Contacts of the helix formed by residues 588 - 603 (chain A) in PDB entry 4RG7
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 GLU 588 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A PHE* 2.6 33.3 + - + +
584A SER* 4.4 1.4 - - - -
586A GLN* 4.4 7.9 - - + +
587A ARG* 1.3 79.4 - - - +
589A HIS* 1.3 63.1 + - - +
590A ASP* 3.7 2.5 - - + +
591A ILE* 4.6 5.4 - - + +
592A ALA* 3.9 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A ARG 3.9 3.9 + - - +
588A GLU* 1.3 73.8 - - - +
590A ASP* 1.3 68.0 + - - +
591A ILE 3.3 2.0 - - - -
592A ALA* 4.2 4.7 - - - +
593A ILE* 3.3 23.4 + - - +
616A GLU* 5.1 11.7 - - + +
619A LEU* 6.5 0.2 - - + -
620A THR* 4.7 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A GLU* 3.7 1.3 - - + +
589A HIS* 1.3 81.2 - - - +
591A ILE* 1.3 60.5 + - - +
593A ILE* 3.7 5.2 + - - +
594A LYS* 3.6 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A PHE* 3.5 37.7 - - + -
588A GLU* 4.4 6.8 + - + +
589A HIS* 3.3 1.0 - - - +
590A ASP* 1.3 77.3 - - - +
592A ALA* 1.3 65.7 + - - +
594A LYS* 3.4 16.1 + - - +
595A PHE* 3.4 22.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A GLY* 3.1 31.1 - - - +
583A PHE* 4.2 7.5 - - + +
584A SER* 4.5 6.5 - - - +
588A GLU 3.9 17.3 + - - +
589A HIS* 3.8 4.9 + - - +
591A ILE* 1.3 76.8 - - - +
593A ILE* 1.3 65.4 + - - +
595A PHE* 3.3 3.9 + - - +
596A PHE* 3.1 37.5 + - + -
616A GLU* 5.6 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 593 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A HIS 3.3 15.8 + - - +
590A ASP* 3.7 7.0 - - - +
591A ILE 3.3 0.4 - - - -
592A ALA* 1.3 78.7 - - - +
594A LYS* 1.3 61.9 + - - +
596A PHE* 3.4 8.7 + - - +
597A GLN* 3.0 21.8 + - - +
613A LEU* 6.0 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 594 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A ASP 3.6 8.1 + - - +
591A ILE* 3.4 12.1 + - - +
592A ALA 3.3 0.4 - - - -
593A ILE* 1.3 79.9 - - - +
595A PHE* 1.3 65.8 + - + +
597A GLN* 3.0 24.1 - - - +
598A ARG* 3.2 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 595 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A TRP* 3.3 55.7 - + + +
579A ALA* 3.6 28.7 - - + -
580A GLY* 3.8 9.4 - - - -
583A PHE* 3.2 33.7 - + - -
591A ILE* 3.4 14.0 + - + -
592A ALA 3.3 3.3 + - - +
594A LYS* 1.3 78.1 - - + +
596A PHE* 1.3 67.0 + - - +
597A GLN 2.9 2.0 - - - -
598A ARG* 2.9 16.6 + - + +
599A ALA 3.2 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 596 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A TRP 4.5 1.3 - - - -
577A CYS* 3.5 31.0 - - - -
580A GLY* 4.0 8.7 - - - -
581A ASN* 3.7 26.5 - - + -
584A SER* 5.6 2.5 - - - -
592A ALA* 3.1 35.0 + - + +
593A ILE* 3.8 6.7 - - - +
595A PHE* 1.3 76.5 - - - +
597A GLN* 1.3 60.9 + - - +
599A ALA* 3.3 9.3 + - - +
600A ILE* 3.2 26.7 + - + +
609A ALA* 4.3 8.2 - - - +
612A LEU* 3.5 49.1 - - + -
613A LEU* 4.3 27.6 - - + -
616A GLU* 4.8 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 597 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A ILE 3.0 13.3 + - - +
594A LYS* 3.0 19.3 - - - +
596A PHE* 1.3 74.6 - - - +
598A ARG* 1.3 58.0 + - - +
600A ILE* 2.9 16.8 + - - +
601A GLN* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 598 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A TRP* 3.9 32.8 - - + -
594A LYS 3.2 7.1 + - - +
595A PHE* 2.9 11.7 + - + +
597A GLN* 1.3 79.9 - - - +
599A ALA* 1.3 56.6 + - - +
601A GLN* 3.8 6.4 - - - +
602A VAL* 2.9 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 599 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A PRO* 3.6 32.3 - - + +
576A TRP* 4.0 5.3 - - + +
577A CYS* 4.0 5.4 - - - +
595A PHE 3.2 8.5 + - - +
596A PHE* 3.3 14.1 - - - +
597A GLN 3.1 0.2 - - - -
598A ARG* 1.3 75.6 - - - +
600A ILE* 1.3 61.5 + - - +
602A VAL* 3.5 11.0 - - - +
603A ASP 3.2 22.5 + - - +
609A ALA* 3.7 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 600 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A PHE* 3.2 19.3 + - + +
597A GLN* 2.9 15.8 + - - +
599A ALA* 1.3 75.7 - - - +
601A GLN* 1.3 64.6 + - - +
603A ASP 4.0 4.3 - - - -
604A PRO* 3.1 26.9 - - + +
609A ALA* 4.3 7.6 - - + +
610A TYR* 3.4 57.9 - - + +
613A LEU* 5.2 6.3 - - + -
629A CYS* 6.3 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 601 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A GLN 2.9 14.7 + - - +
598A ARG* 3.3 8.3 + - - +
600A ILE* 1.3 80.2 - - - +
602A VAL* 1.3 63.9 + - + +
603A ASP 3.4 0.7 + - - -
604A PRO* 4.2 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 602 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A LYS 4.1 17.3 - - - +
571A ASN* 4.4 15.6 - - + +
572A SER 4.0 5.8 - - - +
573A PRO* 3.7 30.0 - - + +
576A TRP* 4.9 2.7 - - + +
598A ARG* 2.9 23.1 + - + +
599A ALA* 3.5 9.9 - - - +
601A GLN* 1.3 78.6 - - + +
603A ASP* 1.3 63.6 + - - +
604A PRO* 4.3 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 603 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A PRO* 4.1 17.4 - - + +
599A ALA 3.2 17.9 + - - +
600A ILE* 3.2 5.9 - - - +
601A GLN 3.2 1.2 - - - -
602A VAL* 1.3 82.9 - - - +
604A PRO* 1.3 65.0 - - - +
605A ASN* 2.9 23.2 + - - +
606A TYR* 3.2 39.0 + - + +
----------------------------------------------------------
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