Contacts of the helix formed by residues 594 - 606 (chain A) in PDB entry 1R4I
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 CYS 594 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577A LEU 4.8 0.2 - - - -
578A CYS* 3.6 9.9 - - - -
579A ALA* 5.3 1.1 - - + +
584A CYS* 3.9 11.0 - - + -
586A ILE* 4.7 5.5 - - + +
590A ARG 4.1 3.4 + - - -
591A ARG 4.3 4.7 + - - +
592A LYS 3.8 0.2 - - - -
593A ASN* 1.3 78.7 - - + +
595A PRO* 1.3 68.7 - - - +
596A SER* 3.7 8.5 - - - -
597A CYS* 3.0 28.9 - - + +
598A ARG* 3.1 18.0 + - - +
651A ZN 2.3 36.8 - - - -
579B ALA* 5.9 1.1 - - + -
593B ASN* 4.8 5.8 - - + +
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Residues in contact with PRO 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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565A PHE* 4.0 6.6 - - + -
576A TYR* 3.2 43.1 - - + -
577A LEU 5.0 1.8 - - - +
591A ARG 4.8 2.2 - - - +
592A LYS 4.1 5.6 - - - +
593A ASN 2.9 20.4 - - - +
594A CYS* 1.3 76.2 - - - +
596A SER* 1.3 69.3 + - - +
598A ARG* 3.0 9.0 + - + +
599A LEU* 2.8 21.8 + - - +
592B LYS* 6.3 3.6 - - - -
593B ASN* 4.6 11.4 - - - +
29D T 3.2 23.6 - - - +
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Residues in contact with SER 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A TYR* 3.5 21.3 + - - +
577A LEU* 4.0 3.8 - - - +
578A CYS* 3.7 33.9 + - - +
582A ASN* 4.1 8.1 + - - -
594A CYS* 3.3 3.6 - - - -
595A PRO* 1.3 81.9 - - - +
597A CYS* 1.3 67.8 + - - +
599A LEU* 3.2 5.6 + - - +
600A ARG* 2.8 24.8 + - - +
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Residues in contact with CYS 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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578A CYS* 3.1 14.4 - - - -
582A ASN* 3.6 5.6 - - - -
583A ASP 3.5 7.2 - - - -
584A CYS* 3.1 24.2 - - + +
586A ILE* 3.9 17.7 - - + -
594A CYS* 3.0 13.4 - - - +
596A SER* 1.3 76.9 + - - +
598A ARG* 1.3 65.6 + - - +
600A ARG* 3.0 19.3 + - - +
601A LYS* 2.7 23.4 + - - +
651A ZN 2.5 32.8 - - - -
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Residues in contact with ARG 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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544A ILE* 4.2 13.4 - - + +
561A SER* 3.4 10.3 + - - -
562A CYS* 3.4 35.9 - - - +
565A PHE* 3.3 43.9 - - + +
586A ILE* 3.9 23.4 - - + +
591A ARG* 3.4 46.6 + - - +
592A LYS* 4.6 1.2 - - - +
594A CYS 3.1 10.6 + - - +
595A PRO* 3.0 8.2 + - + +
597A CYS* 1.3 76.2 - - - +
599A LEU* 1.3 67.1 + - - +
601A LYS* 2.8 17.1 + - - +
602A CYS* 3.1 10.9 + - - -
29D T 4.9 3.0 + - - -
30D G 3.3 27.5 + - - -
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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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565A PHE* 3.8 17.9 - - + -
566A PHE* 5.4 4.5 - - + +
569A ALA* 3.8 31.6 - - + +
570A ALA* 4.2 10.1 - - - +
574A GLN* 5.8 0.7 - - + -
576A TYR* 4.8 8.1 - - + -
595A PRO 2.8 17.9 + - - +
596A SER* 3.8 5.4 - - - +
598A ARG* 1.3 74.4 - - - +
600A ARG* 1.3 59.8 + - + +
602A CYS* 2.7 36.9 + - + +
603A TYR* 3.0 38.8 + - + -
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Residues in contact with ARG 600 (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 ASN* 2.8 51.2 + - - +
583A ASP* 3.8 6.9 - - - +
584A CYS 4.6 2.2 + - - +
596A SER* 2.8 19.4 + - - +
597A CYS* 3.3 27.3 + - - +
599A LEU* 1.3 79.4 - - + +
601A LYS* 1.3 71.7 + - - +
603A TYR* 3.2 8.0 + - + +
604A GLU* 2.5 59.9 + - + +
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Residues in contact with LYS 601 (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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543A LEU 4.0 12.5 + - - +
544A ILE* 3.2 38.8 + - + +
585A THR* 6.0 0.2 - - - +
586A ILE* 3.9 30.1 + - + +
597A CYS 2.7 15.1 + - - +
598A ARG* 2.8 14.0 + - - +
600A ARG* 1.3 80.0 - - - +
602A CYS* 1.3 49.9 + - - +
604A GLU* 3.2 9.3 + - + +
605A ALA* 2.7 36.2 + - + +
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Residues in contact with CYS 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ILE* 3.6 22.2 - - - -
562A CYS* 5.6 3.8 - - - -
565A PHE* 5.0 7.2 - - - -
566A PHE* 3.7 26.0 - - + -
598A ARG* 3.1 17.4 + - - -
599A LEU* 2.7 15.3 + - - +
601A LYS* 1.3 72.4 - - - +
603A TYR* 1.3 60.0 + - - +
604A GLU 2.9 0.9 - - - -
605A ALA* 2.7 24.1 + - - +
606A GLY 3.0 7.6 + - - -
607A MET* 3.2 36.3 + - + +
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Residues in contact with TYR 603 (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 PHE* 4.3 23.0 - + - -
570A ALA* 3.2 28.3 + - - +
571A GLU* 6.0 0.2 - - - -
599A LEU* 3.0 47.5 + - + -
600A ARG* 3.7 9.2 - - + +
602A CYS* 1.3 79.2 - - - +
604A GLU* 1.3 60.3 + - - +
606A GLY* 3.2 12.8 + - - -
607A MET* 4.5 12.4 - - - +
608A THR* 5.7 2.2 - - - -
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Residues in contact with GLU 604 (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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600A ARG* 2.5 51.6 + - + +
601A LYS* 3.3 12.5 - - + +
603A TYR* 1.3 74.2 - - - +
605A ALA* 1.3 57.4 + - - +
606A GLY* 2.8 11.6 + - - -
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Residues in contact with ALA 605 (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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543A LEU* 3.8 33.4 - - + +
544A ILE* 4.7 6.7 - - + -
555A GLY 5.9 0.5 - - - -
556A ALA* 5.0 8.1 - - + +
601A LYS* 2.7 14.3 + - + +
602A CYS* 2.7 16.1 + - - +
604A GLU* 1.3 72.2 - - - +
606A GLY* 1.3 59.3 + - - +
607A MET* 4.8 7.0 - - + +
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Residues in contact with GLY 606 (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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554A TYR 4.5 0.9 - - - +
555A GLY* 4.5 7.1 - - - -
602A CYS 3.0 1.2 + - - -
603A TYR 3.2 8.9 + - - -
604A GLU 2.8 8.2 - - - -
605A ALA* 1.3 80.4 - - - +
607A MET* 1.3 68.9 + - - +
608A THR* 4.0 8.3 - - - +
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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