Contacts of the helix formed by residues 641 - 646 (chain A) in PDB entry 5IYB
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 641 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A LEU* 3.8 11.0 - - - +
546A ARG* 5.0 0.9 - - + -
606A HIS* 5.0 2.7 - - - -
607A SER 5.0 1.1 - - - -
608A THR* 3.9 28.5 - - + -
628A VAL* 6.5 0.2 - - - -
639A ILE* 5.5 1.3 - - + -
640A LEU* 1.3 76.5 - - - +
642A LYS* 1.3 59.2 + - - +
643A LYS* 2.9 44.4 - - - -
644A SER* 2.9 14.2 + - - -
645A LEU* 3.1 25.8 + - - +
646A GLY 3.6 0.5 + - - -
771A VAL* 4.3 8.7 - - + +
772A SER* 3.6 17.9 - - - +
301U CYS 5.2 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 642 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A LEU* 4.9 8.7 - - + -
641A CYS* 1.3 80.8 - - - +
643A LYS* 1.3 60.2 + - - +
646A GLY* 2.9 35.7 + - - +
647A THR* 4.8 16.4 - - - +
648A SER* 3.8 15.1 + - - +
772A SER 3.1 13.1 + - - +
773A GLY* 4.0 23.4 + - - +
282U ASP 4.1 7.6 + - - -
283U GLU* 4.5 11.2 + - - -
284U PRO* 3.7 32.7 - - - +
286U THR* 5.1 2.8 + - - -
299U LYS* 5.0 14.4 - - - +
301U CYS 5.0 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 643 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A THR* 3.5 29.0 - - - +
606A HIS 3.7 7.4 - - - +
607A SER* 3.6 48.7 - - - +
641A CYS* 2.9 16.7 - - - -
642A LYS* 1.3 78.9 - - - +
644A SER* 1.3 59.5 + - - +
648A SER* 4.4 21.0 - - - +
651A SER* 4.6 1.4 + - - -
301U CYS* 3.4 34.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 644 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A THR* 4.1 25.1 - - - -
606A HIS* 5.7 0.2 - - - -
628A VAL* 4.4 8.9 - - - +
639A ILE 4.3 0.9 + - - -
640A LEU* 3.3 25.0 - - - +
641A CYS* 2.9 28.6 + - - -
643A LYS* 1.3 79.5 - - - +
645A LEU* 1.3 57.7 + - - +
646A GLY 3.5 0.4 - - - -
651A SER* 3.1 28.1 - - - -
652A LEU* 3.2 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 645 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A ILE* 3.9 32.0 + - + -
542A LEU* 4.4 3.6 - - + -
545A VAL* 3.5 42.6 - - + -
592A PHE* 4.4 0.2 - - + -
640A LEU* 3.8 9.9 - - + -
641A CYS 3.1 14.6 + - - +
644A SER* 1.3 81.0 + - - +
646A GLY* 1.3 59.6 + - - +
651A SER* 4.7 1.3 - - - -
652A LEU* 3.8 30.7 - - + +
653A VAL* 4.1 14.7 - - + +
668A PHE* 5.0 3.8 - - + -
672A ILE* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A GLY* 4.2 10.5 - - - -
537A ILE 4.6 7.6 - - - -
542A LEU* 5.5 0.7 - - - -
641A CYS 3.6 1.6 + - - -
642A LYS* 2.9 32.7 + - - -
644A SER 3.5 1.0 - - - -
645A LEU* 1.3 74.2 - - - +
647A THR* 1.3 57.2 + - - -
648A SER 2.8 13.5 + - - -
651A SER* 2.8 17.8 + - - -
653A VAL* 3.7 5.0 - - - +
----------------------------------------------------------
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