Contacts of the helix formed by residues 260 - 265 (chain A) in PDB entry 5IHC
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 HIS 260 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A SER* 5.1 2.5 - - - -
238A LEU* 5.9 1.8 - - + -
239A LEU* 3.8 21.7 - - + +
242A GLN* 2.6 32.6 + - - -
252A ILE* 3.6 22.9 - - + -
256A ASN 3.3 15.8 + - - +
257A LEU* 3.3 16.5 + - + +
258A LEU 3.7 0.2 - - - -
259A ASN* 1.3 76.8 - - - +
261A PRO* 1.4 84.0 - - + +
262A TRP* 3.0 39.5 + - + +
263A ILE* 3.0 21.2 + - + +
264A MET* 3.0 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A SER* 6.2 0.7 - - - -
259A ASN 3.5 4.2 - - - +
260A HIS* 1.4 100.7 - - + +
262A TRP* 1.4 59.4 + - - +
264A MET* 3.4 7.4 + - + +
265A GLN* 3.2 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU* 3.6 22.0 - - + -
109A THR* 3.9 6.5 - - + -
110A ARG* 2.6 89.9 + - + +
113A PHE* 4.0 12.1 - + + -
199A LEU* 3.7 22.9 - - + -
203A MET* 4.2 4.5 - - - -
235A SER* 3.3 33.3 - - - +
236A SER* 2.9 33.0 + - - +
239A LEU* 3.5 26.0 - - + -
260A HIS* 3.0 20.9 + - + +
261A PRO* 1.4 74.6 - - - +
263A ILE* 1.3 75.8 + - + +
265A GLN* 3.5 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG* 3.8 7.3 - - - +
113A PHE* 3.7 31.6 - - + -
114A ARG* 2.9 42.8 + - + +
117A VAL* 4.2 14.6 - - + -
239A LEU* 4.6 1.8 - - + -
257A LEU* 3.4 23.8 - - + +
258A LEU 3.4 26.2 - - - +
259A ASN* 4.7 0.4 - - - -
260A HIS* 3.0 15.7 + - + +
262A TRP* 1.3 92.0 - - + +
264A MET* 1.3 59.1 + - + +
265A GLN 3.6 0.3 + - - -
267A TYR* 4.0 0.9 - - - -
271A VAL* 3.7 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ARG* 4.3 2.7 - - - +
258A LEU 4.6 0.2 - - - +
259A ASN* 3.3 28.7 - - + +
260A HIS 3.0 15.8 + - - +
261A PRO* 3.9 7.9 - - + +
263A ILE* 1.3 74.6 - - - +
265A GLN* 1.3 59.7 + - - +
266A ASP 3.3 0.7 + - - -
267A TYR 2.9 5.2 + - - -
268A ASN* 2.7 56.1 + - - +
269A TYR* 3.4 30.5 - - - +
270A PRO* 3.5 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU* 3.9 13.4 - - - +
110A ARG* 3.1 35.1 + - - +
235A SER* 4.3 10.2 + - - -
261A PRO 3.2 12.9 + - - +
262A TRP* 3.5 16.3 - - - +
263A ILE 3.4 0.6 - - - -
264A MET* 1.3 73.6 - - - +
266A ASP* 1.3 77.9 + - - +
267A TYR* 3.2 6.1 + - - -
268A ASN* 4.9 1.8 - - - +
----------------------------------------------------------
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