Contacts of the strand formed by residues 456 - 464 (chain A) in PDB entry 1HMU
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 LEU 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413A THR* 3.8 12.8 - - + +
414A SER* 3.5 38.4 - - - +
415A ARG* 4.0 6.7 - - + +
451A LEU* 3.8 17.5 - - + +
452A ASP* 3.2 4.5 + - - -
453A TYR 3.0 33.9 + - - +
454A ASP* 4.0 4.5 - - + +
455A SER* 1.3 78.7 - - - +
457A GLN* 1.3 69.6 + - - +
476A ILE* 4.5 4.9 - - + -
477A ASN 3.4 17.7 - - - +
478A SER* 3.9 11.4 - - - +
484A ILE* 3.8 23.8 - - + -
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Residues in contact with GLN 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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451A LEU* 3.2 9.2 - - - +
452A ASP* 3.3 30.3 + - + +
455A SER* 3.5 9.4 + - - +
456A LEU* 1.3 104.4 - - - +
458A ALA* 1.3 65.7 + - - +
475A GLY 3.8 6.5 - - - +
476A ILE* 3.3 1.0 - - - -
477A ASN* 3.0 50.7 + - + +
478A SER* 4.5 1.6 + - - -
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Residues in contact with ALA 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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413A THR* 4.6 9.2 - - + -
449A TYR 3.6 1.0 - - - +
450A ALA* 3.5 2.8 - - - -
451A LEU* 2.8 47.0 + - + +
457A GLN* 1.3 79.1 - - - +
459A LYS* 1.3 65.5 + - - +
460A LYS* 3.9 14.1 - - + -
474A ALA 3.8 0.2 - - - -
475A GLY 3.7 9.8 + - - -
476A ILE* 3.8 21.1 - - + -
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Residues in contact with LYS 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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435A PHE* 6.1 0.2 - - - -
449A TYR 3.7 2.0 - - - -
450A ALA* 3.8 24.7 - - + -
458A ALA* 1.3 74.4 - - - +
460A LYS* 1.3 60.4 + - - +
473A GLY* 3.2 5.4 - - - -
474A ALA 2.8 40.2 + - - +
475A GLY* 5.2 1.1 - - - +
607A ASN* 2.8 50.6 + - + +
610A GLN* 3.2 7.9 + - - +
625A TYR* 3.5 44.6 - - + +
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Residues in contact with LYS 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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385A ASP 3.7 21.1 - - - +
411A GLY 2.9 28.3 + - - -
412A ILE 3.8 0.2 - - - -
413A THR* 2.9 38.5 + - - +
448A ALA* 3.3 2.3 - - - -
449A TYR* 2.7 51.6 + - + +
451A LEU* 4.8 7.0 - - + -
458A ALA* 4.4 12.6 - - + -
459A LYS* 1.3 77.7 - - - +
461A ALA* 1.3 60.4 + - - +
462A TRP* 3.5 25.3 - - + -
472A LEU 3.5 4.0 - - - -
486A THR* 4.2 1.4 - - - +
578A TYR* 2.9 31.0 + - + +
610A GLN* 4.1 0.7 - - - -
625A TYR* 3.8 1.1 + - - -
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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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447A SER 3.3 11.4 - - - +
448A ALA* 4.2 7.6 - - + -
460A LYS* 1.3 75.6 - - - +
462A TRP* 1.3 71.7 + - - +
463A PHE* 3.5 28.3 - - + -
471A CYS* 3.6 2.8 - - - +
472A LEU 2.9 29.6 + - - +
578A TYR* 5.0 0.9 + - - -
610A GLN* 3.3 19.5 - - - +
623A ILE* 4.3 2.9 - - + -
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Residues in contact with TRP 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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358A PHE* 4.0 7.6 - + - -
360A VAL* 3.8 16.4 - - + -
362A MET* 4.0 11.9 - - + -
386A GLY* 3.6 37.5 - - - -
388A THR* 3.3 23.5 - - + +
411A GLY 4.7 1.6 + - - -
446A ALA* 3.1 6.1 - - - +
447A SER* 2.9 47.9 + - - -
449A TYR* 3.9 18.4 - - + -
460A LYS* 3.5 43.1 - - + -
461A ALA* 1.3 78.8 + - - +
463A PHE* 1.3 63.2 + - - +
464A PHE* 3.3 23.7 - - + -
469A ILE* 4.5 2.9 - - + -
470A VAL 3.4 3.8 - - - -
471A CYS* 3.7 27.2 - - + +
578A TYR* 5.4 2.7 + - - -
580A TYR* 4.9 2.4 + - - -
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Residues in contact with PHE 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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446A ALA* 3.8 4.7 - - + -
461A ALA* 3.5 32.8 - - + -
462A TRP* 1.3 71.0 - - - +
464A PHE* 1.3 62.0 + - - +
465A PHE* 3.6 18.2 - - + -
469A ILE* 3.2 5.1 - - - -
470A VAL* 2.8 51.6 + - + +
472A LEU* 3.8 20.4 - - + -
610A GLN* 3.4 34.5 - - + -
611A ALA* 4.0 3.6 - - - -
612A VAL* 3.6 14.4 - - + -
621A GLN* 3.1 49.4 - - + +
623A ILE* 4.0 11.2 - - + -
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Residues in contact with PHE 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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340A HIS* 3.6 15.7 - + + -
349A VAL* 3.9 11.9 - - + -
351A HIS* 3.4 42.3 - + + +
358A PHE* 3.5 34.5 - + - -
360A VAL* 3.9 14.1 - - + -
444A TYR* 3.7 9.2 - - - -
445A GLY 3.0 25.8 + - - +
447A SER* 4.1 13.5 - - - -
462A TRP* 3.3 37.2 - - + -
463A PHE* 1.3 72.0 - - - +
465A PHE* 1.3 62.7 + - - +
468A GLU 4.3 1.6 - - - -
469A ILE* 4.0 12.1 - - + +
621A GLN* 3.0 21.1 + - - -
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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