Contacts of the helix formed by residues 432 - 436 (chain A) in PDB entry 3LC4
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 THR 432 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS* 5.6 4.5 - - + -
90A LEU* 3.5 35.8 - - + +
91A LEU* 3.3 35.4 - - + +
370A HIS* 5.3 0.3 - - - -
428A LYS* 4.0 24.0 - - + -
431A SER* 1.3 81.3 + - - +
433A GLY* 1.3 71.8 + - - +
434A LYS 3.9 0.9 + - - -
435A ARG 4.5 1.2 + - - -
436A VAL* 3.6 17.1 + - - +
500A HEM 4.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU 3.5 17.9 - - - -
91A LEU* 3.6 9.6 - - - +
94A LYS* 4.5 8.7 - - - -
126A ARG* 5.4 0.3 + - - -
432A THR* 1.3 83.6 + - - +
434A LYS* 1.3 64.4 + - - -
436A VAL* 3.4 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU 4.5 2.8 + - - -
94A LYS* 4.2 31.7 - - + +
95A ASP* 2.5 38.8 + - - +
98A SER* 4.4 11.8 + - - +
122A TRP* 3.3 29.8 - - + -
123A LYS* 4.0 25.5 - - - +
126A ARG* 3.2 22.2 + - - +
370A HIS* 5.8 1.8 - - + -
432A THR 3.9 0.6 + - - -
433A GLY* 1.3 74.6 - - - -
435A ARG* 1.3 61.3 + - + +
436A VAL 3.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A SER* 2.9 30.2 + - - +
99A GLY* 4.0 6.7 - - - -
100A ARG* 3.2 39.9 - - - +
114A ILE 3.1 12.9 + - - -
115A ILE 3.9 1.2 + - - -
117A ASN 2.6 30.7 + - - -
118A ASN* 4.6 1.2 + - - +
122A TRP* 2.9 40.3 - - + +
126A ARG* 3.3 5.4 - - - +
370A HIS* 4.0 13.8 - - + -
432A THR 4.5 1.8 + - - -
434A LYS* 1.3 84.0 - - + +
436A VAL* 1.3 68.6 + - - +
437A CYS 3.2 0.3 + - - -
500A HEM 2.5 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ARG* 2.5 36.2 + - - +
430A PHE 3.9 4.7 - - - +
431A SER 3.3 26.2 - - - +
432A THR* 3.6 16.2 + - - +
433A GLY 3.4 19.6 + - - +
434A LYS 3.4 1.2 - - - -
435A ARG* 1.3 74.6 - - - +
437A CYS* 1.3 75.6 + - - +
438A ALA* 3.1 0.3 + - - -
440A GLU* 3.7 21.5 - - - +
500A HEM 4.4 0.8 - - - +
----------------------------------------------------------
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