Contacts of the helix formed by residues 453 - 469 (chain A) in PDB entry 1HXK
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 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A ASP 4.1 0.4 + - - -
450A GLY 3.1 15.2 + - - +
451A MET* 3.1 13.1 - - - +
452A ALA* 1.3 80.8 - - - +
454A ILE* 1.3 64.2 + - - +
455A GLU* 3.5 2.9 - - - -
456A GLU* 2.8 48.6 + - - +
457A ARG* 3.1 65.3 + - - +
500A VAL* 5.2 0.2 - - - +
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Residues in contact with ILE 454 (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 SER* 3.9 17.0 - - - +
448A TRP* 3.5 49.1 - - + -
449A ASP 5.2 0.2 + - - -
452A ALA* 3.7 18.1 - - + +
453A ARG* 1.3 73.9 - - - +
455A GLU* 1.3 78.5 + - + +
457A ARG* 3.2 3.3 + - - +
458A LEU* 2.9 43.9 + - + +
499A MET* 6.2 1.3 - - + -
500A VAL* 4.1 29.8 - - + +
503A GLN* 4.8 10.3 - - + -
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Residues in contact with GLU 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A TRP* 4.4 20.9 + - - +
449A ASP 5.1 2.6 - - - +
450A GLY* 5.2 6.1 - - - -
453A ARG* 4.8 0.7 - - - -
454A ILE* 1.3 88.9 + - + +
456A GLU* 1.3 57.1 + - - +
458A LEU* 3.9 5.9 - - - +
459A GLU* 2.9 32.7 + - - +
462A ARG* 4.9 1.6 + - - -
964A ARG* 6.0 1.0 - - - -
966A THR 4.4 5.1 - - - +
967A LYS* 3.9 49.5 - - + +
968A SER 4.6 0.2 + - - -
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Residues in contact with GLU 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ARG* 2.8 62.8 + - - +
455A GLU* 1.3 80.9 - - - +
457A ARG* 1.3 66.4 + - - +
459A GLU* 3.4 6.2 + - - +
460A GLN* 3.1 24.4 + - - +
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Residues in contact with ARG 457 (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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452A ALA 4.4 5.9 + - - -
453A ARG* 3.1 71.3 + - - +
456A GLU* 1.3 85.4 + - - +
458A LEU* 1.3 60.1 + - - +
460A GLN* 3.4 14.3 + - - +
461A ALA* 3.0 23.6 + - - +
496A ALA* 3.6 32.8 - - + +
499A MET* 3.5 31.7 - - + +
500A VAL* 3.7 21.5 - - + -
519A PHE 5.0 4.9 + - - -
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Residues in contact with LEU 458 (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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436A VAL* 6.0 0.7 - - + -
439A ALA* 3.7 33.7 - - + -
440A GLU* 4.1 19.5 - - + +
443A SER* 3.4 22.9 - - - +
454A ILE* 2.9 29.2 + - + +
455A GLU* 3.9 6.1 - - + +
457A ARG* 1.3 74.9 - - - +
459A GLU* 1.3 61.3 + - - +
461A ALA* 3.3 8.6 + - + +
462A ARG* 2.9 50.8 + - - +
497A CYS* 5.4 1.8 - - - -
500A VAL* 4.0 14.6 - - + -
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Residues in contact with GLU 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A GLU* 4.1 5.6 - - - +
455A GLU 2.9 18.5 + - - +
456A GLU* 3.7 6.9 - - - +
458A LEU* 1.3 75.9 - - - +
460A GLN* 1.3 64.4 + - - +
462A ARG* 3.4 21.4 + - - +
463A ARG* 2.9 75.3 + - - +
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Residues in contact with GLN 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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456A GLU* 3.1 10.9 + - + +
457A ARG* 3.5 17.9 + - - +
458A LEU 3.2 0.2 - - - -
459A GLU* 1.3 79.9 - - - +
461A ALA* 1.3 64.3 + - - +
463A ARG* 3.2 6.1 + - - +
464A GLU* 3.0 42.9 + - + +
492A GLU* 3.7 30.5 + - - +
493A ALA* 5.3 0.9 - - - -
496A ALA* 3.8 22.2 - - - +
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Residues in contact with ALA 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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436A VAL* 4.1 9.3 - - + +
457A ARG 3.0 17.4 + - - +
458A LEU* 3.7 9.4 - - + +
460A GLN* 1.3 76.9 - - - +
462A ARG* 1.3 62.2 + - + +
464A GLU* 3.4 0.3 + - - -
465A LEU* 3.1 25.6 + - - +
493A ALA* 3.8 25.1 - - + +
496A ALA* 4.5 1.8 - - + +
497A CYS* 3.7 30.3 - - - -
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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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180A LEU* 3.8 35.2 - - + +
184A GLU* 3.0 26.9 + - - +
436A VAL* 4.2 7.6 - - + -
440A GLU* 2.8 42.4 + - + +
455A GLU 4.9 2.0 + - - -
458A LEU* 2.9 38.9 + - - +
459A GLU* 3.6 28.0 + - - +
461A ALA* 1.3 77.4 - - - +
463A ARG* 1.3 55.1 + - - +
465A LEU* 4.0 1.3 - - - +
466A SER* 2.7 37.6 + - - -
963A ARG* 4.1 15.8 - - - +
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Residues in contact with ARG 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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135A ALA* 5.5 1.8 - - - +
139A HIS* 5.5 6.9 + - - -
165A TRP* 3.4 45.4 + - + +
184A GLU* 2.8 29.4 + - + +
188A TRP* 3.9 28.1 - - - +
459A GLU* 2.9 54.3 + - - +
460A GLN* 3.2 4.9 + - - +
462A ARG* 1.3 75.0 - - - +
464A GLU* 1.3 65.6 + - + +
466A SER* 4.2 4.9 - - - -
467A LEU* 2.9 29.3 + - - +
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Residues in contact with GLU 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A GLN* 3.0 33.7 + - + +
463A ARG* 1.3 76.7 - - - +
465A LEU* 1.3 65.5 + - - +
467A LEU* 3.4 7.1 + - - +
468A PHE* 3.2 20.6 + - - +
486A TYR* 6.1 0.2 - - - -
489A ARG* 2.9 75.7 + - + +
490A MET* 4.5 6.3 - - - +
492A GLU* 4.0 10.7 - - - +
493A ALA* 3.9 12.3 - - + -
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Residues in contact with LEU 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ASN* 3.4 24.2 - - + +
180A LEU* 3.6 17.7 - - + -
429A ASP* 3.6 24.7 - - - +
432A LEU* 3.7 26.2 - - + +
433A MET* 3.7 18.2 - - - +
436A VAL* 3.9 14.4 - - + -
461A ALA 3.1 16.9 + - - +
462A ARG 4.0 2.9 - - - +
464A GLU* 1.3 74.4 - - - +
466A SER* 1.3 65.0 + - - +
468A PHE* 3.2 11.6 + - + +
469A GLN* 3.0 36.1 - - - +
490A MET* 4.8 3.8 - - - -
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Residues in contact with SER 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TRP* 3.7 17.0 - - - -
166A VAL* 3.6 10.9 - - - +
180A LEU* 3.8 10.7 + - - +
181A GLN* 3.3 37.4 + - - +
184A GLU* 4.0 4.4 - - - +
462A ARG 2.7 25.7 + - - -
463A ARG* 3.7 5.6 - - - -
464A GLU 3.3 0.2 - - - -
465A LEU* 1.3 77.9 - - - +
467A LEU* 1.3 62.6 + - - +
469A GLN* 3.1 21.5 + - - +
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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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93A PRO* 3.6 31.4 - - + +
99A PHE* 3.9 19.1 - - + -
132A SER* 4.4 10.1 - - - +
165A TRP* 3.7 4.7 - - + +
166A VAL* 3.8 9.9 - - + +
463A ARG 2.9 17.4 + - - +
464A GLU* 3.6 7.9 - - - +
466A SER* 1.3 76.6 - - - +
468A PHE* 1.3 63.0 + - - +
470A HIS* 3.1 24.9 + - - +
485A ASP* 5.4 0.2 - - - +
486A TYR* 4.0 20.6 - - + -
489A ARG* 3.6 45.3 - - - +
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Residues in contact with PHE 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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425A HIS* 3.4 47.1 - + + -
429A ASP* 3.8 15.9 - - + +
464A GLU 3.2 10.1 + - - +
465A LEU* 3.2 11.4 + - - +
467A LEU* 1.3 75.4 - - - +
469A GLN* 1.3 57.0 + - - +
470A HIS 3.0 7.4 + - - +
473A GLY* 3.3 21.7 - - - -
474A ILE* 2.9 59.0 + - + +
483A VAL* 6.3 0.9 - - + -
486A TYR* 3.7 39.7 - + + -
490A MET* 3.5 28.9 - - + -
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Residues in contact with GLN 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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166A VAL* 4.0 3.4 - - + -
168A PRO* 3.1 18.2 - - + +
169A ASP* 2.8 25.3 + - - +
173A SER* 3.6 27.5 - - - +
174A HIS 4.5 0.2 - - - +
177A ASN* 3.5 40.4 - - + +
181A GLN* 4.3 3.1 - - + -
429A ASP* 2.7 27.5 + - - +
465A LEU* 3.0 28.0 - - - +
466A SER* 3.1 16.0 + - - +
468A PHE* 1.3 73.5 - - - +
470A HIS* 1.3 67.5 + - - +
474A ILE* 4.2 6.4 - - - +
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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
------------------------------------------------------------
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