Contacts of the helix formed by residues 586 - 599 (chain A) in PDB entry 2RC4
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 586 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566A PRO* 3.4 34.5 - - - +
567A ALA* 4.9 1.9 + - - +
581A VAL* 3.7 11.8 - - - +
582A ASP 3.2 7.1 + - - -
583A GLY 3.9 1.8 - - - -
585A VAL* 1.3 85.3 - - - +
587A THR* 1.3 66.2 + - - +
588A ILE* 3.8 2.9 - - - -
589A TYR* 3.7 7.1 - - - +
590A CYS* 3.5 18.4 + - - -
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Residues in contact with THR 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 GLY 2.6 24.9 - - - +
584A ASN* 3.5 12.7 + - - +
585A VAL 3.8 1.6 + - - -
586A SER* 1.3 71.6 - - - +
588A ILE* 1.3 63.0 + - - +
590A CYS* 2.5 32.2 + - - -
591A GLN* 2.9 20.4 + - - +
610A VAL* 3.6 17.7 - - + -
611A GLU* 3.7 19.3 - - + +
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Residues in contact with ILE 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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546A TYR* 5.7 3.8 - - + +
586A SER* 5.2 1.6 - - - -
587A THR* 1.3 80.9 + - - +
589A TYR* 1.3 57.4 + - + +
591A GLN* 3.2 24.9 - - - +
592A ASN* 2.8 56.0 + - - +
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Residues in contact with TYR 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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542A PHE 3.1 28.1 + - - -
543A CYS* 4.1 14.8 - - - +
544A LEU* 3.7 18.3 - - + +
564A HIS 5.7 0.2 - - - -
565A PRO* 3.8 20.5 - - + +
566A PRO* 3.5 41.5 - - + -
581A VAL* 4.2 13.5 - - + -
586A SER* 3.7 11.2 - - - +
587A THR 2.7 4.0 + - - -
588A ILE* 1.3 78.8 - - + +
590A CYS* 1.3 55.5 + - - +
592A ASN* 2.7 29.1 + - - +
593A LEU* 2.7 21.0 + - + +
617A VAL* 4.1 21.6 - - + +
628A LEU* 3.9 19.4 - - - +
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Residues in contact with CYS 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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581A VAL* 3.4 30.1 - - - -
583A GLY* 3.9 10.5 - - - -
586A SER 3.5 8.7 - - - -
587A THR 2.5 11.8 + - - +
589A TYR* 1.3 75.5 - - - +
591A GLN* 1.3 62.1 + - - +
593A LEU* 2.9 19.9 + - - +
594A CYS* 3.0 18.4 + - - -
610A VAL* 3.6 12.6 - - + -
615A PHE* 3.3 42.8 - - + -
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Residues in contact with GLN 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 THR* 2.9 15.4 + - - +
588A ILE* 3.2 33.4 - - - +
590A CYS* 1.3 76.0 - - - +
592A ASN* 1.3 66.6 + - - +
594A CYS* 3.5 5.0 + - - +
595A LEU* 3.3 24.1 + - - +
607A TYR* 3.8 15.2 - - - +
608A TYR* 3.4 24.9 + - - +
610A VAL* 3.5 27.2 - - + +
611A GLU* 5.4 1.4 + - - -
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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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527A TYR* 3.8 2.7 + - - +
543A CYS 3.8 10.2 - - - +
544A LEU* 3.4 34.7 - - + +
545A LYS* 4.4 4.9 - - - +
546A TYR* 3.6 28.1 + - + -
588A ILE* 2.8 39.5 + - - +
589A TYR* 2.7 10.8 + - - +
591A GLN* 1.3 75.8 - - - +
593A LEU* 1.3 61.4 + - - +
595A LEU* 3.3 10.1 + - - +
596A LEU* 2.9 29.5 + - - +
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Residues in contact with LEU 593 (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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544A LEU* 3.9 21.9 - - + +
589A TYR* 2.7 19.3 + - + +
590A CYS* 2.9 11.6 + - - +
592A ASN* 1.3 77.3 - - - +
594A CYS* 1.3 50.2 + - - +
596A LEU* 3.2 9.6 + - + +
597A ALA* 2.7 38.0 + - + +
615A PHE* 3.6 29.4 - - + -
617A VAL* 3.7 26.5 - - + -
628A LEU* 4.2 14.8 - - + -
631A TYR* 3.7 32.5 - - + -
648A MET* 5.2 2.9 - - + -
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Residues in contact with CYS 594 (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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590A CYS 3.0 20.8 + - - -
591A GLN 3.6 6.5 - - - +
593A LEU* 1.3 73.2 - - - +
595A LEU* 1.3 59.8 + - - +
597A ALA* 3.6 6.1 - - - +
598A LYS* 2.8 33.5 + - - +
604A LYS* 4.2 15.3 - - - +
606A LEU 4.1 20.9 - - - +
607A TYR* 4.1 15.4 - - + -
610A VAL* 3.9 11.7 - - - -
615A PHE* 3.7 26.9 - - - -
631A TYR* 5.1 0.9 - - - -
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Residues in contact with LEU 595 (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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525A SER* 2.7 28.2 + - - +
526A PRO* 3.6 30.1 - - + -
527A TYR* 3.3 52.6 - - + +
528A PRO* 4.5 3.6 - - + -
546A TYR* 3.8 22.2 - - + +
591A GLN 3.3 13.8 + - - +
592A ASN* 3.3 10.0 + - - +
594A CYS* 1.3 80.4 - - - +
596A LEU* 1.3 63.3 + - - +
598A LYS* 3.4 3.9 + - - -
599A LEU 3.6 0.7 + - - -
607A TYR* 3.8 16.8 - - + -
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Residues in contact with LEU 596 (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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512A ILE* 3.9 18.6 - - + -
514A PHE* 3.5 32.5 - - + -
527A TYR* 2.9 11.3 + - - +
539A LEU* 3.8 21.1 - - + -
544A LEU* 4.1 17.9 - - + -
592A ASN 2.9 14.2 + - - +
593A LEU* 3.5 10.8 - - + +
595A LEU* 1.3 74.3 - - - +
597A ALA* 1.3 64.4 - - - +
599A LEU* 3.2 25.6 + - + +
600A PHE* 3.6 13.8 - - + -
628A LEU* 4.5 12.6 - - + -
648A MET* 5.0 1.8 - - + -
650A LEU* 4.3 12.6 - - + -
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Residues in contact with ALA 597 (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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593A LEU 2.7 20.8 + - - +
594A CYS* 3.2 6.7 + - - +
596A LEU* 1.3 73.0 - - - +
598A LYS* 1.3 58.2 + - - +
600A PHE* 2.8 24.1 + - - +
601A LEU* 3.3 21.8 + - + +
604A LYS* 5.0 1.8 - - - -
631A TYR* 3.3 37.5 - - + +
648A MET* 4.3 12.0 - - + +
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Residues in contact with LYS 598 (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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523A TYR* 3.6 11.3 - - - +
524A SER* 2.8 33.9 + - - +
525A SER* 3.5 17.9 - - - +
526A PRO* 4.1 1.8 - - + -
594A CYS 2.8 17.0 + - - +
596A LEU 3.3 0.4 - - - -
597A ALA* 1.3 71.7 - - - +
599A LEU* 1.3 57.6 + - - +
600A PHE 2.9 10.6 + - - -
601A LEU* 2.9 43.5 + - - +
602A ASP 3.3 18.8 + - - -
604A LYS* 3.5 22.9 - - + +
607A TYR* 3.5 31.0 - - + +
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Residues in contact with LEU 599 (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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508A CYS 4.1 1.1 - - - +
509A PRO* 4.0 21.5 - - + -
512A ILE* 4.0 20.4 - - + -
521A THR* 3.2 32.8 - - + +
522A TRP 2.8 28.6 + - - -
523A TYR 3.0 15.9 + - - +
525A SER* 3.8 14.8 - - - -
527A TYR* 3.8 18.2 - - + +
539A LEU* 5.2 0.4 - - + -
595A LEU 3.6 7.1 + - - +
596A LEU* 3.3 32.3 - - + +
597A ALA 3.0 0.8 - - - -
598A LYS* 1.3 77.6 - - - +
600A PHE* 1.3 65.1 + - + +
601A LEU 3.8 0.2 - - - -
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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