Contacts of the helix formed by residues 208 - 214 (chain A) in PDB entry 4IRQ
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 LYS 208 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PHE* 3.6 42.3 + - + -
152A SER* 5.1 3.0 + - - -
153A SER 4.1 16.6 + - - -
154A ASN* 4.3 12.9 + - - +
156A THR* 3.2 38.6 + - - +
157A ASP* 3.1 20.4 + - - +
158A TYR* 4.4 3.6 - - - +
159A ILE* 4.6 2.9 - - + -
206A LEU 3.7 1.0 + - - -
207A SER* 1.3 71.8 - - - +
209A GLN* 1.3 63.9 + - - +
211A TYR 3.1 2.4 + - - -
212A ARG* 3.0 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A SER* 3.2 6.7 + - - +
208A LYS* 1.3 78.5 - - - +
210A HIS* 1.3 63.8 + - + +
212A ARG* 3.3 17.6 + - - +
213A LEU* 3.0 56.9 + - + +
288B ASN* 4.5 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PRO 4.4 2.2 + - - -
179A GLU 3.5 24.7 + - - -
180A ALA 4.1 2.9 - - - -
181A GLY* 3.6 28.9 - - - -
182A PRO* 3.9 5.6 - - + +
206A LEU* 4.2 11.2 - - + -
207A SER* 3.0 28.0 + - - +
209A GLN* 1.3 84.5 - - + +
211A TYR* 1.3 61.4 + - - +
213A LEU* 3.5 14.7 + - + +
214A CYS* 3.4 27.0 + - - -
240A LEU* 3.6 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE* 3.6 12.1 - - + +
146A ASN* 2.5 39.5 + - - -
149A PHE* 3.3 53.8 - + + -
159A ILE* 4.1 15.9 - - + -
161A MET* 4.0 21.1 - - + -
206A LEU* 4.0 14.3 - - + +
207A SER 3.1 12.2 + - - +
208A LYS 3.6 1.6 - - - +
210A HIS* 1.3 74.6 - - - +
212A ARG* 1.3 63.0 + - - +
214A CYS* 3.2 8.6 + - - +
216A GLY* 2.9 44.0 + - - -
217A MET* 3.5 6.9 + - + +
231A PHE* 4.1 16.6 - + - -
287A LEU* 4.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PHE* 3.7 20.8 - - + -
208A LYS* 3.0 60.0 + - - +
209A GLN* 3.7 20.3 + - - +
211A TYR* 1.3 73.8 - - - +
213A LEU* 1.3 56.4 + - + +
215A ASN* 2.8 23.3 + - - +
287A LEU* 4.1 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLN* 3.0 45.0 + - + +
210A HIS* 3.5 27.1 - - + +
211A TYR 3.3 0.4 - - - -
212A ARG* 1.3 76.7 - - - +
214A CYS* 1.3 58.1 + - - +
215A ASN 3.2 0.4 - - - -
238A ALA* 4.2 10.8 - - + +
240A LEU* 4.2 13.9 - - + -
150B LEU* 6.1 1.8 - - + -
212B ARG* 3.7 45.1 + - - +
288B ASN* 5.1 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 4.7 0.9 - - - -
210A HIS 3.4 15.7 - - - -
211A TYR 3.2 9.3 + - - +
212A ARG 3.1 0.8 - - - -
213A LEU* 1.3 77.4 - - - +
215A ASN* 1.3 68.9 + - - +
216A GLY 3.3 8.9 - - - +
231A PHE* 3.9 21.1 - - + -
234A ARG* 3.5 38.7 + - + +
235A ILE* 4.1 17.0 - - - -
238A ALA* 4.6 1.1 - - - -
240A LEU* 3.6 20.4 - - - -
----------------------------------------------------------
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