Contacts of the helix formed by residues 583 - 599 (chain A) in PDB entry 3RC3
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 583 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580A ASN* 3.1 27.1 + - + +
581A LYS 3.2 0.4 - - - -
582A LYS* 1.4 83.6 + - - +
584A PRO* 1.3 76.6 - - - +
585A PHE* 3.2 1.6 + - - +
586A VAL* 3.1 33.1 + - + +
587A CYS* 3.3 15.1 + - - -
623A LYS* 5.8 1.4 + - - -
626A MSE 3.5 41.2 - - - +
627A ASP* 4.9 5.2 - - - +
630A ALA* 3.7 25.0 - - + +
633A ASP* 5.3 2.0 - - - +
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Residues in contact with PRO 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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582A LYS 3.4 10.3 - - - +
583A GLN* 1.3 90.3 - - + +
585A PHE* 1.3 57.0 + - - +
587A CYS* 3.2 9.8 + - + +
588A SER* 2.9 34.4 + - - +
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Residues in contact with PHE 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A GLN* 3.2 1.8 + - - +
584A PRO* 1.3 76.5 - - - +
586A VAL* 1.3 58.0 + - - +
588A SER* 3.8 6.9 - - - -
589A SER* 2.7 38.0 + - - -
611A TYR* 3.5 52.9 - + - -
612A ILE* 4.3 10.3 - - + -
630A ALA* 4.5 15.0 - - + -
631A VAL* 4.2 26.7 - - + -
634A VAL* 3.6 28.7 - - + -
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Residues in contact with VAL 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A ILE* 3.6 36.6 - - + -
580A ASN* 3.9 12.6 - - + +
583A GLN* 3.1 25.4 + - + +
585A PHE* 1.3 77.6 - - - +
587A CYS* 1.3 56.7 + - - +
589A SER* 3.2 3.5 + - - -
590A LEU* 2.9 27.0 + - - +
630A ALA* 3.9 24.2 - - - +
633A ASP* 4.0 22.9 - - + +
634A VAL* 3.9 10.5 - - + -
637A LEU* 4.4 6.8 - - + +
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Residues in contact with CYS 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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556A PHE* 3.8 26.5 - - - -
560A LEU* 3.6 28.6 - - + +
579A ILE* 4.6 4.9 - - - -
581A LYS* 3.6 30.3 - - - -
583A GLN 3.3 9.4 + - - -
584A PRO* 3.2 11.5 + - + +
586A VAL* 1.3 75.8 - - - +
588A SER* 1.3 63.5 + - - +
590A LEU* 3.2 3.6 + - - +
591A LEU* 3.1 22.0 + - - +
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Residues in contact with SER 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A PRO* 2.9 19.6 + - - +
585A PHE* 3.8 11.7 - - - -
587A CYS* 1.3 76.6 - - - +
589A SER* 1.3 56.2 + - - +
591A LEU* 3.5 13.8 + - - +
592A GLN* 3.0 27.7 + - - +
611A TYR* 3.7 9.1 + - - -
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Residues in contact with SER 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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585A PHE* 2.7 24.7 + - - -
586A VAL 3.2 5.4 + - - -
588A SER* 1.3 73.9 - - - +
590A LEU* 1.3 66.4 + - - +
592A GLN* 3.3 2.4 + - - +
593A PHE* 2.9 36.2 + - - -
611A TYR* 2.8 29.9 + - - -
634A VAL* 3.4 32.2 - - - +
637A LEU* 4.6 2.0 - - - -
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Residues in contact with LEU 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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557A SER* 3.6 32.5 - - - +
560A LEU* 4.0 11.9 - - + -
561A ILE* 4.2 13.9 - - + -
574A PHE* 3.9 38.8 - - + +
577A ALA* 4.8 1.3 - - + +
579A ILE* 3.9 17.3 - - + -
586A VAL 2.9 12.8 + - - +
587A CYS* 3.2 8.3 + - - +
589A SER* 1.3 78.3 - - - +
591A LEU* 1.3 62.6 + - - +
593A PHE* 3.9 1.7 - - - -
594A ALA* 3.0 22.9 + - - +
637A LEU* 3.9 30.6 - - + +
641A LEU* 5.1 1.1 - - + -
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Residues in contact with LEU 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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560A LEU* 3.3 46.9 - - + +
561A ILE* 4.3 12.7 - - + +
564A ILE* 4.5 10.6 - - + +
587A CYS 3.1 15.4 + - - +
588A SER* 3.5 15.9 - - - +
590A LEU* 1.3 75.8 - - - +
592A GLN* 1.3 58.4 + - - +
594A ALA* 3.8 0.9 - - - +
595A ARG* 2.8 55.8 + - - +
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Residues in contact with GLN 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 SER 3.0 15.6 + - - +
589A SER* 3.7 4.7 - - - +
591A LEU* 1.3 80.0 - - - +
593A PHE* 1.3 63.4 + - + +
595A ARG* 3.3 25.3 + - - +
596A GLN* 3.0 55.3 + - - +
607A TRP* 3.6 35.3 - - + +
611A TYR* 4.2 20.6 - - + +
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Residues in contact with PHE 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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574A PHE* 4.0 3.8 - - + -
589A SER* 2.9 27.1 + - - +
590A LEU* 3.9 3.4 - - - +
592A GLN* 1.3 73.1 - - + +
594A ALA* 1.3 63.0 + - - +
596A GLN* 4.0 1.2 - - - +
597A TYR* 3.1 25.1 + - - +
603A LEU* 3.7 23.8 - - + +
607A TRP* 3.9 26.0 - + - -
608A LEU* 4.1 11.4 - - + -
611A TYR* 4.9 2.9 - + - -
634A VAL* 3.8 28.7 - - + -
637A LEU* 3.8 26.5 - - + -
638A TYR* 3.9 24.5 - + + -
641A LEU* 3.7 23.3 - - + -
649A PHE* 4.0 15.9 - + + -
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Residues in contact with ALA 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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561A ILE* 4.2 18.4 - - + -
564A ILE* 3.6 19.0 - - + +
566A LEU* 4.0 8.8 - - + +
574A PHE* 3.6 28.9 - - + -
590A LEU 3.0 16.8 + - - +
591A LEU* 3.9 2.9 - - - +
593A PHE* 1.3 76.5 - - - +
595A ARG* 1.3 63.6 + - - +
597A TYR* 3.5 2.6 - - - +
598A SER* 3.0 18.5 + - - -
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Residues in contact with ARG 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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564A ILE* 3.9 30.0 - - + +
591A LEU* 2.8 41.2 + - - +
592A GLN* 3.7 36.5 + - - +
593A PHE 3.3 0.2 - - - -
594A ALA* 1.3 78.0 - - - +
596A GLN* 1.3 63.2 + - - +
598A SER* 2.5 25.4 + - - +
599A ARG* 3.2 52.7 + - - +
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Residues in contact with GLN 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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592A GLN* 3.0 38.9 + - + +
595A ARG* 1.3 71.4 - - - +
597A TYR* 1.3 67.0 + - - +
599A ARG* 3.0 26.8 + - - +
601A GLU* 3.0 66.8 + - - +
602A PRO 5.0 1.6 + - - -
603A LEU* 3.5 28.0 - - + +
607A TRP* 4.6 16.4 - - + +
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Residues in contact with TYR 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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566A LEU* 3.8 17.3 - - + -
570A VAL* 3.5 37.2 - - + +
574A PHE* 3.8 15.3 - + + -
593A PHE 3.1 19.3 + - - +
594A ALA 3.5 4.5 - - - +
596A GLN* 1.3 75.0 - - - +
598A SER* 1.3 60.1 + - - +
600A ASN* 2.8 22.0 + - - -
603A LEU* 4.2 2.0 - - - +
645A PHE* 3.6 35.7 - + + -
648A MSE 3.5 33.8 - - + +
649A PHE* 4.3 2.9 - + + -
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Residues in contact with SER 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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564A ILE* 3.7 10.2 - - - +
565A PRO* 3.1 41.0 - - - +
566A LEU* 3.9 1.1 - - - -
594A ALA 3.0 14.1 + - - -
595A ARG* 2.5 29.7 + - - +
597A TYR* 1.3 81.6 - - - +
599A ARG* 1.3 64.0 + - - +
600A ASN 3.7 0.2 + - - -
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Residues in contact with ARG 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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595A ARG* 3.4 50.7 - - - +
596A GLN* 3.0 20.3 + - - +
597A TYR 3.0 1.2 + - - -
598A SER* 1.3 81.9 + - - +
600A ASN* 1.3 72.2 + - - +
601A GLU* 3.1 11.3 - - + +
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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