Contacts of the strand formed by residues 577 - 584 (chain A) in PDB entry 1OMW
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 GLN 577 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566A SER* 3.0 4.9 - - - -
567A LYS* 2.9 61.9 + - + +
568A MET 6.2 0.4 - - - -
576A TRP* 1.3 85.6 + - - +
578A ARG* 1.3 60.2 + - - +
579A ARG* 3.4 35.6 + - - +
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Residues in contact with ARG 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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36A GLU* 5.4 3.0 + - - +
564A TYR* 3.5 51.3 - - + +
565A MET* 4.3 4.6 - - - +
566A SER* 3.4 21.6 + - - +
577A GLN* 1.3 69.3 - - - +
579A ARG* 1.3 73.0 + - - +
591A ARG 4.7 0.3 - - - +
592A GLY* 5.1 1.7 - - - -
593A GLU* 4.7 5.3 + - - -
635A ASP* 3.0 39.7 + - - -
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Residues in contact with ARG 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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564A TYR* 3.3 10.9 - - - -
565A MET 2.9 30.9 + - - +
567A LYS* 4.5 12.4 - - + +
577A GLN* 3.4 38.6 + - - +
578A ARG* 1.3 88.9 + - - +
580A TYR* 1.3 61.1 + - - +
581A PHE* 3.7 15.6 - - + -
590A TRP* 3.9 25.1 - - + -
591A ARG 3.2 15.7 - - - +
592A GLY* 3.7 24.3 - - - +
595A GLU* 5.9 0.6 + - - -
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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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38A SER* 3.3 33.2 - - - -
552A ASP* 5.6 1.1 - - - -
562A HIS* 3.0 23.5 + - + -
563A GLY* 3.4 17.5 + - - -
564A TYR* 3.4 48.4 - + + +
579A ARG* 1.3 71.2 - - - +
581A PHE* 1.3 62.3 + - - +
582A TYR* 3.6 35.4 - + - -
590A TRP* 3.4 2.3 - - - -
591A ARG* 3.0 70.7 + - - +
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Residues in contact with PHE 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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562A HIS* 3.1 22.5 - - - +
563A GLY 3.1 19.4 + - - +
565A MET* 3.7 42.6 - - + -
566A SER* 5.1 0.4 - - - -
567A LYS* 4.7 10.5 - - + -
579A ARG* 3.7 21.3 - - + -
580A TYR* 1.3 74.6 - - - +
582A TYR* 1.3 65.9 + - - +
583A LEU 4.1 0.2 - - - -
588A LEU* 3.7 29.8 - - + -
589A GLU 3.2 9.2 - - - -
590A TRP* 3.6 32.1 - + + -
630A PHE* 4.7 2.2 - + - -
632A LEU* 3.6 25.8 - - + -
643A TRP* 3.9 13.9 - - + -
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Residues in contact with TYR 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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550A GLU* 3.8 3.6 + - - -
552A ASP* 3.2 20.9 + - - -
553A TYR* 3.9 31.4 - + + +
554A ALA* 3.9 26.5 - - + -
559A CYS* 4.4 3.8 - - - -
561A MET 3.8 3.4 - - - -
562A HIS* 3.4 19.5 - + + -
580A TYR* 3.6 29.5 - + - -
581A PHE* 1.3 75.1 - - - +
583A LEU* 1.3 61.0 + - - +
584A PHE* 3.6 24.7 - - + -
588A LEU* 3.6 2.2 - - - -
589A GLU* 2.8 36.7 + - + +
591A ARG* 3.3 40.8 + - + -
597A PRO* 4.2 9.9 - - + -
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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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559A CYS* 3.6 3.6 - - - -
560A ILE* 2.8 46.0 + - + +
561A MET* 2.8 20.5 + - + +
581A PHE 4.1 0.4 - - - -
582A TYR* 1.3 71.2 - - - +
584A PHE* 1.3 74.1 + - - +
587A ARG 3.6 7.4 - - - +
588A LEU* 3.8 6.5 - - + +
603A MET* 3.8 12.3 - - + -
643A TRP* 3.6 21.7 - - + -
646A GLU* 3.7 35.9 - - + +
647A LEU* 3.6 33.9 - - + +
650A ALA* 4.3 5.8 - - + -
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Residues in contact with PHE 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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553A TYR* 4.1 7.0 - + - -
557A LYS* 3.9 33.9 - - + -
558A ASP* 3.6 17.7 - - - -
559A CYS* 3.7 30.1 - - + -
560A ILE* 3.9 5.8 - - - +
582A TYR* 3.6 29.8 - + + -
583A LEU* 1.3 85.4 - - - +
585A PRO* 1.3 75.2 - - + +
586A ASN 3.2 0.9 - - - +
587A ARG* 2.9 65.6 + - + +
589A GLU* 3.6 22.0 - - + -
603A MET* 4.3 0.3 - - - +
650A ALA* 4.6 0.5 - - - +
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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