Contacts of the helix formed by residues 581 - 592 (chain A) in PDB entry 1OAI
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 ASN 581 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575A SER* 3.9 1.8 - - - -
579A GLY 4.0 0.6 + - - -
580A MET* 1.4 72.4 - - - +
582A LEU* 1.3 63.1 + - - +
583A GLU* 3.4 14.3 + - - +
584A TRP* 3.0 39.9 + - - -
585A SER* 2.9 25.5 + - - -
615A VAL 3.1 22.4 + - - -
616A ALA 3.0 12.6 + - - -
617A PHE* 4.7 1.4 - - - +
618A MET* 2.9 30.7 + - - +
619A LYS* 4.6 10.3 - - - +
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Residues in contact with LEU 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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568A GLN* 5.6 3.1 - - - +
571A LEU* 3.4 35.8 - - + +
572A GLN* 4.5 13.9 - - + -
575A SER* 3.8 24.8 + - - +
581A ASN* 1.3 75.3 - - - +
583A GLU* 1.3 66.9 + - - +
585A SER* 3.3 2.4 + - - -
586A GLN* 2.9 28.3 + - - +
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Residues in contact with GLU 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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581A ASN* 3.3 13.4 + - - +
582A LEU* 1.3 84.1 + - - +
584A TRP* 1.3 64.7 + - + +
586A GLN* 3.4 9.3 + - - +
587A LYS* 3.0 25.3 + - - +
619A LYS 5.8 0.3 - - - +
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Residues in contact with TRP 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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580A MET* 3.9 8.9 - - - +
581A ASN* 3.0 31.3 + - - +
583A GLU* 1.3 78.0 - - + +
585A SER* 1.3 59.6 + - - +
587A LYS* 3.3 22.7 + - + +
588A CYS* 3.0 28.1 + - - +
613A PRO* 3.8 26.9 - - + -
615A VAL* 3.9 24.7 + - + +
616A ALA* 3.6 42.1 - - + +
13B PHE* 3.9 31.4 - + + -
15B PHE* 3.7 23.5 - + - -
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Residues in contact with SER 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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571A LEU* 3.7 13.9 - - - -
574A PHE* 4.1 7.5 - - - -
575A SER* 3.1 32.4 + - - -
578A SER* 3.7 2.4 + - - -
580A MET* 3.3 19.1 + - - +
581A ASN 2.9 21.1 + - - -
582A LEU 3.6 4.3 - - - -
584A TRP* 1.3 74.9 - - - +
586A GLN* 1.3 64.7 + - - +
588A CYS* 3.3 2.3 + - - +
589A LEU* 3.0 28.1 + - - +
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Residues in contact with GLN 586 (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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561A PRO* 5.3 11.5 + - - +
563A LEU* 3.7 27.7 - - - +
571A LEU* 3.4 17.0 - - + +
582A LEU 2.9 18.0 + - - +
583A GLU* 3.6 8.8 - - - +
585A SER* 1.3 77.2 - - - +
587A LYS* 1.3 56.0 + - - +
589A LEU* 3.4 1.0 + - - +
590A GLN* 2.8 65.2 + - + +
594A TRP* 4.2 13.7 - - + -
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Residues in contact with LYS 587 (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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583A GLU 3.0 14.3 + - - +
584A TRP* 3.5 42.8 - - + +
585A SER 3.2 0.2 - - - -
586A GLN* 1.3 77.1 - - - +
588A CYS* 1.3 62.1 + - - +
590A GLN* 3.8 11.3 - - - +
591A ASP* 2.9 55.0 + - - +
13B PHE* 2.7 34.3 + - - -
14B SER* 3.8 2.2 - - - +
15B PHE* 4.2 6.1 - - + -
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Residues in contact with CYS 588 (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 PHE* 3.8 17.0 - - + -
580A MET* 4.0 8.5 - - + -
584A TRP 3.0 15.5 + - - +
585A SER 3.3 4.2 + - - +
587A LYS* 1.3 77.8 - - - +
589A LEU* 1.3 60.7 + - - +
591A ASP 3.4 0.5 + - - -
592A ASN* 3.0 33.3 + - - +
599A SER* 3.7 24.0 - - - -
603A PHE* 4.2 3.1 - - - -
15B PHE* 3.5 48.0 - - + -
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Residues in contact with LEU 589 (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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570A MET* 3.8 24.2 - - + +
571A LEU* 3.8 23.8 - - + +
574A PHE* 3.8 25.8 - - + -
585A SER 3.0 23.0 + - - +
586A GLN 3.8 1.8 - - - +
588A CYS* 1.3 75.6 - - - +
590A GLN* 1.3 60.8 + - - +
592A ASN 3.1 8.3 + - - -
593A ASN 3.1 0.2 + - - -
594A TRP* 2.8 60.6 + - + -
596A TYR* 4.4 8.3 - - + -
599A SER* 3.5 25.1 - - - +
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Residues in contact with GLN 590 (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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563A LEU* 4.6 2.6 - - - +
586A GLN* 2.8 53.3 + - - +
587A LYS* 3.8 12.1 - - - +
589A LEU* 1.3 70.4 - - - +
591A ASP* 1.3 65.7 + - - +
592A ASN 3.1 0.9 + - - -
593A ASN* 3.3 10.7 + - - -
594A TRP* 3.5 31.2 + - + +
18B LYS* 3.7 6.2 + - - -
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Residues in contact with ASP 591 (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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587A LYS* 2.9 50.6 + - - +
588A CYS 3.6 5.2 - - - +
590A GLN* 1.3 77.1 + - - +
592A ASN* 1.3 60.8 + - - +
14B SER* 3.4 8.0 - - - -
15B PHE* 2.9 46.8 + - + +
18B LYS* 2.9 31.0 + - - +
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Residues in contact with ASN 592 (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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588A CYS* 3.0 18.1 + - - +
589A LEU 3.1 2.0 + - - -
590A GLN 3.1 0.4 - - - -
591A ASP* 1.3 77.0 - - - +
593A ASN* 1.3 71.9 + - - +
594A TRP 3.2 2.7 - - - -
595A ASP* 3.1 18.5 + - - +
598A ARG* 3.0 41.3 + - + +
599A SER* 3.2 27.0 - - - +
602A ALA* 3.7 9.9 - - - +
15B PHE* 3.5 29.0 + - - +
16B GLY* 3.4 17.7 - - - -
18B LYS* 4.1 0.7 - - - +
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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