Contacts of the helix formed by residues 186 - 208 (chain A) in PDB entry 3W8I
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 186 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A TYR* 3.6 11.2 - - - +
184A ASP* 3.1 39.2 + - - +
185A GLY* 1.3 75.4 - - - +
187A ALA* 1.3 64.2 + - - +
188A ILE* 3.3 12.5 + - + -
189A ASN* 3.6 30.8 + - - +
190A VAL* 4.1 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 3.6 26.0 - - + -
122A ASN* 6.1 0.7 - - - +
181A TYR* 4.0 13.9 - - + +
185A GLY 3.4 5.5 + - - +
186A LYS* 1.3 68.8 - - - +
188A ILE* 1.3 61.1 + - - +
189A ASN 3.2 2.5 - - - -
190A VAL* 2.9 22.9 + - - +
191A PHE* 3.0 29.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN* 3.3 35.2 - - - +
77A THR* 3.6 23.1 - - + +
186A LYS* 4.4 14.4 - - + -
187A ALA* 1.3 77.6 - - - +
189A ASN* 1.3 71.8 + - - +
191A PHE* 3.2 14.1 + - + +
192A VAL* 2.9 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A THR* 3.5 19.6 + - + +
180A THR* 5.2 7.3 - - + +
181A TYR* 6.2 0.9 - - + -
184A ASP* 4.5 8.9 + - - -
186A LYS* 3.6 33.0 + - - +
187A ALA 3.2 0.6 - - - -
188A ILE* 1.3 82.5 - - - +
190A VAL* 1.3 61.0 + - + +
192A VAL* 3.3 10.1 + - - +
193A SER* 2.9 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 4.4 10.8 - - + -
121A ILE* 4.2 10.8 - - + -
127A PHE* 4.3 11.7 - - + -
174A PHE* 4.0 14.0 - - + -
177A THR* 3.8 12.8 - - + -
178A LEU* 4.0 22.7 - - + -
181A TYR* 3.6 44.0 - - + -
186A LYS 4.1 0.9 - - - +
187A ALA* 2.9 11.8 + - - +
189A ASN* 1.3 73.8 - - + +
191A PHE* 1.3 62.9 + - + +
193A SER* 3.9 0.7 - - - -
194A ALA* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN* 4.7 0.7 - - - -
77A THR* 3.4 18.2 - - - +
78A GLU* 3.9 37.0 - - + -
81A LEU* 3.7 23.6 - - + +
117A ILE* 3.7 23.6 - - + -
118A PRO* 3.9 19.1 - - + -
121A ILE* 3.9 23.8 - - + -
187A ALA* 3.0 30.7 + - + -
188A ILE* 3.2 21.3 + - + +
190A VAL* 1.3 78.8 - - - +
192A VAL* 1.3 56.9 + - - +
194A ALA* 3.4 2.1 + - - +
195A ASN* 3.0 33.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
77A THR* 4.3 15.9 - - + +
188A ILE* 2.9 27.8 + - + +
189A ASN* 3.3 13.2 + - - +
191A PHE* 1.3 75.9 - - - +
193A SER* 1.3 63.4 + - - +
195A ASN* 3.2 8.7 + - - +
196A ARG* 2.9 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A TYR 5.2 1.6 - - - +
173A SER* 3.8 12.6 + - - -
174A PHE* 3.7 24.8 - - - +
177A THR* 2.8 30.8 + - - +
189A ASN 2.9 15.6 + - - -
190A VAL 3.9 0.9 - - - -
192A VAL* 1.3 78.1 - - - +
194A ALA* 1.3 58.1 + - - +
196A ARG* 3.3 9.7 + - - +
197A LEU* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 3.8 24.2 - - + -
114A LEU* 3.9 7.6 - - + +
117A ILE* 3.8 19.7 - - + -
174A PHE* 3.8 9.6 - - + -
190A VAL 2.9 19.2 + - - +
191A PHE 3.6 4.5 - - - +
193A SER* 1.3 77.1 - - - +
195A ASN* 1.3 62.9 + - - +
197A LEU* 3.2 6.0 + - - +
198A ILE* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET* 3.3 31.6 - - - +
77A THR* 3.1 34.4 + - - -
80A LEU* 3.7 22.5 - - + +
81A LEU* 3.2 29.3 + - - +
84A ALA* 4.4 0.2 - - - +
191A PHE 3.0 17.4 + - - +
192A VAL* 3.4 9.5 - - - +
194A ALA* 1.3 76.3 - - - +
196A ARG* 1.3 57.8 + - + +
198A ILE* 3.2 3.6 + - - +
199A HIS 2.9 23.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
170A TYR* 4.2 33.9 + - + -
192A VAL* 2.9 37.7 + - + +
193A SER* 3.3 11.0 + - - +
195A ASN* 1.3 75.7 - - + +
197A LEU* 1.3 57.4 + - - +
199A HIS* 3.3 8.4 + - - +
200A GLN* 2.9 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 4.6 2.2 - - + -
114A LEU* 3.9 23.6 - - + -
138A ILE* 3.9 29.4 - - + -
167A PHE* 3.7 21.1 - - + -
170A TYR* 4.0 12.5 - - + +
171A SER* 3.7 31.0 - - - +
174A PHE* 4.3 22.0 - - + -
193A SER 2.9 16.5 + - - +
194A ALA* 3.6 5.6 - - - +
196A ARG* 1.3 74.3 - - - +
198A ILE* 1.3 60.6 + - - +
200A GLN* 3.3 3.2 + - + +
201A THR* 2.9 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET* 3.7 12.8 - - + -
81A LEU* 3.8 28.5 - - + -
84A ALA* 3.7 34.5 - - + +
111A LYS* 3.7 29.6 - - + +
114A LEU* 3.6 24.9 - - + -
115A SER* 4.5 1.3 - - - +
194A ALA 2.9 14.7 + - - +
195A ASN* 3.4 8.7 - - - +
197A LEU* 1.3 73.7 - - - +
199A HIS* 1.3 60.1 + - - +
201A THR* 3.1 9.7 + - - -
202A ASN* 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A MET* 4.0 17.5 - - + +
18A VAL 3.9 12.3 - - - -
19A SER* 5.0 1.1 - - - -
20A MET* 3.9 17.3 - - + +
23A TYR* 2.8 44.2 + + - +
195A ASN 2.9 13.6 + - - +
196A ARG* 3.5 11.4 - - - +
198A ILE* 1.3 75.9 - - - +
200A GLN* 1.3 68.1 + - - +
202A ASN* 3.3 4.6 + - - +
203A LEU* 2.9 44.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLN* 4.1 6.6 + - - +
166A GLU* 3.8 21.1 + - - +
167A PHE* 4.4 16.3 + - + -
170A TYR* 3.5 50.3 + - + -
196A ARG* 2.9 21.0 + - - +
197A LEU* 3.6 7.0 - - - +
198A ILE 3.2 0.2 - - - -
199A HIS* 1.3 86.1 - - - +
201A THR* 1.3 60.4 + - - +
203A LEU* 3.2 27.8 + - - +
204A ILE* 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ALA* 3.6 33.7 - - + +
110A LEU* 3.4 24.3 - - + +
111A LYS* 3.9 21.2 - - + +
114A LEU* 5.4 0.2 - - - +
141A LEU* 5.3 3.8 - - + -
167A PHE* 3.6 9.1 - - + -
197A LEU 2.9 15.6 + - - -
198A ILE* 3.1 10.1 + - - -
200A GLN* 1.3 76.5 - - - +
202A ASN* 1.3 58.5 + - - +
204A ILE* 3.2 11.0 + - + +
205A LEU* 2.9 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A MET* 3.4 23.3 - - + +
23A TYR* 3.1 34.9 + - + +
84A ALA 5.3 0.8 + - - -
88A VAL* 4.4 8.7 - - - +
91A TYR* 4.7 5.6 - - + +
92A MET* 5.8 0.3 - - - +
111A LYS* 2.8 31.4 + - - +
198A ILE* 2.9 29.8 + - - +
199A HIS 3.5 7.4 - - - +
201A THR* 1.3 76.5 - - - +
203A LEU* 1.3 56.8 + - - +
205A LEU* 3.3 15.1 - - - +
206A GLN* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A MET* 3.6 31.9 - - + -
163A GLN* 3.5 25.6 - - - +
199A HIS* 2.9 29.3 + - + +
200A GLN* 3.2 39.0 + - - +
202A ASN* 1.3 75.2 - - - +
204A ILE* 1.3 59.1 + - - +
206A GLN* 3.9 10.8 - - - +
207A THR* 2.9 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 4.2 23.3 - - + -
107A ALA* 6.4 0.2 - - + -
141A LEU* 5.1 5.6 - - + -
145A VAL* 4.4 14.4 - - + -
163A GLN* 3.4 40.8 + - + +
164A LYS* 4.0 6.1 - - - +
167A PHE* 4.1 24.2 - - + -
200A GLN 2.9 18.3 + - - +
201A THR* 3.3 10.8 - - + +
203A LEU* 1.3 75.0 - - - +
205A LEU* 1.3 65.8 + - + +
207A THR* 3.3 1.4 + - - -
208A PHE* 2.9 50.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 3.8 12.1 - - + +
92A MET* 3.8 28.5 - - + -
93A ILE* 3.6 16.8 - - + +
103A LEU* 4.2 17.3 - - + +
104A ASN* 4.1 17.3 - - - +
107A ALA* 3.8 31.9 - - + -
111A LYS* 5.0 5.4 - - - -
201A THR* 2.9 21.9 + - + +
202A ASN* 3.3 24.2 - - - +
204A ILE* 1.3 77.9 - - + +
206A GLN* 1.3 62.0 + - - +
209A LYS* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A MET* 3.5 42.2 + - + +
90A GLU 5.7 0.2 - - - +
91A TYR* 3.5 44.3 + - + -
202A ASN 2.9 16.9 + - - +
203A LEU* 3.9 11.5 - - - +
204A ILE 3.3 0.2 - - - -
205A LEU* 1.3 73.0 - - - +
207A THR* 1.3 68.4 + - - +
209A LYS* 3.1 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 4.0 22.4 - - + +
163A GLN* 3.3 30.3 + - + +
203A LEU* 2.9 20.5 + - - +
204A ILE 3.9 2.9 - - - -
206A GLN* 1.3 77.5 + - - +
208A PHE* 1.3 71.0 + - + +
209A LYS 3.0 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 4.0 9.6 - - + +
95A ARG* 5.4 2.6 - - - -
100A PHE* 3.9 18.5 - + + -
103A LEU* 3.7 27.4 - - + -
145A VAL* 3.6 21.1 - - + -
148A VAL* 3.5 39.7 - - + -
149A PHE* 3.4 31.4 - + - -
160A LEU* 4.4 13.9 - - + -
163A GLN* 4.9 0.9 - - + -
204A ILE* 2.9 43.6 + - + +
205A LEU 3.8 0.7 - - - -
207A THR* 1.3 87.8 - - + +
209A LYS* 1.3 58.5 + - - +
----------------------------------------------------------
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