Contacts of the helix formed by residues 576 - 589 (chain A) in PDB entry 2RD0
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 SER 576 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A ASP* 3.4 7.0 - - - -
573A LYS* 3.3 9.6 + - - -
574A TRP 3.2 2.6 + - - -
575A ASN* 1.3 81.4 - - - +
577A ARG* 1.3 54.9 + - - +
578A ASP* 2.7 21.5 + - - +
579A GLU* 3.1 38.4 + - - +
580A VAL* 3.2 22.6 + - - +
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Residues in contact with ARG 577 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A TRP* 3.4 39.3 - - + -
392A TYR* 4.3 18.0 - - - +
394A PRO* 3.2 41.9 - - - +
395A ASP* 2.7 62.3 + - - +
494A GLU* 4.9 2.0 - - - +
576A SER* 1.3 70.3 - - - +
578A ASP* 1.3 74.7 + - - +
580A VAL* 4.5 5.3 - - - +
581A ALA* 3.2 30.3 + - - +
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Residues in contact with ASP 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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395A ASP* 5.7 0.4 - - - -
494A GLU* 4.1 11.0 - - - +
497A ASN* 3.9 24.2 + - - +
576A SER* 2.7 11.5 + - - +
577A ARG* 1.3 99.7 + - - +
579A GLU* 1.3 69.3 + - + +
581A ALA* 3.7 1.0 + - - +
582A GLN* 3.5 29.8 + - - +
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Residues in contact with GLU 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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552A TRP* 2.9 64.5 + - + +
571A SER 5.4 0.3 - - - +
572A VAL* 4.1 11.7 - - + -
573A LYS* 3.3 35.8 + - - +
576A SER* 3.1 17.5 + - - +
578A ASP* 1.3 79.6 - - + +
580A VAL* 1.3 63.8 + - - +
582A GLN* 3.1 7.3 + - - +
583A MET* 3.0 18.4 + - - +
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Residues in contact with VAL 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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397A PRO* 5.1 10.8 - - + -
572A VAL* 3.8 13.5 - - + -
574A TRP* 3.7 49.1 - - + +
576A SER 3.2 17.2 + - - +
577A ARG* 4.5 5.2 - - - +
579A GLU* 1.3 76.1 - - - +
581A ALA* 1.3 57.5 + - - +
583A MET* 3.2 7.8 - - - +
584A TYR* 3.0 60.7 + - + +
608A ASP* 5.2 0.2 - - - +
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Residues in contact with ALA 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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328A TRP* 5.3 5.4 - - + -
491A VAL* 4.0 26.4 - - + +
494A GLU* 3.5 30.9 - - + +
577A ARG 3.2 20.6 + - - +
578A ASP 4.3 1.1 - - - +
579A GLU 3.3 0.4 - - - -
580A VAL* 1.3 74.7 - - - +
582A GLN* 1.3 66.8 + - - +
584A TYR* 3.5 15.6 - - - +
585A CYS* 3.7 11.4 + - - +
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Residues in contact with GLN 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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494A GLU* 3.9 11.4 - - - +
497A ASN* 3.1 31.7 - - - +
498A TRP* 3.5 40.4 - - + +
552A TRP* 4.0 9.9 - - + -
555A ARG* 3.1 35.8 + - - +
578A ASP* 3.5 18.2 + - - +
579A GLU* 3.1 9.3 + - - +
581A ALA* 1.3 75.1 - - - +
583A MET* 1.3 65.3 + - - +
585A CYS* 2.9 16.1 + - - +
586A LEU* 3.2 16.4 + - + +
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Residues in contact with MET 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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552A TRP* 3.6 15.3 - - + -
565A LEU* 5.0 1.3 - - - -
568A LEU* 3.6 39.0 - - + +
569A LEU* 3.9 26.0 - - + -
572A VAL* 3.3 32.8 - - + -
574A TRP* 4.8 7.0 - - + -
579A GLU 3.0 11.5 + - - +
580A VAL* 3.2 15.3 - - + +
582A GLN* 1.3 71.0 - - - +
584A TYR* 1.3 57.3 + - + +
585A CYS 2.7 16.0 + - - -
586A LEU* 2.9 26.0 + - + +
587A VAL* 3.0 24.2 + - + +
611A VAL* 6.1 0.2 - - + -
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Residues in contact with TYR 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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398A ARG* 3.9 21.9 + - + +
485A LYS* 4.3 14.2 + - - -
488A ASP* 4.4 13.5 - - - +
491A VAL* 3.8 28.5 - - + -
574A TRP* 5.0 2.0 - + - -
580A VAL* 3.0 45.1 + - + +
581A ALA* 3.5 12.1 - - - +
583A MET* 1.3 76.7 - - + +
585A CYS* 1.3 57.6 + - + +
587A VAL* 3.7 10.5 - - + +
588A LYS* 3.2 22.2 + - - +
608A ASP* 3.0 36.4 + - - -
609A PRO* 4.9 0.3 - - - +
610A MET* 3.7 43.5 - - + +
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Residues in contact with CYS 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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488A ASP* 5.6 0.9 - - - -
491A VAL* 5.9 0.2 - - - -
492A ILE* 3.6 52.7 - - - -
495A HIS* 5.2 1.6 - - - -
498A TRP* 4.0 20.9 - - + -
581A ALA 4.0 7.9 - - - +
582A GLN 2.9 11.8 + - - +
583A MET 2.7 6.3 + - - -
584A TYR* 1.3 76.6 - - - +
586A LEU* 1.3 64.2 + - - +
587A VAL 3.3 0.4 - - - -
588A LYS* 3.5 14.5 + - - +
589A ASP* 3.3 16.5 - - - +
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Residues in contact with LEU 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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498A TRP* 5.3 4.5 - - + -
552A TRP* 5.4 0.4 - - + -
555A ARG* 4.5 33.9 - - + +
556A HIS* 4.0 30.7 - - + +
559A VAL* 4.1 21.3 - - + +
568A LEU* 4.9 5.2 - - + -
582A GLN* 3.2 15.1 + - + +
583A MET* 2.9 25.5 + - + +
585A CYS* 1.3 74.8 - - - +
587A VAL* 1.3 64.9 - - - +
588A LYS 3.1 1.0 + - - -
589A ASP* 3.2 9.2 + - - +
590A TRP* 3.0 37.0 + - + -
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Residues in contact with VAL 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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565A LEU* 4.7 12.1 - - + -
569A LEU* 4.6 10.5 - - + -
583A MET* 3.0 38.6 + - + +
584A TYR* 3.7 9.6 - - - +
586A LEU* 1.3 76.9 - - - +
588A LYS* 1.3 64.2 + - - +
589A ASP 3.4 0.2 + - - -
590A TRP* 3.4 19.7 + - - +
610A MET* 3.6 32.8 - - + +
611A VAL* 4.6 7.9 - - + +
614A PHE* 4.1 24.7 - - + -
617A ARG* 4.4 4.8 + - - +
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Residues in contact with LYS 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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488A ASP* 5.3 5.4 - - - +
492A ILE* 3.3 38.8 - - + +
584A TYR 3.2 13.1 + - - +
585A CYS* 3.5 16.6 - - - +
586A LEU 3.1 1.4 + - - -
587A VAL* 1.3 81.2 - - - +
589A ASP* 1.3 68.1 + - - +
590A TRP 3.9 0.7 + - - +
617A ARG* 4.4 12.3 + - - +
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Residues in contact with ASP 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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559A VAL* 4.3 13.0 - - - +
585A CYS 3.3 15.1 - - - +
586A LEU* 3.2 7.7 + - - +
588A LYS* 1.3 86.5 + - - +
590A TRP* 1.3 64.0 + - - +
591A PRO 4.2 0.3 - - - -
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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