Contacts of the helix formed by residues 181 - 199 (chain A) in PDB entry 1CI1
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 PRO 181 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ALA 3.6 2.7 - - - +
180A THR* 1.3 83.7 - - - +
182A GLN* 1.3 71.1 + - - +
184A ALA* 3.2 1.7 + - - +
185A GLN* 2.9 30.3 + - - +
222A THR* 4.3 27.4 - - - +
223A LEU* 3.8 19.5 - - + -
226A MET* 3.7 33.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A THR* 3.0 19.2 + - - +
181A PRO* 1.3 97.1 - - - +
183A GLN* 1.3 60.0 + - + +
185A GLN* 3.8 6.4 - - - +
186A GLU* 3.1 25.1 + - - +
226A MET* 4.6 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ARG* 4.2 28.5 + - - +
167A TYR* 4.9 0.8 - - - -
171A TRP* 3.9 10.8 - - + -
177A LYS* 5.7 2.4 - - - -
178A VAL 5.0 0.3 - - - +
179A ALA* 3.7 14.5 - - + -
180A THR* 2.7 52.7 + - - +
182A GLN* 1.3 71.9 - - + +
184A ALA* 1.3 64.0 + - - +
186A GLU* 3.7 9.0 + - - +
187A VAL* 3.5 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A TYR* 4.7 7.9 - - - -
179A ALA* 4.3 2.8 - - + +
180A THR 3.0 6.3 + - - +
181A PRO 3.7 4.7 - - - +
183A GLN* 1.3 73.3 - - - +
185A GLN* 1.3 67.8 + - - +
187A VAL* 3.2 3.8 + - - +
188A HIS* 2.9 32.3 + - + -
211A TYR* 4.0 21.8 - - + -
223A LEU* 3.9 16.2 - - + -
229A ILE* 3.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A PRO 2.9 17.5 + - - +
182A GLN* 3.8 6.7 - - - +
184A ALA* 1.3 76.5 - - - +
186A GLU* 1.3 53.3 - - - +
188A HIS* 3.2 3.7 + - - +
189A GLU* 2.8 55.2 + - - +
226A MET* 3.0 39.9 - - + +
227A ARG* 3.6 15.5 - - - +
228A ASP* 2.7 43.7 + - - +
229A ILE* 4.3 2.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ARG* 5.3 7.3 + - - -
140A THR* 6.1 0.9 - - - +
182A GLN 3.1 16.0 + - - +
183A GLN* 3.7 11.0 - - - +
184A ALA 3.2 0.2 - - - -
185A GLN* 1.3 79.6 - - - +
187A VAL* 1.3 69.8 + - + +
189A GLU* 3.3 12.3 - - - +
190A LEU* 3.0 21.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ARG* 4.1 12.1 - - - +
140A THR* 4.3 10.8 - - + -
144A VAL* 4.6 17.3 - - + -
167A TYR* 3.7 55.9 - - + +
183A GLN 3.5 13.4 + - - +
184A ALA 3.2 3.4 + - - +
186A GLU* 1.3 80.0 - - + +
188A HIS* 1.3 60.7 + - - +
190A LEU* 3.1 12.1 + - + +
191A LEU* 2.9 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A TYR* 3.7 30.3 - + + +
184A ALA* 2.9 32.0 + - + +
185A GLN* 3.6 5.2 - - - +
187A VAL* 1.3 75.4 - - - +
189A GLU* 1.3 63.4 + - - +
191A LEU* 3.2 10.1 + - - +
192A ARG* 3.0 25.1 + - - +
209A ILE* 3.3 30.4 + - + +
210A LEU 3.4 25.6 - - - -
211A TYR* 3.7 18.9 - - + +
228A ASP* 3.3 30.7 + - + +
229A ILE* 3.7 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLN* 2.8 35.1 + - - +
186A GLU* 3.3 11.9 - - - +
188A HIS* 1.3 78.5 - - - +
190A LEU* 1.3 62.1 + - - +
192A ARG* 3.4 1.9 + - - +
193A ARG* 3.1 69.6 + - - +
227A ARG* 3.3 28.9 + - - -
228A ASP* 4.0 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A THR* 5.8 1.3 - - + -
141A ALA* 3.8 37.0 - - + -
144A VAL* 4.0 17.5 - - + -
145A LEU* 4.2 22.0 - - + -
186A GLU* 3.0 10.9 + - + +
187A VAL* 3.3 15.3 - - + +
189A GLU* 1.3 80.6 - - - +
191A LEU* 1.3 61.3 + - + +
193A ARG* 3.5 9.4 + - + +
194A TRP* 3.2 22.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 4.5 12.3 - - + -
144A VAL* 4.2 23.3 - - + +
145A LEU* 4.0 19.7 - - + -
148A LEU* 4.1 17.7 - - + +
165A ILE* 4.5 11.2 - - + -
167A TYR* 4.4 13.0 - - + -
187A VAL* 2.9 30.3 + - + +
188A HIS* 3.2 8.3 + - - +
190A LEU* 1.3 78.4 - - + +
192A ARG* 1.3 61.2 + - - +
194A TRP* 3.5 5.0 + - - +
195A VAL* 3.2 28.0 + - - +
209A ILE* 4.2 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 5.1 2.1 - - - +
188A HIS 3.0 14.0 + - - +
189A GLU* 4.0 3.1 - - - +
191A LEU* 1.3 74.5 - - - +
193A ARG* 1.3 61.8 + - + +
195A VAL* 3.3 6.6 + - + +
196A ARG* 2.8 49.2 + - - +
204A ALA* 2.8 42.6 + - + +
205A ALA* 4.2 8.8 + - - +
207A LEU* 2.7 27.6 + - + +
209A ILE* 3.5 17.0 - - + +
227A ARG 5.0 1.3 + - - -
228A ASP* 2.7 46.0 + - - +
230A ASN* 2.5 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLU* 3.1 59.8 + - - +
190A LEU* 3.9 7.9 - - + +
191A LEU 3.3 0.2 - - - -
192A ARG* 1.3 74.2 - - + +
194A TRP* 1.3 61.4 + - - +
196A ARG* 3.6 27.2 - - - +
197A SER* 2.9 31.6 + - - -
227A ARG* 5.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 3.6 39.4 + - + +
148A LEU* 3.8 26.2 - - + -
149A ALA* 4.0 34.5 - - + +
152A ALA* 4.0 22.4 - - + -
153A GLN* 4.6 7.0 - - - -
160A TRP* 5.3 0.7 - + - -
190A LEU 3.2 16.1 + - - +
191A LEU 3.8 4.7 - - - +
192A ARG 3.3 0.2 - - - -
193A ARG* 1.3 79.1 - - - +
195A VAL* 1.3 66.7 + - + +
197A SER* 2.9 20.2 + - - -
198A LYS* 3.1 61.7 + - + +
199A LEU* 5.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LEU* 4.1 10.8 - - + -
160A TRP* 4.7 10.5 - - + -
191A LEU 3.2 15.5 + - - +
192A ARG* 3.5 8.7 - - - +
193A ARG 3.2 0.2 - - - -
194A TRP* 1.3 92.3 - - + +
196A ARG* 1.3 57.1 + - - +
198A LYS* 4.5 1.8 - - - -
199A LEU* 2.7 42.0 + - + +
200A GLY 3.6 0.3 + - - +
203A ILE* 4.1 17.9 - - + -
204A ALA* 3.9 21.3 - - + -
207A LEU* 3.9 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ARG* 2.8 45.2 + - - +
193A ARG* 3.2 32.6 + - - +
195A VAL* 1.3 75.4 - - - +
197A SER* 1.3 62.4 + - - +
200A GLY* 2.8 47.7 + - - +
201A THR* 4.2 23.9 - - + +
204A ALA* 3.6 9.2 - - + +
205A ALA* 6.2 0.8 - - - +
228A ASP* 5.4 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ARG 2.9 13.4 + - - -
194A TRP* 2.9 20.4 + - - -
196A ARG* 1.3 77.4 - - - +
198A LYS* 1.3 74.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LYS* 5.6 2.1 + - - -
194A TRP* 3.1 71.4 + - + +
195A VAL* 4.0 2.0 - - - +
196A ARG 3.0 0.6 - - - -
197A SER* 1.3 94.6 - - - +
199A LEU* 1.3 68.6 + - + +
200A GLY 3.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ALA* 5.3 4.0 - - + -
155A LEU 5.9 0.9 - - - +
156A SER 5.4 0.4 - - - -
157A LYS* 3.7 45.8 - - + +
160A TRP* 3.5 52.9 - - + +
194A TRP* 5.3 2.0 - - + -
195A VAL* 2.7 29.6 + - + +
198A LYS* 1.3 83.4 - - + +
200A GLY* 1.3 57.9 + - - +
202A ASP* 3.8 4.3 - - - +
203A ILE* 3.7 28.1 - - + +
----------------------------------------------------------
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