Contacts of the helix formed by residues 594 - 605 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A ALA* 5.5 2.7 - - + -
593A ASN* 4.7 6.5 - - + +
577B LEU 5.2 0.2 - - - -
578B CYS* 4.1 7.4 - - - -
579B ALA* 4.9 2.5 - - + +
584B CYS* 4.7 5.2 - - + -
586B ILE* 5.4 1.2 - - - +
590B ARG 4.1 0.8 + - - -
591B ARG 4.0 5.1 + - - +
592B LYS 2.9 6.4 + - - -
593B ASN* 1.3 80.3 - - + +
595B PRO* 1.3 69.6 - - - +
596B SER* 3.7 11.9 - - - -
597B CYS* 3.1 20.5 - - + +
598B ARG* 3.1 15.2 + - - +
653B ZN 2.4 36.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 595 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A ASN* 4.1 19.1 - - - +
565B PHE* 4.0 23.6 - - + -
576B TYR* 3.7 41.7 - - + -
577B LEU 5.9 0.9 - - - +
591B ARG 5.1 1.1 - - - +
592B LYS 4.0 9.3 - - - +
594B CYS* 1.3 84.1 - - - +
596B SER* 1.3 60.5 + - - +
598B ARG* 2.9 3.9 + - + -
599B LEU* 2.7 36.5 + - - +
12C A 5.2 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 596 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B TYR* 2.9 36.3 + - - +
577B LEU* 3.7 2.0 - - - -
578B CYS* 3.4 28.5 + - - +
582B ASN* 4.8 2.8 + - - -
594B CYS* 3.3 5.1 - - - -
595B PRO* 1.3 82.8 - - - +
597B CYS* 1.3 64.2 + - - +
599B LEU* 3.6 5.2 - - - +
600B ARG* 3.2 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 597 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B CYS* 3.3 12.1 - - - -
582B ASN* 3.5 25.1 - - - +
583B ASP 5.4 0.2 - - - -
584B CYS* 3.1 30.3 - - + +
586B ILE* 3.6 5.4 - - + +
594B CYS* 3.1 6.9 - - + +
596B SER* 1.3 78.3 - - - +
598B ARG* 1.3 67.0 + - - +
600B ARG* 3.4 14.5 + - - +
601B LYS* 3.1 19.9 + - - +
653B ZN 2.3 35.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 598 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B ILE* 4.5 10.1 - - + -
561B SER* 3.0 27.3 + - - -
562B CYS* 3.3 28.3 - - - +
565B PHE* 3.4 48.9 - - + +
586B ILE* 3.3 23.2 - - + +
591B ARG* 3.5 43.4 + - - +
592B LYS* 4.8 1.4 - - - +
594B CYS 3.1 11.8 + - - +
595B PRO* 2.9 7.6 + - + +
597B CYS* 1.3 75.5 - - - +
599B LEU* 1.3 66.7 + - - +
601B LYS* 2.8 21.0 + - - +
602B CYS* 3.3 7.1 + - - -
12C A 4.5 6.3 + - - -
13C G 3.2 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 599 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B PHE* 3.7 13.0 - - + -
566B PHE* 4.3 18.2 - - + -
569B ALA* 4.4 18.6 - - + +
570B ALA* 4.6 7.0 - - + +
574B GLN 5.3 2.9 - - - +
576B TYR* 4.1 24.7 - - + -
595B PRO 2.7 20.6 + - - +
596B SER* 3.6 4.9 - - - +
598B ARG* 1.3 71.7 - - - +
600B ARG* 1.3 57.9 + - - +
602B CYS* 2.7 29.3 + - - +
603B TYR* 3.4 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 600 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B ASN* 2.8 36.9 + - - +
583B ASP* 4.4 4.2 - - - +
596B SER 3.2 12.8 + - - +
597B CYS* 3.4 14.0 + - - +
599B LEU* 1.3 79.5 - - - +
601B LYS* 1.3 98.9 + - - +
603B TYR* 4.0 12.5 - - + +
604B GLU* 2.8 61.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 601 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B LEU 5.1 2.5 - - - +
544B ILE* 3.4 29.0 - - + +
583B ASP 4.7 6.7 + - - -
584B CYS 4.6 5.7 + - - -
585B THR* 5.6 1.0 - - - +
586B ILE* 3.6 31.9 - - + +
597B CYS* 3.1 7.5 + - - +
598B ARG 2.8 15.1 + - - +
600B ARG* 1.3 116.7 - - - +
602B CYS* 1.3 55.3 + - - +
604B GLU* 3.7 12.8 - - - +
605B ALA* 2.8 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 602 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B ILE* 3.4 28.5 - - - -
562B CYS* 5.2 2.5 - - - -
565B PHE* 4.8 8.3 - - - -
566B PHE* 3.5 22.0 - - + -
598B ARG 3.3 7.8 + - - -
599B LEU* 2.7 17.6 + - - +
601B LYS* 1.3 74.2 - - - +
603B TYR* 1.3 67.3 + - - +
604B GLU 3.1 0.9 - - - -
605B ALA* 3.0 4.5 + - - +
606B GLY 2.9 24.1 + - - +
607B MET* 3.5 33.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 603 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B PHE* 3.9 17.9 - + - -
570B ALA* 2.9 33.0 + - + +
599B LEU* 3.4 36.6 + - + +
600B ARG* 4.1 9.6 - - + +
602B CYS* 1.3 77.4 - - - +
604B GLU* 1.3 58.9 + - - +
606B GLY* 2.9 21.5 + - - -
607B MET 4.0 18.4 + - - +
608B THR* 5.5 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 604 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B ARG* 2.8 50.5 + - + +
601B LYS* 3.7 17.1 - - - +
603B TYR* 1.3 78.6 - - - +
605B ALA* 1.3 60.1 + - + +
606B GLY 3.1 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 605 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B LEU* 4.3 27.0 - - + +
544B ILE* 4.4 11.2 - - + -
556B ALA* 4.2 13.7 - - + +
601B LYS* 2.8 25.0 + - + +
602B CYS 3.0 2.2 + - - +
604B GLU* 1.3 73.7 - - + +
606B GLY* 1.3 65.6 + - - +
607B MET* 6.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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