Contacts of the helix formed by residues 183 - 196 (chain A) in PDB entry 3IH9
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 SER 183 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ARG* 4.0 8.1 - - - +
180A LEU* 5.4 0.2 - - - -
182A ASP* 1.3 77.5 - - - +
184A ALA* 1.3 65.8 + - - +
185A GLU* 3.9 9.8 + - - +
186A GLU* 3.1 36.4 + - - +
187A ILE* 3.1 15.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
168A LEU* 4.1 4.5 - - + +
171A ALA* 3.7 23.9 - - + +
172A HIS* 3.4 50.8 - - + +
175A ARG* 3.6 11.6 - - - +
180A LEU* 4.8 2.0 - - - -
183A SER* 1.3 72.2 - - - +
185A GLU* 1.3 60.4 + - - +
187A ILE 3.6 0.3 + - - -
188A VAL* 3.0 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ARG* 3.0 32.2 + - - -
161A MET* 4.7 14.7 - - + +
168A LEU* 3.9 17.2 - - + +
183A SER* 3.1 8.6 + - - +
184A ALA* 1.3 78.7 - - - +
186A GLU* 1.3 68.6 + - - +
188A VAL* 3.4 1.7 + - - +
189A ALA* 3.0 24.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
121A HIS* 5.6 0.2 - - - -
129A ALA 5.2 1.4 - - - +
130A SER 5.0 0.2 - - - -
131A ARG* 3.7 56.6 + - + +
134A ARG* 4.5 3.8 + - - -
182A ASP* 3.4 33.7 - - - +
183A SER* 3.1 22.6 + - - +
185A GLU* 1.3 88.1 + - - +
187A ILE* 1.3 67.2 + - + +
189A ALA* 3.4 2.8 + - - +
190A GLY* 3.1 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 3.4 40.4 - - + +
121A HIS* 4.5 11.4 + - + +
122A GLN* 3.6 45.3 - - - +
134A ARG* 4.7 6.7 - - - +
171A ALA* 5.1 0.2 - - + -
180A LEU* 4.0 21.5 - - + -
182A ASP* 4.2 15.7 - - + +
183A SER 3.1 14.9 + - - +
184A ALA 4.2 1.6 - - - +
186A GLU* 1.3 82.0 - - + +
188A VAL* 1.3 58.7 + - - +
190A GLY* 3.3 2.1 + - - +
191A TYR* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 4.1 10.3 - - + -
161A MET* 4.8 4.9 - - + -
164A SER* 4.0 17.0 - - - -
167A ASN* 3.6 44.9 - - + +
168A LEU* 3.8 16.4 - - + -
171A ALA* 3.7 10.5 - - + -
184A ALA 3.0 19.6 + - - +
185A GLU 3.9 3.1 - - - +
187A ILE* 1.3 73.1 - - - +
189A ALA* 1.3 59.7 + - - +
191A TYR* 3.8 1.1 - - + +
192A VAL* 2.8 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ARG* 3.9 21.1 - - - +
157A TYR* 3.5 17.6 - - - +
161A MET* 3.6 27.8 - - + +
185A GLU* 3.0 20.1 + - - +
186A GLU 3.7 4.5 - - - +
188A VAL* 1.3 75.8 - - - +
190A GLY* 1.3 58.7 + - - +
192A VAL 3.3 0.3 + - - -
193A ALA* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A HIS* 3.1 34.8 + - - -
131A ARG* 5.8 6.4 - - - +
135A LEU* 4.7 7.4 - - - +
186A GLU 3.1 13.4 + - - -
187A ILE 3.3 1.5 + - - -
188A VAL 3.2 0.2 - - - -
189A ALA* 1.3 78.9 - - - +
191A TYR* 1.3 60.1 + - - +
193A ALA* 3.4 6.0 + - - +
194A GLN* 3.0 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 4.0 3.6 + - - -
67A LYS* 2.9 28.5 + - + -
114A ASN* 3.3 15.8 + - + -
117A ALA* 3.4 31.9 - - + -
118A LEU* 3.7 24.2 - - + -
121A HIS* 3.8 13.6 - - + -
167A ASN* 4.3 26.7 - - + -
187A ILE 2.9 17.4 + - - +
188A VAL 3.9 2.0 - - - +
190A GLY* 1.3 76.4 - - - +
192A VAL* 1.3 65.1 + - + +
194A GLN* 3.1 24.4 - - - +
195A CYS* 3.0 53.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A TYR* 3.4 23.6 - - + +
160A GLU* 3.2 46.9 - - + +
161A MET* 4.1 9.4 - - - -
164A SER* 4.3 2.2 - - - +
167A ASN* 4.7 4.9 - - - +
188A VAL* 2.8 39.9 + - + +
189A ALA 3.8 3.4 - - - +
191A TYR* 1.3 85.5 - - + +
193A ALA* 1.3 64.7 + - - +
195A CYS* 3.3 7.7 + - - +
196A ALA* 3.2 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 3.8 29.2 - - + -
152A VAL* 3.8 16.8 - - + +
154A TRP* 4.4 11.0 - - + -
157A TYR* 3.8 16.1 - - + -
189A ALA 3.0 17.2 + - - +
190A GLY* 3.8 4.7 - - - +
192A VAL* 1.3 75.4 - - - +
194A GLN* 1.3 59.3 + - - +
196A ALA* 2.9 23.6 + - - +
197A VAL* 3.5 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 3.9 6.2 - - - +
66A SER* 2.9 27.3 + - - +
67A LYS* 4.2 3.4 - - - +
70A THR* 3.3 40.2 + - + +
117A ALA* 5.1 2.5 + - - +
121A HIS* 2.8 37.9 - - + +
135A LEU* 4.5 6.7 - - + +
138A ALA* 4.3 8.7 - - + -
142A MET* 4.5 2.8 - - - +
190A GLY 3.0 12.2 + - - +
191A TYR* 3.1 33.4 - - - +
193A ALA* 1.3 76.9 - - - +
195A CYS* 1.3 60.9 + - - +
197A VAL* 3.3 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 3.4 10.2 - - - -
62A ILE 3.5 0.5 + - - -
63A GLN* 2.7 71.3 + - - +
64A SER* 4.3 0.7 - - - -
66A SER* 4.1 3.4 - - - -
160A GLU* 5.4 2.7 - - - +
191A TYR* 3.0 57.1 + - - +
192A VAL* 3.3 8.0 + - - +
193A ALA 3.2 0.4 - - - -
194A GLN* 1.3 75.7 - - - +
196A ALA* 1.3 55.7 + - - +
197A VAL 3.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 3.4 19.2 - - + +
63A GLN* 4.8 1.3 - - - +
152A VAL* 3.8 9.4 - - + -
153A ASP* 2.8 44.7 + - - +
156A THR* 4.7 3.4 - - + -
157A TYR* 4.3 11.7 - - + +
192A VAL 3.2 11.6 + - - +
193A ALA* 2.9 14.1 + - - +
195A CYS* 1.3 75.6 - - - +
197A VAL* 1.3 66.1 + - - +
198A LEU 3.3 0.5 + - - -
----------------------------------------------------------
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