Contacts of the helix formed by residues 464 - 478 (chain A) in PDB entry 4ASQ
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 ASN 464 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A VAL* 3.9 11.0 - - + -
461A ASP* 2.8 29.4 + - - +
463A ALA* 1.3 94.0 + - - +
465A TRP* 1.3 62.3 + - - +
467A CYS* 4.5 0.8 - - + +
468A ALA* 3.0 24.7 + - + +
487A GLU* 3.2 13.6 + - - +
614A SER* 5.5 11.1 + - - +
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Residues in contact with TRP 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ARG* 4.8 4.0 - - - +
181A PHE* 4.1 6.5 - + - -
182A GLU* 3.7 37.0 - - + -
185A VAL* 3.8 39.9 - - + -
451A TYR* 2.8 31.3 + - - +
455A LEU* 3.5 34.9 - - + +
460A VAL* 3.0 27.1 + - + -
461A ASP 3.1 18.8 - - - -
462A LYS* 3.5 37.8 + - + +
464A ASN* 1.3 78.3 - - - +
466A ASN* 1.3 62.2 + - - +
468A ALA* 3.6 0.2 - - - +
469A PHE 3.4 2.9 + - - -
487A GLU* 3.4 3.2 + - - +
490A PHE* 3.8 28.5 - + + -
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Residues in contact with ASN 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ARG* 4.3 2.5 - - - +
451A TYR* 4.6 0.7 - - - -
465A TRP* 1.3 71.6 - - - +
467A CYS* 1.3 60.6 + - - +
469A PHE* 3.1 26.6 + - - +
470A TRP* 3.3 15.7 + - - +
485A ARG* 4.2 2.4 - - - +
486A SER 2.9 22.0 - - - +
487A GLU* 2.9 18.9 + - - +
489A ASP* 3.2 25.1 - - - +
490A PHE* 3.5 7.7 - - + +
491A ASP* 2.9 50.0 + - - +
492A ALA 4.5 2.2 - - - +
612A CYS* 4.2 1.1 - - - -
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Residues in contact with CYS 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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464A ASN* 4.5 1.1 - - + +
466A ASN* 1.3 71.0 - - - +
468A ALA* 1.3 60.0 + - - +
470A TRP* 4.2 0.6 - - - +
471A LYS* 2.8 48.7 + - + +
486A SER* 4.6 0.7 - - - -
487A GLU* 2.9 25.8 + - - +
612A CYS* 2.0 62.8 - - + +
613A VAL 3.6 17.3 - - - -
614A SER* 4.2 11.9 - - - +
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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
----------------------------------------------------------
451A TYR* 4.0 9.9 - - + -
454A SER* 5.6 0.2 - - - +
460A VAL* 3.8 27.6 - - + -
464A ASN* 3.0 20.6 + - + +
465A TRP 3.6 7.2 - - - +
466A ASN 3.2 0.2 - - - -
467A CYS* 1.3 78.0 - - - +
469A PHE* 1.3 60.8 + - - +
471A LYS* 3.8 11.3 - - - +
472A LEU* 3.4 27.1 + - + +
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Residues in contact with PHE 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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170A TYR* 5.4 2.5 - + - -
444A PHE* 6.1 0.2 - + - -
447A THR 5.4 0.2 - - - -
448A MET* 3.7 32.5 - - + -
451A TYR* 3.5 45.3 - + + +
465A TRP 3.4 2.4 + - - +
466A ASN* 3.1 14.6 + - - +
468A ALA* 1.3 78.5 - - - +
470A TRP* 1.3 103.7 + + - +
472A LEU* 3.2 7.7 + - + +
473A ARG* 3.1 36.8 + - + +
491A ASP* 4.6 3.1 - - + -
492A ALA* 3.8 33.9 - - + -
495A LYS* 5.9 2.2 - - + -
498A ILE* 4.3 8.3 - - + -
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Residues in contact with TRP 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A TRP* 3.7 20.6 - + - -
170A TYR* 3.9 10.5 - + - -
256A MET* 3.6 37.7 - - + -
466A ASN* 3.3 27.3 + - - +
467A CYS 4.2 1.3 - - - +
469A PHE* 1.3 90.9 - + - +
471A LYS* 1.3 61.0 + - - +
473A ARG* 3.7 20.9 - - + +
474A ASP* 2.9 30.5 + - - +
479A ILE* 4.2 6.1 - - + +
480A GLU* 5.1 0.4 - - - -
481A PRO* 3.5 30.7 - - + +
485A ARG* 4.1 3.5 - - + +
491A ASP* 2.8 42.7 + - + +
609A SER* 5.8 0.2 - - - -
611A LYS 6.0 0.2 - - - -
612A CYS* 4.0 26.9 - - + -
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Residues in contact with LYS 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A CYS* 2.8 37.0 + - + +
468A ALA* 3.8 10.5 - - - +
469A PHE 3.3 0.2 - - - -
470A TRP* 1.3 77.4 - - - +
472A LEU* 1.3 58.0 + - + +
474A ASP* 3.4 6.5 + - - +
475A GLU* 2.8 31.2 + - - +
608A THR* 6.1 4.9 - - + +
612A CYS* 6.4 0.9 - - + -
614A SER* 4.7 10.5 + - - -
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Residues in contact with LEU 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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447A THR* 3.6 16.0 - - + +
450A LYS* 4.0 15.0 - - + +
451A TYR* 3.6 44.4 - - + +
454A SER* 5.2 2.9 - - - +
468A ALA* 3.4 14.5 + - + +
469A PHE* 3.2 8.3 + - + +
471A LYS* 1.3 77.0 - - + +
473A ARG* 1.3 65.7 + - + +
475A GLU* 4.2 9.6 - - - +
476A TYR* 3.0 56.1 + - + +
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Residues in contact with ARG 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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256A MET* 5.7 0.6 - - - +
263A TRP 3.8 10.7 + - - -
264A ALA 4.4 4.9 + - - -
444A PHE* 3.3 35.1 - - - +
447A THR* 3.0 31.0 + - - +
448A MET* 3.8 15.3 - - - +
469A PHE* 3.1 29.3 + - + +
470A TRP* 3.7 26.8 - - + +
472A LEU* 1.3 75.0 - - - +
474A ASP* 1.3 57.0 + - - +
477A SER* 2.9 61.3 + - - -
478A GLY 3.2 6.2 + - - -
479A ILE* 3.7 37.0 + - + +
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Residues in contact with ASP 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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253A PRO* 4.3 2.6 - - - +
470A TRP 2.9 17.6 + - - +
471A LYS* 3.4 8.1 - - - +
473A ARG* 1.3 74.1 - - - +
475A GLU* 1.3 68.3 + - - +
478A GLY 2.9 12.5 + - - +
479A ILE 3.7 13.6 + - - +
606A TRP* 2.9 41.8 + - - -
607A THR 4.2 0.3 - - - +
608A THR* 3.5 15.0 - - - +
609A SER* 2.8 41.3 + - - -
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Residues in contact with GLU 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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225A ARG* 2.9 24.6 + - - +
471A LYS 2.8 21.0 + - - +
472A LEU* 3.9 12.6 - - - +
474A ASP* 1.3 76.6 + - - +
476A TYR* 1.3 88.1 + - + +
606A TRP* 3.6 12.4 + - - +
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Residues in contact with TYR 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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218A GLU* 4.7 5.5 + - - -
221A PHE* 3.5 36.1 - + - -
225A ARG* 3.7 18.9 + - - +
228A TYR* 3.6 12.8 - - - -
229A GLN* 4.7 1.6 + - - -
443A PRO* 3.5 21.0 - - + +
446A PHE* 4.8 3.6 - + + -
447A THR* 3.5 28.0 - - + -
450A LYS* 3.2 38.3 + - + -
472A LEU* 3.0 33.0 + - + -
475A GLU* 1.3 108.6 + - + +
477A SER* 1.3 61.5 + - - +
478A GLY 3.7 0.2 - - - -
606A TRP* 4.2 5.0 - - - -
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Residues in contact with SER 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A TYR* 2.5 33.4 + - - -
232A HIS* 3.3 8.8 - - - -
264A ALA 6.0 0.4 - - - -
440A VAL 4.9 0.9 + - - -
443A PRO* 3.6 5.9 - - - +
444A PHE* 3.5 17.5 + - - +
473A ARG* 2.9 49.3 + - - -
476A TYR* 1.3 77.4 - - - +
478A GLY* 1.3 64.7 + - - +
479A ILE* 3.4 10.1 + - - +
606A TRP* 4.0 0.9 - - - -
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Residues in contact with GLY 478 (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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232A HIS* 2.8 20.9 + - - -
253A PRO* 3.4 7.0 - - - +
254A ILE 2.9 14.4 + - - -
473A ARG 3.2 0.6 + - - -
474A ASP 2.9 12.8 + - - -
477A SER* 1.3 78.3 - - - +
479A ILE* 1.3 59.5 + - - +
606A TRP* 3.2 36.1 - - - -
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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