Contacts of the strand formed by residues 576 - 584 (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 ALA 576 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475A GLY 3.2 7.8 + - - -
476A ILE* 3.0 43.3 + - + +
569A HIS* 4.3 15.5 - - + +
573A PRO* 3.7 20.2 - - + -
574A GLU 3.1 4.1 - - - +
575A ASN* 1.3 81.4 - - - +
577A GLN* 1.3 60.7 + - - +
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Residues in contact with GLN 577 (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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473A GLY 3.1 16.2 - - - +
474A ALA* 4.1 5.8 - - + -
476A ILE* 3.9 7.4 - - - +
531A GLU* 4.2 22.8 + - - -
567A ILE* 5.4 0.9 - - - +
569A HIS* 3.6 11.1 + - - -
575A ASN* 4.6 7.9 + - - +
576A ALA* 1.3 78.8 - - - +
578A TYR* 1.3 67.3 + - - +
579A ALA* 6.1 0.6 - - - +
605A ASN* 4.0 26.7 + - - +
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Residues in contact with TYR 578 (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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411A GLY 4.8 0.3 + - - -
413A THR* 3.7 7.9 - - - -
460A LYS* 2.9 36.0 + - + +
461A ALA 4.8 1.6 + - - -
462A TRP* 5.2 3.3 + - - -
471A CYS* 3.6 16.2 - - + +
472A LEU* 3.3 11.5 + - - -
473A GLY* 2.9 48.6 + - - -
476A ILE* 3.7 14.6 - - + -
486A THR* 3.5 34.3 - - + -
567A ILE* 3.7 21.3 - - + -
569A HIS* 3.9 4.3 - + + -
577A GLN* 1.3 78.9 - - - +
579A ALA* 1.3 63.3 + - - +
580A TYR* 3.7 23.7 + + - -
605A ASN* 3.1 11.9 + - - -
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Residues in contact with ALA 579 (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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470A VAL* 6.0 0.2 - - + -
471A CYS 3.4 7.4 - - - -
472A LEU* 3.4 20.2 - - + -
529A PHE* 4.1 11.3 - - - +
530A PRO* 3.7 23.8 - - + +
531A GLU* 5.1 16.4 + - + +
532A GLY 4.6 4.9 - - - +
533A ALA* 5.6 0.5 - - - +
567A ILE* 5.0 1.2 - - - +
577A GLN* 6.1 0.7 - - - +
578A TYR* 1.3 78.6 - - - +
580A TYR* 1.3 62.1 + - - +
602A VAL* 4.8 7.9 - - + -
605A ASN* 4.6 3.8 - - - +
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Residues in contact with TYR 580 (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* 5.6 0.8 - + - -
388A THR* 4.8 5.0 + - - +
411A GLY* 4.0 24.4 + - - -
462A TRP* 4.9 1.4 + - - -
469A ILE 4.0 0.2 - - - +
470A VAL* 4.5 0.6 - - - +
471A CYS* 2.8 66.0 + - + +
472A LEU* 4.9 0.6 - - - +
486A THR* 4.3 10.8 - - + -
487A THR 4.1 2.4 + - - -
488A LEU* 3.7 44.4 + - + -
528A TYR 3.4 7.2 - - - +
529A PHE* 3.9 23.3 - - + -
530A PRO* 4.3 0.7 - - - -
567A ILE* 4.4 4.0 - - + -
578A TYR* 3.7 27.2 + + - -
579A ALA* 1.3 74.1 - - - +
581A ILE* 1.3 66.8 + - - +
582A VAL* 3.6 21.5 - - + -
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Residues in contact with ILE 581 (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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468A GLU* 3.5 30.7 - - + -
469A ILE 3.6 5.6 - - - +
470A VAL* 4.1 25.4 - - + -
527A TYR* 3.4 4.2 - - - -
528A TYR* 2.7 66.2 + - + +
530A PRO* 3.9 16.8 - - + -
580A TYR* 1.3 78.0 - - - +
582A VAL* 1.3 63.9 + - - +
583A LEU* 3.3 10.9 - - + +
595A TYR* 3.7 8.3 - - + +
599A ALA* 4.4 0.2 - - + -
600A PRO* 4.1 25.8 - - + +
602A VAL* 5.9 0.9 - - + -
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Residues in contact with VAL 582 (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 28.3 - - + -
390A ILE* 4.3 12.3 - - + -
468A GLU* 3.1 7.4 - - - +
469A ILE* 3.0 37.4 + - + +
471A CYS* 4.2 0.9 - - - -
488A LEU 5.8 0.2 - - - +
525A ILE* 3.8 22.9 - - + -
526A GLY 3.5 2.9 - - - -
527A TYR* 4.5 9.9 - - + -
580A TYR* 3.6 30.7 - - + -
581A ILE* 1.3 73.8 - - - +
583A LEU* 1.3 62.5 - - - +
584A PRO* 3.3 18.1 - - + +
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Residues in contact with LEU 583 (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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467A LYS* 3.6 13.0 - - + +
468A GLU* 4.2 4.0 - - + -
525A ILE* 3.5 2.0 - - - -
526A GLY* 2.7 45.2 + - - +
528A TYR* 3.9 14.8 - - + -
581A ILE* 3.3 30.7 - - + +
582A VAL* 1.3 75.2 - - - +
584A PRO* 1.3 66.1 - - - +
586A ILE* 3.4 22.6 - - + +
591A GLU 5.6 0.4 - - - +
592A ILE* 3.9 20.0 - - + -
595A TYR* 3.6 39.5 - - + -
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Residues in contact with PRO 584 (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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355A ALA* 5.0 1.6 - - - +
356A TYR* 3.3 56.7 - - + -
390A ILE* 4.9 5.8 - - + -
392A LEU* 4.2 11.2 - - + -
467A LYS* 3.6 14.9 - - - +
469A ILE* 3.8 16.2 - - + -
524A ALA 3.9 2.9 - - - +
525A ILE* 4.4 4.7 - - + -
582A VAL* 3.3 22.7 - - + +
583A LEU* 1.3 84.8 - - - +
585A GLY* 1.3 61.9 + - - +
586A ILE* 5.1 1.4 - - - +
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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
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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