Contacts of the helix formed by residues 570 - 585 (chain A) in PDB entry 3OPY
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 ASP 570 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A GLY 5.7 1.0 + - - -
367A THR 3.4 22.3 + - - +
368A ASP* 3.6 20.4 - - - +
534A LEU* 6.3 0.7 - - + -
568A LEU 4.2 1.0 + - - -
569A ARG* 1.3 77.7 - - - +
571A GLN* 1.4 65.5 + - - +
572A GLU* 3.1 34.3 - - + +
573A PHE* 3.0 21.0 + - - +
574A ALA* 3.1 9.1 + - - +
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Residues in contact with GLN 571 (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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569A ARG 5.5 1.4 + - - -
570A ASP* 1.4 72.7 - - - +
572A GLU* 1.4 54.6 + - - +
574A ALA* 4.0 14.4 - - - +
575A THR* 2.7 62.5 + - + +
943A SER* 5.8 3.8 - - - +
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Residues in contact with GLU 572 (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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362A ASN* 4.3 0.5 + - - -
368A ASP* 3.3 35.3 - - + +
374A TYR* 3.6 16.8 + - - +
409A TRP* 2.7 42.0 + - - -
413A MET* 4.2 5.3 - - + +
570A ASP* 3.2 21.8 - - - +
571A GLN* 1.4 77.8 - - - +
573A PHE* 1.4 59.5 + - - +
575A THR* 3.2 10.7 + - - -
576A SER* 2.9 25.8 + - - +
943A SER* 5.5 7.6 + - - +
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Residues in contact with PHE 573 (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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407A CYS* 3.9 6.1 - - - -
408A GLY 3.8 7.9 - - - -
409A TRP* 3.4 46.0 - + + -
412A LEU* 3.6 16.2 - - + +
425A ILE* 4.1 10.3 - - + -
427A GLU* 3.3 44.6 - - + -
566A LEU* 4.6 12.8 - - + -
569A ARG* 3.7 31.2 - - + -
570A ASP* 3.0 17.5 + - - +
572A GLU* 1.4 82.2 + - - +
574A ALA* 1.3 59.2 + - - +
576A SER* 3.5 3.8 + - - -
577A TYR* 3.0 28.3 + - + +
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Residues in contact with ALA 574 (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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566A LEU* 5.4 14.1 - - + +
569A ARG* 4.9 4.5 - - + +
570A ASP 3.1 11.2 + - - +
571A GLN* 3.1 29.1 + - - +
573A PHE* 1.3 79.6 - - - +
575A THR* 1.4 56.9 + - - +
577A TYR* 3.4 6.5 + - - +
578A GLU* 3.0 29.2 + - - +
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Residues in contact with THR 575 (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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571A GLN* 2.7 45.8 + - + +
572A GLU* 3.2 8.7 + - - -
574A ALA* 1.4 70.5 - - - +
576A SER* 1.4 58.4 + - - +
578A GLU* 3.5 6.6 + - - +
579A ASN* 3.1 36.4 + - - +
881A ARG* 3.8 31.7 + - - +
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Residues in contact with SER 576 (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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412A LEU* 3.9 11.9 - - - -
413A MET* 3.7 20.9 - - - +
416A ILE* 3.3 27.9 - - - +
572A GLU* 2.9 22.2 + - - +
573A PHE* 3.7 5.4 - - - -
575A THR* 1.4 76.2 + - - +
577A TYR* 1.3 59.9 + - - +
579A ASN* 3.4 4.5 + - - +
580A PHE* 3.1 22.9 + - - +
877A VAL* 4.6 7.1 - - - +
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Residues in contact with TYR 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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412A LEU* 3.7 24.4 - - + +
423A ILE* 4.8 9.0 - - + -
425A ILE* 4.1 20.3 - - + +
428A ARG* 3.2 65.4 + - + +
566A LEU* 3.8 22.7 - - + -
573A PHE* 3.0 21.0 + + + +
574A ALA* 3.7 6.3 - - - +
576A SER* 1.3 74.5 - - - +
578A GLU* 1.4 58.5 + - - +
580A PHE* 3.3 2.5 + + - +
581A LEU* 2.9 58.7 + - + +
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Residues in contact with GLU 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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574A ALA 3.0 17.1 + - - +
575A THR* 3.6 9.4 - - - +
577A TYR* 1.4 77.7 - - - +
579A ASN* 1.3 55.5 + - - +
581A LEU* 3.5 7.9 + - - +
582A SER* 2.7 38.8 + - - +
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Residues in contact with ASN 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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416A ILE* 5.1 4.0 - - + -
575A THR* 3.1 22.8 + - - +
576A SER* 3.6 8.3 - - - +
577A TYR 3.3 0.2 - - - -
578A GLU* 1.3 77.5 - - - +
580A PHE* 1.3 63.7 + - - +
582A SER* 3.4 6.8 + - - -
583A VAL* 3.1 31.5 + - - +
880A CYS* 4.1 9.1 - - - -
881A ARG* 3.3 37.8 + - - +
884A ILE* 3.4 28.6 - - + +
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Residues in contact with PHE 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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412A LEU* 3.9 14.4 - - + -
415A GLY* 3.7 37.0 - - - -
416A ILE* 3.8 13.1 - - + +
419A GLY 5.4 0.2 - - - -
420A ALA 3.6 24.5 - - - -
421A ASP 4.4 5.8 - - - -
422A TYR* 4.4 2.5 - - - -
423A ILE* 3.5 46.2 - - + -
576A SER 3.1 13.6 + - - +
577A TYR* 3.6 7.6 - + - +
579A ASN* 1.3 74.2 - - - +
581A LEU* 1.3 74.9 + - + +
583A VAL* 3.6 3.6 + - - +
584A SER* 3.0 39.4 + - - -
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Residues in contact with LEU 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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428A ARG* 3.5 30.7 - - - +
577A TYR* 2.9 55.0 + - + +
578A GLU* 3.7 7.6 - - - +
580A PHE* 1.3 87.6 - - + +
582A SER* 1.4 66.1 + - - +
584A SER* 3.6 5.6 + - - -
585A LYS* 3.1 22.3 + - - +
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Residues in contact with SER 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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578A GLU* 2.7 24.2 + - - +
579A ASN* 3.5 10.3 + - - -
581A LEU* 1.4 73.4 - - - +
583A VAL* 1.4 60.0 + - - +
585A LYS 2.9 19.1 + - - -
586A TYR* 3.2 30.3 + - - -
591A TYR* 3.2 24.1 + - - -
884A ILE* 5.1 3.4 - - - -
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Residues in contact with VAL 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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446A HIS* 5.3 0.2 - - - -
579A ASN 3.1 17.1 + - - +
580A PHE* 4.2 3.8 - - - +
582A SER* 1.4 77.1 - - - +
584A SER* 1.3 64.0 + - - +
586A TYR* 3.2 45.2 + - + +
587A ASP* 4.3 3.3 - - - +
618A ARG* 5.0 9.0 - - - +
619A VAL* 4.4 7.9 - - + -
622A LEU* 4.2 20.2 - - + -
880A CYS* 4.2 12.3 - - - -
884A ILE* 3.9 18.2 - - + -
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Residues in contact with SER 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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420A ALA 4.8 2.7 + - - -
421A ASP 3.2 23.4 + - - -
442A VAL* 4.2 5.5 - - - +
445A ARG* 2.6 23.9 + - - -
446A HIS* 3.1 23.6 + - - -
580A PHE* 3.0 29.9 + - - -
581A LEU* 3.8 7.2 - - - -
583A VAL* 1.3 76.9 - - - +
585A LYS* 1.3 52.5 + - - +
586A TYR 3.3 3.3 + - - -
587A ASP* 3.6 2.8 - - - +
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Residues in contact with LYS 585 (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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445A ARG* 3.6 9.4 - - - +
581A LEU 3.1 16.2 + - - +
582A SER 2.9 8.3 + - - +
584A SER* 1.3 72.4 - - - +
586A TYR* 1.4 60.9 + - - +
587A ASP 3.2 3.1 - - - -
588A ASP* 3.2 36.4 - - - +
591A TYR* 3.3 18.3 - - + +
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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