Contacts of the helix formed by residues 458 - 472 (chain A) in PDB entry 5AM8
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 458 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453A ARG 3.8 11.5 + - - -
454A THR* 3.8 2.5 - - - -
455A PRO* 2.8 42.6 + - + +
457A SER* 1.3 93.8 + - - +
459A TYR* 1.3 63.4 + - - +
460A ASN 3.3 2.7 - - - -
461A PHE* 3.8 28.7 - - + -
462A ASP* 2.9 39.6 + - - +
481A GLU* 3.5 6.3 - - - -
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Residues in contact with TYR 459 (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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172A LYS* 3.8 20.9 - - + -
175A TYR* 3.7 26.5 + + - -
176A GLU* 3.4 39.3 - - + +
179A THR* 4.1 2.1 + - - +
445A TRP* 2.9 29.9 + + + +
449A VAL* 3.6 40.1 - - + +
454A THR* 3.8 8.1 - - + -
455A PRO 3.3 15.3 + - - -
456A PRO* 3.2 33.2 + - + +
458A ARG* 1.3 74.6 - - - +
460A ASN* 1.3 57.1 + - - +
463A TRP* 3.1 13.2 + - - +
481A GLU* 3.5 2.0 + - - +
483A HIS 5.6 0.7 - - - +
484A PHE* 3.5 29.6 - + + -
486A ALA* 5.4 0.3 - - - +
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Residues in contact with ASN 460 (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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459A TYR* 1.3 71.2 - - - +
461A PHE* 1.3 67.2 + - - +
462A ASP 3.2 1.3 - - - -
463A TRP* 4.1 4.1 - - - +
464A TRP* 2.9 38.8 + - - +
479A ARG* 3.5 22.0 - - - +
480A ASN* 3.5 12.9 + - - +
481A GLU* 2.9 21.7 + - - +
483A HIS* 3.4 19.0 - - - +
484A PHE* 3.8 1.0 - - - -
485A ASP* 2.9 52.1 + - - +
486A ALA 4.4 0.5 + - - -
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Residues in contact with PHE 461 (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 ARG* 3.8 28.3 - - + +
460A ASN* 1.3 71.9 - - - +
462A ASP* 1.3 77.2 + - - +
464A TRP* 4.0 2.5 - - - +
465A TYR* 3.0 33.8 + + + +
481A GLU* 2.8 22.2 + - - +
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Residues in contact with ASP 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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445A TRP* 3.9 7.2 - - + -
453A ARG* 3.6 14.0 + - - +
454A THR* 2.6 39.2 + - + +
458A ARG* 2.9 27.2 + - - +
461A PHE* 1.3 94.3 - - - +
463A TRP* 1.3 64.5 + - - +
465A TYR* 3.6 9.6 - - + +
466A LEU* 3.2 31.0 + - + +
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Residues in contact with TRP 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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164A HIS* 5.9 1.0 + - - -
257A TRP* 5.8 3.4 - + - -
438A PHE* 4.2 21.3 - + - -
441A LEU* 4.0 19.7 - - + -
442A VAL* 4.4 16.6 - - + -
445A TRP* 3.5 31.8 - + + +
459A TYR 3.1 21.6 + - - +
460A ASN* 3.3 6.3 + - - +
462A ASP* 1.3 76.2 - - - +
464A TRP* 1.3 84.5 + + - +
466A LEU* 3.1 6.3 + - - +
467A ARG* 2.9 64.0 + - + +
485A ASP* 3.7 25.8 - - + +
486A ALA* 3.6 37.7 - - + -
489A LYS* 5.0 8.5 - - + -
492A VAL* 5.4 1.8 - - + -
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Residues in contact with TRP 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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160A TRP* 3.7 30.5 - + - -
164A HIS* 5.6 0.2 - - - -
250A ALA* 4.1 3.6 - - + -
460A ASN* 2.9 39.3 + - - +
461A PHE* 4.3 2.9 - - - +
463A TRP* 1.3 91.0 - + - +
465A TYR* 1.3 65.3 + - - +
467A ARG* 3.6 46.0 - - + -
468A THR* 2.9 32.6 + - - +
473A ILE* 4.3 11.0 - - + -
474A CYS* 4.1 6.3 - - - -
475A PRO* 3.6 44.2 - - + -
479A ARG* 4.1 8.2 - - + +
485A ASP* 2.9 24.1 + - + -
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Residues in contact with TYR 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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461A PHE* 3.0 26.2 + + + +
462A ASP* 3.6 13.0 - - + +
464A TRP* 1.3 77.9 - - - +
466A LEU* 1.3 74.3 + - + +
468A THR* 3.8 3.5 - - - -
469A LYS* 2.8 70.3 + - + +
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Residues in contact with LEU 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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441A LEU* 3.9 18.8 - - + +
444A GLN* 4.0 16.6 - - + +
445A TRP* 3.6 41.7 - - + +
453A ARG* 5.7 4.9 - - - +
462A ASP* 3.2 15.4 + - + +
463A TRP* 3.1 7.2 + - - +
465A TYR* 1.3 94.4 - - + +
467A ARG* 1.3 61.0 + - - +
469A LYS* 4.2 3.1 - - + +
470A TYR* 2.9 61.0 + - + +
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Residues in contact with ARG 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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160A TRP* 4.7 6.5 - - - +
164A HIS* 4.7 7.9 + - - -
250A ALA* 4.4 6.1 - - - +
257A TRP* 2.8 39.5 + - - +
438A PHE* 3.4 11.1 - - - -
441A LEU* 4.0 15.0 - - + -
463A TRP* 2.9 62.5 + - + +
464A TRP* 3.6 39.3 - - + -
466A LEU* 1.3 77.4 - - - +
468A THR* 1.3 56.7 + - - +
471A GLN* 2.9 54.5 + - - +
472A GLY 3.2 1.7 + - - -
473A ILE* 3.4 19.9 - - + +
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Residues in contact with THR 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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247A PRO* 4.1 20.9 - - + -
464A TRP* 2.9 22.9 + - - +
465A TYR* 3.9 3.6 - - - -
467A ARG* 1.3 74.8 - - - +
469A LYS* 1.3 59.5 + - - +
472A GLY* 3.0 10.2 + - - +
473A ILE 3.0 21.6 + - - +
474A CYS* 4.7 3.5 - - - +
475A PRO* 5.4 0.7 - - - +
594A TRP* 2.8 34.7 + - + -
597A TYR* 4.3 18.2 - - + +
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Residues in contact with LYS 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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219A GLU* 5.0 6.8 - - - +
444A GLN* 5.1 2.0 + - - -
465A TYR* 2.8 58.3 + - + +
466A LEU* 3.7 7.5 - - + +
468A THR* 1.3 75.2 - - - +
470A TYR* 1.3 98.7 + - + +
594A TRP* 3.4 15.9 + - - +
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Residues in contact with TYR 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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212A GLU* 4.2 8.5 + - - -
215A TYR* 3.8 32.1 + + - -
219A GLU* 5.5 2.6 - - - +
222A TYR* 3.4 16.8 - - - -
437A PRO* 3.5 25.5 - - + +
440A TYR* 3.7 22.5 + + - -
441A LEU* 4.0 16.2 - - + -
444A GLN* 3.1 32.2 + - - -
466A LEU* 2.9 44.2 + - + +
469A LYS* 1.3 106.4 + - + +
471A GLN* 1.3 63.4 + - - +
472A GLY 3.5 0.4 + - - -
594A TRP* 3.8 6.2 - - - -
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Residues in contact with GLN 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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222A TYR* 2.5 29.9 + - - +
226A HIS* 3.3 7.8 - - - -
257A TRP 3.7 9.3 + - - -
258A ALA* 3.0 27.7 + - - +
259A GLN* 4.3 0.4 - - - +
261A TRP* 5.1 0.6 - - - +
434A ALA 4.8 3.6 + - - -
437A PRO* 4.0 16.8 - - + -
438A PHE* 3.3 23.9 - - - +
441A LEU* 3.6 11.7 - - + +
467A ARG* 2.9 48.5 + - - +
470A TYR* 1.3 79.0 - - - +
472A GLY* 1.3 63.1 + - - +
473A ILE* 3.4 19.4 - - + +
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Residues in contact with GLY 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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226A HIS* 3.0 12.5 + - - -
247A PRO* 3.2 6.7 - - - +
248A ILE 2.8 20.6 + - - -
467A ARG 3.2 0.8 + - - -
468A THR* 3.0 12.7 + - - -
471A GLN* 1.3 78.3 - - - +
473A ILE* 1.3 60.5 + - - +
594A TRP* 3.2 37.6 - - - -
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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