Contacts of the strand formed by residues 469 - 478 (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 ILE 469 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A HIS* 4.7 0.7 - - + -
356A TYR* 3.7 33.0 - - + +
358A PHE* 3.8 51.6 - - + -
462A TRP* 4.5 2.7 - - + -
463A PHE 3.2 15.0 - - - +
464A PHE* 4.0 24.2 - - + -
468A GLU* 1.3 81.0 - - - +
470A VAL* 1.3 65.2 + - - +
471A CYS* 3.6 11.0 + - - -
581A ILE* 4.5 0.7 - - - -
582A VAL* 3.0 29.3 + - + +
584A PRO* 3.8 14.6 - - + -
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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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462A TRP* 3.4 2.8 - - - -
463A PHE* 2.8 51.2 + - + -
465A PHE* 4.2 12.8 - - + -
468A GLU* 4.7 0.4 - - + -
469A ILE* 1.3 72.1 - - - +
471A CYS* 1.3 61.1 + - - +
472A LEU* 3.8 25.1 - - + -
580A TYR 3.9 3.6 - - - +
581A ILE* 4.1 31.6 - - + +
600A PRO* 4.1 23.6 - - + +
602A VAL* 4.5 7.6 - - + -
612A VAL* 3.9 17.0 - - + -
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Residues in contact with CYS 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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358A PHE* 4.1 15.5 - - - -
461A ALA 3.6 6.7 - - - +
462A TRP* 3.7 24.0 - - + +
469A ILE* 3.9 12.1 - - - -
470A VAL* 1.3 75.6 - - - +
472A LEU* 1.3 61.1 + - - +
578A TYR* 3.6 6.6 - - + +
579A ALA* 3.4 4.0 - - - -
580A TYR* 2.8 79.1 + - + +
582A VAL* 4.2 1.1 - - - -
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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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460A LYS* 3.5 1.9 - - - -
461A ALA 2.9 34.4 + - - +
463A PHE* 3.8 28.7 - - + -
470A VAL* 3.8 17.0 + - + -
471A CYS* 1.3 76.9 - - - +
473A GLY* 1.3 58.7 + - - +
578A TYR* 3.3 9.4 + - - +
579A ALA* 3.4 29.8 - - + -
602A VAL* 3.8 29.4 - - + -
604A ALA 3.9 13.2 - - - +
605A ASN* 3.7 16.6 - - - +
610A GLN* 3.3 10.7 + - + +
611A ALA 4.3 0.2 - - - +
612A VAL* 4.1 10.3 - - + -
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Residues in contact with GLY 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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459A LYS 3.2 8.1 - - - -
460A LYS* 5.0 0.7 - - - -
472A LEU* 1.3 76.6 - - - +
474A ALA* 1.3 59.6 + - - -
476A ILE* 4.5 2.0 - - - -
577A GLN* 3.1 8.8 - - - +
578A TYR* 2.9 55.9 + - - -
605A ASN* 3.1 6.8 + - - -
610A GLN* 3.5 1.6 - - - -
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Residues in contact with ALA 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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458A ALA* 3.8 0.7 - - - -
459A LYS* 2.8 34.2 + - + +
473A GLY* 1.3 75.2 - - - +
475A GLY* 1.3 65.0 + - - +
476A ILE* 3.1 6.1 + - - +
576A ALA 3.6 6.5 - - - -
577A GLN* 4.1 3.6 - - + -
605A ASN* 3.3 24.7 - - - +
606A THR* 3.5 30.5 - - - +
607A ASN* 4.5 0.7 - - - -
610A GLN* 3.7 3.6 - - - +
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Residues in contact with GLY 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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457A GLN* 3.4 9.7 - - - +
458A ALA* 3.7 5.1 + - - -
459A LYS* 5.2 1.4 - - - +
474A ALA* 1.3 77.0 - - - +
476A ILE* 1.3 59.7 + - - +
477A ASN* 3.0 23.3 + - - -
575A ASN* 3.6 24.4 + - - -
576A ALA 3.2 5.0 + - - -
577A GLN* 5.2 0.2 - - - +
607A ASN* 4.1 17.8 - - - +
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Residues in contact with ILE 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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413A THR* 4.4 7.9 - - + -
456A LEU* 4.5 2.0 - - + -
457A GLN 3.3 9.0 - - - +
458A ALA* 3.8 16.4 - - + -
473A GLY 4.5 1.3 - - - -
474A ALA 4.0 6.7 - - - +
475A GLY* 1.3 74.9 - - - +
477A ASN* 1.3 60.7 + - - +
484A ILE* 4.2 18.2 - - + -
486A THR* 4.6 0.9 - - - +
569A HIS* 3.5 34.1 - - + +
573A PRO* 3.7 21.2 - - + -
575A ASN 3.1 5.9 + - - -
576A ALA* 3.0 45.7 + - + +
577A GLN* 3.9 6.7 - - - -
578A TYR* 3.7 21.1 - - + -
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Residues in contact with ASN 477 (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 LEU* 3.4 3.6 - - - +
457A GLN* 3.0 47.9 + - + +
475A GLY* 3.0 28.3 + - - -
476A ILE* 1.3 73.7 - - - +
478A SER* 1.3 64.0 + - - +
573A PRO* 3.4 7.8 - - - +
574A GLU* 3.1 13.5 - - - +
575A ASN* 2.6 28.7 + - - +
607A ASN* 6.0 1.2 - - - +
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Residues in contact with SER 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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415A ARG* 4.7 0.5 - - - +
455A SER 2.9 20.8 + - - -
456A LEU* 3.9 14.9 - - - +
457A GLN* 4.7 2.2 - - - -
477A ASN* 1.3 78.9 - - - +
479A ASN* 1.3 59.7 + - - +
480A ALA* 3.2 20.6 + - - +
484A ILE* 3.9 16.7 - - - +
572A ARG* 3.1 27.4 - - - +
573A PRO* 3.4 14.0 + - - +
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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