Contacts of the helix formed by residues 589 - 597 (chain A) in PDB entry 3VF1
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 ASN 589 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A TRP* 3.8 22.0 - - + +
587A LYS 3.7 7.9 + - - -
588A SER* 1.3 76.7 - - - +
590A HIS* 1.3 65.0 + - - +
591A LYS* 3.0 21.8 + - - +
592A VAL* 3.1 30.3 + - - +
593A ILE* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ASP 4.9 1.6 - - - -
209A CYS* 3.5 18.6 - - + +
210A LEU* 3.1 43.9 + - + +
211A GLU* 5.6 2.5 - - + -
233A ARG* 4.8 6.5 - - - -
351A TRP* 3.6 35.4 - + + +
589A ASN* 1.3 76.3 - - - +
591A LYS* 1.3 68.3 + - + +
593A ILE* 3.2 5.7 + - + +
594A MET* 3.1 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASP* 5.0 1.2 - - - +
207A TRP 5.1 0.4 + - - +
208A ASP* 3.1 40.9 + - - +
589A ASN* 3.0 7.8 + - - +
590A HIS* 1.3 80.5 - - + +
592A VAL* 1.3 66.6 + - + +
594A MET* 3.3 8.7 + - + +
595A ALA* 3.2 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A MET* 4.0 17.5 - - + -
587A LYS 3.8 15.3 - - - +
588A SER* 4.7 3.8 - - - +
589A ASN* 3.1 37.0 + - - +
591A LYS* 1.3 76.2 - - + +
593A ILE* 1.3 63.5 + - - +
595A ALA* 3.1 20.2 + - + +
596A SER* 3.4 10.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
210A LEU* 4.1 12.8 - - + -
351A TRP* 3.6 44.4 - - + +
354A ILE* 3.9 20.0 - - + -
355A MET* 3.4 30.7 - - + +
358A LEU* 3.7 21.3 - - + -
588A SER* 5.2 0.2 - - - -
589A ASN 3.1 14.3 + - - +
590A HIS* 3.5 8.3 - - - +
592A VAL* 1.3 77.1 - - - +
594A MET* 1.3 62.6 + - - +
596A SER* 3.1 13.1 + - - +
597A LEU* 3.1 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 594 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASP* 3.7 10.2 - - + +
207A TRP* 3.4 49.5 + - + +
208A ASP 3.8 9.2 - - - +
209A CYS 3.5 12.6 - - - +
210A LEU* 3.6 37.5 - - - +
213A PHE* 3.9 17.0 - - + -
578A ARG* 3.1 17.8 + - - -
590A HIS* 3.1 25.1 + - + +
591A LYS* 3.3 13.0 + - + +
593A ILE* 1.3 75.7 - - - +
595A ALA* 1.3 57.7 + - - +
596A SER 3.6 0.2 + - - -
597A LEU* 3.6 10.8 + - + +
598A ALA 4.9 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 595 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASP* 3.4 16.8 + - - +
578A ARG* 3.4 19.0 + - - +
579A GLN* 3.5 27.4 + - + +
591A LYS 3.2 10.4 + - - +
592A VAL* 3.1 13.8 + - - +
593A ILE 3.1 0.8 - - - -
594A MET* 1.3 77.5 - - - +
596A SER* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 596 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A MET* 4.4 14.0 - - - +
359A TRP* 4.6 6.2 - - - -
577A MET* 3.3 25.6 - - - -
578A ARG* 2.8 28.2 + - - +
579A GLN* 3.5 25.4 + - - +
580A PRO 4.7 1.9 + - - -
592A VAL* 3.4 9.3 + - - +
593A ILE* 3.1 10.6 + - - -
595A ALA* 1.3 77.4 - - - +
597A LEU* 1.3 68.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 597 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU* 3.5 31.6 - - + -
213A PHE* 3.9 26.0 - - + -
358A LEU* 4.3 11.7 - - + -
570A HIS* 4.9 4.3 - - + -
571A PRO* 4.6 8.3 - - + -
574A PRO* 4.1 20.9 - - + -
576A LEU 4.5 0.9 - - - -
577A MET* 3.9 26.7 - - + -
578A ARG* 2.8 24.4 + - - -
593A ILE* 3.1 22.2 + - + +
594A MET* 3.6 9.7 + - + +
595A ALA 3.6 0.2 - - - -
596A SER* 1.3 77.3 - - - +
598A ALA* 1.3 67.4 + - - +
----------------------------------------------------------
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