* 3.3 32.3 + - + -
468B ARG* 1.3 81.8 + - - +
470B SER* 1.3 61.8 + - - +
472B SER* 3.3 6.6 + - - -
473B LEU* 3.3 17.5 + - - +
24F G 3.6 17.3 + - - -
25F C 3.2 22.6 + - - -
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Residues in contact with SER 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B CYS* 5.5 1.1 - - - -
461B PHE* 5.1 2.3 - - - -
466B PHE* 2.8 57.4 + - - -
467B GLY* 3.6 3.8 + - - -
469B TYR* 1.3 74.6 - - - +
471B ASP* 1.3 58.1 + - - +
473B LEU* 3.0 11.8 + - - +
474B VAL* 2.7 43.9 + - - +
480B VAL* 4.4 11.9 - - - -
517B ILE* 4.7 5.4 - - - +
527B LEU 4.9 0.5 + - - -
528B GLU* 5.2 3.5 - - - +
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Residues in contact with ASP 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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1A MET* 3.4 29.3 - - - +
4A GLN* 4.0 8.7 + - - +
467B GLY 3.1 17.8 + - - +
468B ARG* 3.2 8.0 + - - +
470B SER* 1.3 81.5 + - - +
472B SER* 1.3 58.2 + - - +
474B VAL* 4.6 4.9 - - - -
475B GLN* 3.0 46.6 + - - +
522B GLN* 4.2 7.3 - - - +
524B TYR* 5.3 0.3 - - - -
529B GLY* 4.2 23.9 + - - +
530B ASP 4.3 10.6 + - - +
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Residues in contact with SER 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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1A MET* 3.0 16.4 + - - +
2A ALA 3.0 23.6 + - - -
3A VAL* 3.5 20.8 + - - -
447B LEU* 3.8 10.5 - - - +
468B ARG 3.3 8.9 + - - -
469B TYR 3.3 10.2 + - - -
470B SER 3.0 0.4 - - - -
471B ASP* 1.3 76.1 - - - +
473B LEU* 1.3 60.1 + - - +
475B GLN 3.3 2.1 + - - -
476B LYS* 2.9 43.6 + - - +
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Residues in contact with LEU 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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424B VAL* 4.2 14.8 - - + -
426B CYS* 5.3 5.2 - - - -
435B LEU* 5.0 5.2 - - + -
442B ILE* 3.8 28.7 - - + -
446B GLU* 4.3 5.2 - - + -
447B LEU* 3.7 40.4 - - + -
461B PHE* 5.8 2.0 - - + -
469B TYR* 3.3 6.0 + - + +
470B SER* 3.0 10.6 + - - +
472B SER* 1.3 79.1 - - - +
474B VAL* 1.3 62.1 + - - +
476B LYS* 3.3 10.0 + - - +
477B GLY 3.3 0.2 + - - -
478B TYR* 3.1 39.2 + - + +
480B VAL* 3.7 26.7 - - + -
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Residues in contact with VAL 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 SER* 2.7 30.3 + - - +
471B ASP* 4.3 5.8 - - - +
473B LEU* 1.3 71.2 - - - +
475B GLN* 1.3 58.1 + - - +
477B GLY* 3.1 20.1 + - - -
478B TYR 3.6 8.4 - - - +
480B VAL* 4.5 11.2 - - + -
517B ILE* 3.9 33.7 - - + +
518B THR 4.0 2.9 - - - -
519B LYS* 3.7 31.2 + - - +
522B GLN* 3.7 33.9 - - + +
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Residues in contact with GLN 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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1A MET* 3.6 31.4 - - + +
471B ASP* 3.0 29.2 + - - +
472B SER 3.3 4.5 + - - +
474B VAL* 1.3 71.7 - - - +
476B LYS* 1.3 60.3 + - - +
477B GLY* 3.1 5.7 + - - -
519B LYS* 3.4 31.4 + - - +
522B GLN* 2.7 35.6 + - - +
524B TYR* 4.8 1.0 + - - -
532B SER* 3.6 14.0 + - - -
537B LYS* 3.3 24.0 - - - +
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Residues in contact with LYS 476 (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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1A MET* 3.4 12.6 - - - +
2A ALA* 3.8 12.5 - - - +
446B GLU* 3.1 56.4 + - + +
472B SER* 2.9 41.2 + - - +
473B LEU* 3.6 7.9 - - + +
474B VAL 3.2 0.4 - - - -
475B GLN* 1.3 76.6 - - - +
477B GLY* 1.3 56.8 + - - +
478B TYR* 3.6 15.8 + - + -
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Residues in contact with GLY 477 (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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474B VAL 3.1 10.5 + - - -
475B GLN 3.1 2.3 - - - -
476B LYS* 1.3 80.2 - - - +
478B TYR* 1.3 66.2 + - - +
479B LYS* 3.6 2.3 + - - +
519B LYS* 5.5 3.1 - - - +
617B LEU* 3.7 33.2 - - - +
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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