Contacts of the helix formed by residues 179 - 184 (chain A) in PDB entry 8ICQ
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 GLY 179 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A CYS* 1.3 76.6 - - - +
180A SER* 1.4 53.3 + - - -
181A PHE* 3.1 6.1 - - - -
182A ARG* 2.7 30.3 + - - +
183A ARG* 3.3 2.8 + - - -
192A ASP* 5.1 7.0 - - - +
272A PHE* 3.6 17.9 + - - +
273A THR* 3.9 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ARG* 5.3 2.0 + - - -
179A GLY* 1.4 65.0 - - - -
181A PHE* 1.3 64.5 + - - +
182A ARG 3.0 1.8 - - - -
183A ARG* 2.9 47.0 + - - +
184A GLY 3.1 0.2 + - - -
185A ALA* 2.8 44.0 + - - +
187A SER 4.4 3.3 + - - -
188A SER* 4.2 11.6 + - - -
189A GLY 5.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ARG* 2.5 52.4 + - - +
155A MET* 3.6 40.8 - - + -
156A LEU* 3.7 29.2 - - + -
159A GLN* 3.6 32.1 - - + -
177A VAL* 3.7 37.7 - - + -
178A CYS 4.2 5.8 - - - +
180A SER* 1.3 82.1 + - - +
182A ARG* 1.3 62.5 + - + +
185A ALA* 4.3 3.8 - - - -
188A SER* 3.6 18.5 + - - +
191A MET* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ARG* 4.5 1.9 + - - -
176A THR* 3.9 17.4 - - - +
177A VAL 3.1 24.9 - - - +
178A CYS* 3.8 2.9 - - - +
179A GLY 2.7 16.7 + - - +
181A PHE* 1.3 89.6 - - + +
183A ARG* 1.4 51.9 - - - +
184A GLY 3.3 4.1 + - - -
269A VAL* 3.7 14.7 + - - +
273A THR* 2.3 58.4 + - + +
316A GLU* 2.3 35.8 + - - -
327A TYR* 5.0 1.0 + - - -
330A PRO* 3.7 27.6 - - + +
331A LYS 5.0 0.3 + - - -
333A ARG* 4.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLY 3.3 0.8 + - - +
180A SER* 2.9 43.6 + - - +
182A ARG* 1.4 75.6 - - - +
184A GLY* 1.4 52.0 + - - +
185A ALA* 3.5 3.6 + - + +
273A THR* 2.9 34.0 + - + +
274A GLY* 4.7 0.4 - - - -
275A SER* 2.8 52.7 - - - +
276A ASP 4.5 0.6 - - - +
330A PRO 3.7 23.3 - - - +
331A LYS* 3.7 23.6 - - - +
333A ARG* 4.2 8.7 - - + -
334A SER* 4.9 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ARG* 3.2 29.0 + - - -
180A SER 3.1 1.4 + - - -
181A PHE 3.6 0.8 + - - -
182A ARG 3.3 7.1 + - - -
183A ARG* 1.4 75.7 - - - +
185A ALA* 1.3 66.9 + - - +
186A GLU* 3.6 5.0 + - - +
331A LYS* 5.5 2.7 - - - -
----------------------------------------------------------
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