Contacts of the helix formed by residues 461 - 476 (chain A) in PDB entry 5I73
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 ARG 461 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458A TRP* 4.5 6.1 - - - -
459A ALA* 4.2 8.4 - - - -
460A LYS* 1.4 101.6 + - + +
462A ARG* 1.3 63.6 + - - +
463A GLU* 3.6 5.2 - - + +
464A ARG* 4.0 23.0 + - + +
465A PHE* 4.1 4.0 + - - +
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Residues in contact with ARG 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ILE* 3.6 7.1 + - - +
271A TRP 3.4 13.7 - - - +
272A LYS 4.6 0.7 - - - -
273A GLY* 3.2 37.4 - - - +
274A VAL* 4.1 6.9 - - - +
350A TYR* 4.5 13.7 + - - -
444A GLU* 2.1 39.6 + - - -
447A ILE* 4.0 19.2 - - + +
448A THR* 4.3 6.6 + - - +
451A LEU* 4.5 23.3 - - + +
459A ALA* 5.0 2.2 + - - +
461A ARG* 1.3 69.4 - - - +
463A GLU* 1.4 60.7 + - - +
464A ARG 3.1 2.5 + - - -
465A PHE* 3.2 5.8 + - - +
466A VAL* 2.9 41.0 + - + +
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Residues in contact with GLU 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A TYR* 2.8 32.8 + - - +
271A TRP* 3.7 39.8 + - + +
461A ARG* 3.6 2.9 - - + -
462A ARG* 1.4 77.6 - - - +
464A ARG* 1.3 58.1 + - - +
466A VAL* 4.4 0.2 - - - -
467A LEU* 3.0 17.9 + - - +
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Residues in contact with ARG 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A TRP* 4.8 9.0 - - + -
460A LYS* 5.7 4.5 - - + -
461A ARG* 4.0 21.5 + - + +
462A ARG 3.1 1.0 - - - -
463A GLU* 1.3 80.6 - - - +
465A PHE* 1.3 57.8 + - - +
467A LEU* 3.8 6.5 - - - +
468A ALA* 2.9 29.0 + - - +
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Residues in contact with PHE 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A VAL* 5.0 2.2 - - + -
447A ILE* 3.6 51.8 - - + -
450A VAL* 3.4 39.3 - - + -
451A LEU* 4.5 9.9 - - + -
458A TRP* 3.3 49.6 - + + -
461A ARG 4.1 2.4 + - - +
462A ARG* 3.2 7.4 + - + +
464A ARG* 1.3 75.3 - - - +
466A VAL* 1.3 61.1 + - - +
468A ALA* 3.1 7.4 + - + +
469A VAL* 2.9 52.0 + - + +
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Residues in contact with VAL 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A TYR* 3.6 28.3 - - + -
270A ILE* 4.0 29.2 - - + -
271A TRP* 4.1 6.3 - - - +
443A LEU* 6.3 0.9 - - + -
447A ILE* 3.6 31.6 - - + -
462A ARG* 2.9 39.2 + - + +
465A PHE* 1.3 74.3 - - - +
467A LEU* 1.3 58.6 + - - +
469A VAL* 3.2 4.4 + - - +
470A VAL* 2.9 39.3 + - + +
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Residues in contact with LEU 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A TYR* 3.4 35.9 - - + +
463A GLU 3.0 20.7 + - - +
464A ARG* 3.8 6.1 - - - +
466A VAL* 1.3 77.9 - - - +
468A ALA* 1.3 60.7 + - + +
470A VAL* 3.7 5.8 - - + +
471A ILE* 2.9 62.6 + - + +
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Residues in contact with ALA 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A TRP* 5.5 4.0 - - + -
464A ARG 2.9 19.9 + - - +
465A PHE* 3.1 13.7 + - + +
467A LEU* 1.3 81.3 - - + +
469A VAL* 1.3 56.6 + - + +
471A ILE* 4.5 3.7 - - - +
472A THR* 2.7 31.5 + - - -
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Residues in contact with VAL 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A LEU* 4.0 19.7 - - + -
446A VAL* 6.0 7.6 - - + -
447A ILE* 4.6 10.5 - - + -
465A PHE* 2.9 50.0 + - + +
466A VAL* 3.5 8.5 - - - +
468A ALA* 1.3 77.9 - - + +
470A VAL* 1.3 59.0 + - - +
472A THR* 3.3 5.3 + - - -
473A CYS* 2.9 48.3 + - - -
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Residues in contact with VAL 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A PHE* 3.4 45.9 - - + +
266A ILE* 4.5 16.6 - - + -
267A TYR* 4.8 9.0 - - + -
443A LEU* 4.6 10.8 - - + -
466A VAL* 2.9 33.0 + - + +
467A LEU* 3.2 7.6 + - + +
469A VAL* 1.3 76.8 - - + +
471A ILE* 1.3 61.5 + - + +
473A CYS* 3.2 8.7 + - - +
474A PHE* 2.9 26.7 + - + +
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Residues in contact with ILE 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A LEU* 2.9 45.4 + - + +
468A ALA* 4.5 4.0 - - - +
470A VAL* 1.3 78.0 - - + +
472A THR* 1.3 59.5 + - - +
474A PHE* 3.0 11.6 + - + +
475A PHE* 2.9 53.3 + - + -
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Residues in contact with THR 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A PHE* 3.8 24.8 - - + -
468A ALA 2.7 23.3 + - - -
469A VAL* 3.3 6.0 + - - -
471A ILE* 1.3 79.1 - - - +
473A CYS* 1.3 57.6 + - - +
475A PHE* 3.4 8.3 + - + +
476A GLY* 2.9 24.6 + - - -
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Residues in contact with CYS 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ALA 6.0 0.4 - - - -
170A PHE* 4.9 17.9 - - - -
173A ALA* 3.7 30.4 - - + +
174A SER* 4.9 0.9 - - - -
263A PHE* 4.1 12.3 - - + -
443A LEU* 4.3 10.1 - - + -
469A VAL* 2.9 39.4 + - - +
470A VAL* 3.5 8.5 - - - +
472A THR* 1.3 75.9 - - - +
474A PHE* 1.3 53.9 + - - +
476A GLY* 3.3 3.3 + - - +
477A SER* 2.7 37.0 + - - -
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Residues in contact with PHE 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ALA* 3.9 8.5 - - + -
259A ILE* 3.8 18.4 - - + -
260A MET* 3.5 37.5 - - + -
263A PHE* 3.4 30.0 - + + -
470A VAL* 2.9 13.8 + - + +
471A ILE* 3.0 14.6 + - + +
473A CYS* 1.3 75.1 - - - +
475A PHE* 1.3 87.3 + + - +
477A SER* 3.1 11.3 + - - -
478A LEU* 3.4 36.4 + - + +
481A LEU* 4.4 2.0 - - + -
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Residues in contact with PHE 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A ILE* 2.9 46.5 + - + +
472A THR* 3.9 7.4 - - + +
474A PHE* 1.3 91.1 - + - +
476A GLY* 1.3 59.6 + - - +
477A SER 3.2 0.7 + - - -
478A LEU* 3.6 38.7 + - + +
479A VAL* 4.9 4.0 + - - +
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Residues in contact with GLY 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A PHE* 4.2 22.2 - - - -
174A SER* 3.2 21.4 + - - -
472A THR 2.9 15.8 + - - -
473A CYS* 3.6 4.5 - - - -
474A PHE 3.1 0.4 - - - -
475A PHE* 1.3 77.0 - - - +
477A SER* 1.3 59.8 + - - +
478A LEU 3.4 0.4 - - - -
479A VAL* 4.3 15.0 + - - +
480A THR* 4.6 0.3 + - - -
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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