Contacts of the helix formed by residues 179 - 206 (chain A) in PDB entry 3H90
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 ASP 179 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A HIS* 4.4 19.4 + - + +
110A PRO* 5.8 4.0 - - - +
111A MET 6.0 0.2 + - - -
112A THR* 4.2 19.1 + - - -
161A ASN* 5.3 4.1 + - - +
164A ILE* 3.4 29.2 - - - +
178A ALA* 1.3 78.2 - - - +
180A ALA* 1.3 57.4 + - - +
182A PHE* 2.8 11.8 + - + +
183A ALA* 2.7 40.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLY 3.7 19.4 - - - +
104A HIS* 3.8 23.2 - - - +
105A LEU* 3.8 24.5 - - + -
106A ILE* 5.8 0.4 - - + -
178A ALA* 3.1 10.4 - - + +
179A ASP* 1.3 76.7 - - - +
181A LEU* 1.3 56.8 + - - +
183A ALA* 4.7 4.5 - - - +
184A LEU* 2.9 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ARG* 4.4 28.9 - - + +
178A ALA 4.1 8.0 + - - +
179A ASP 3.0 1.0 + - - -
180A ALA* 1.3 79.0 - - - +
182A PHE* 1.3 77.9 + - + +
184A LEU* 4.4 5.3 - - - +
185A GLY* 3.3 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ASN* 3.2 38.4 - - - +
163A ALA* 5.0 12.6 - - + -
178A ALA 5.5 3.1 - - - -
179A ASP* 2.8 9.1 + - - +
181A LEU* 1.3 95.2 - - + +
183A ALA* 1.3 59.6 + - - +
184A LEU 3.1 1.3 - - - -
185A GLY* 3.0 2.8 + - - -
186A ILE* 3.0 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 3.0 39.6 - - + +
100A THR* 5.7 1.6 - - + -
101A GLY* 4.4 5.8 - - - +
104A HIS* 4.9 8.5 - - + +
179A ASP* 2.7 32.0 + - + +
180A ALA* 4.5 2.5 - - - +
182A PHE* 1.3 72.1 - - - +
184A LEU* 1.3 58.0 + - - +
186A ILE* 4.4 8.5 - - - +
187A GLY 3.7 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU 4.5 1.3 - - - -
98A PHE* 3.8 23.4 - - + -
101A GLY* 3.8 21.7 - - - +
102A ILE* 3.6 32.1 - - + +
105A LEU* 5.8 2.5 - - + -
180A ALA 2.9 21.0 + - - +
181A LEU* 4.7 4.7 - - - +
183A ALA* 1.3 76.9 - - - +
185A GLY* 1.3 65.6 + - - +
187A GLY* 3.2 10.7 + - - -
188A ILE* 3.2 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU 3.3 12.5 + - - -
182A PHE* 3.0 6.7 + - - -
184A LEU* 1.3 77.2 - - - +
186A ILE* 1.3 64.0 + - - +
188A ILE* 3.3 23.6 + - - +
189A TYR* 3.3 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 4.7 15.3 - - + -
156A SER* 4.6 5.8 - - - +
159A MET* 3.5 58.3 - - + +
161A ASN* 5.4 7.2 - - - +
182A PHE* 3.0 31.6 + - + +
183A ALA* 4.5 7.4 - - - +
185A GLY* 1.3 73.7 - - - +
187A GLY* 1.3 59.1 + - - +
189A TYR* 3.2 5.8 + - - -
190A ILE* 2.9 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ALA* 3.5 25.6 - - - +
97A LEU* 4.7 4.0 - - - +
98A PHE* 4.1 13.2 - - - +
183A ALA 3.7 9.5 + - - -
184A LEU 3.2 9.1 + - - -
186A ILE* 1.3 80.3 - - - +
188A ILE* 1.3 59.6 + - - +
191A LEU* 3.2 26.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
98A PHE* 3.7 22.0 - - + -
184A LEU* 3.2 37.9 + - + +
185A GLY* 3.9 11.9 - - - +
186A ILE 3.3 0.4 - - - -
187A GLY* 1.3 74.6 - - - +
189A TYR* 1.3 64.2 + - - +
191A LEU* 3.9 9.2 - - + +
192A TYR* 3.1 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 5.8 0.9 - - + -
155A GLN* 5.8 1.7 + - + -
159A MET* 4.1 21.8 - - + -
185A GLY 3.3 9.6 + - - +
186A ILE* 3.2 7.5 + - - +
188A ILE* 1.3 79.8 - - - +
190A ILE* 1.3 78.9 + - + +
192A TYR* 3.3 14.0 + + - +
193A SER* 2.7 48.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ILE* 4.0 23.1 - - + -
94A ALA* 4.0 13.7 - - + -
152A LEU* 4.0 21.5 - - + -
155A GLN* 4.8 3.8 - - + -
156A SER* 3.2 37.0 - - - +
159A MET* 4.8 5.6 - - + -
186A ILE* 2.9 33.4 + - + +
187A GLY* 5.3 0.2 - - - -
189A TYR* 1.3 95.6 - - + +
191A LEU* 1.3 60.4 + - - +
193A SER* 3.9 1.8 - - - -
194A ALA* 2.8 28.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
91A SER* 3.4 37.0 + - - +
94A ALA* 3.5 13.2 - - + +
95A LEU* 4.4 24.2 - - + -
98A PHE* 6.2 4.9 - - + -
187A GLY 3.2 22.5 + - - +
188A ILE* 3.9 8.7 - - + +
190A ILE* 1.3 75.4 - - - +
192A TYR* 1.3 58.7 + - - +
194A ALA* 3.4 2.8 + - - +
195A LEU* 2.9 49.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE* 3.1 17.8 + - + +
189A TYR* 3.4 14.1 - + - +
191A LEU* 1.3 82.7 - - + +
193A SER* 1.3 61.6 + - - +
195A LEU* 3.3 9.4 + - + +
196A ARG* 3.0 55.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
152A LEU* 3.7 23.4 - - - +
189A TYR* 2.7 37.5 + - - -
190A ILE* 3.2 13.0 + - - -
192A TYR* 1.3 81.6 - - - +
194A ALA* 1.3 55.9 + - - +
196A ARG* 3.9 4.3 - - - +
197A MET* 3.1 26.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
87A SER* 3.4 18.2 - - - +
90A ILE* 3.8 8.1 - - + -
91A SER* 3.7 31.2 - - - +
152A LEU* 3.4 19.9 - - + +
190A ILE 2.8 21.0 + - - +
191A LEU 3.9 0.4 - - - +
193A SER* 1.3 71.1 - - - +
195A LEU* 1.3 60.3 + - - +
197A MET* 3.3 3.4 - - - +
198A GLY* 2.9 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A SER* 4.2 11.8 + - - +
191A LEU* 2.9 44.3 + - + +
192A TYR* 3.3 9.8 + - + +
194A ALA* 1.3 77.0 - - - +
196A ARG* 1.3 57.3 + - - +
198A GLY* 4.0 0.9 - - - -
199A TYR* 3.1 27.6 + - + +
----------------------------------------------------------
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 TYR* 3.0 44.6 + - + +
193A SER* 3.9 5.6 - - - +
195A LEU* 1.3 72.6 - - - +
197A MET* 1.3 67.2 + - - +
199A TYR* 3.2 42.3 + - - +
200A GLU* 3.1 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA* 4.3 8.7 - - + +
87A SER* 4.0 14.4 - - - -
90A ILE* 6.5 0.2 - - + -
145A GLN* 3.4 41.5 - - - +
148A ARG* 3.6 35.9 - - - +
149A ALA* 3.7 30.1 - - + -
152A LEU* 4.2 13.2 - - + -
193A SER 3.1 19.8 + - - +
194A ALA* 3.3 7.0 - - - +
196A ARG* 1.3 75.2 - - - +
198A GLY* 1.3 62.0 + - - +
200A GLU* 3.3 12.8 + - - +
201A ALA* 3.2 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 4.4 3.6 - - - -
87A SER* 3.2 26.0 - - - -
194A ALA 2.9 15.0 + - - -
195A LEU 4.0 1.3 - - - -
197A MET* 1.3 71.1 - - - +
199A TYR* 1.3 58.4 + - - +
201A ALA* 2.8 27.9 + - - +
202A VAL* 2.9 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 3.1 19.4 + - + +
196A ARG* 3.2 41.7 + - - +
198A GLY* 1.3 75.3 - - - +
200A GLU* 1.3 64.9 + - + +
202A VAL* 3.7 12.7 + - + +
203A GLN* 3.0 63.5 + - + +
208A ARG* 4.1 12.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLN* 3.7 4.8 - - - +
148A ARG* 2.9 40.6 + - - +
196A ARG* 3.1 37.4 + - + +
197A MET* 3.5 8.9 - - - +
199A TYR* 1.3 82.5 - - + +
201A ALA* 1.3 56.6 + - - +
203A GLN* 3.3 8.5 + - - +
204A SER* 2.6 32.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A SER* 3.5 23.6 - - - +
83A ALA* 4.0 9.0 - - + -
84A LEU* 3.7 19.5 - - + +
145A GLN* 3.5 11.8 + - - +
197A MET 3.2 10.2 + - - +
198A GLY* 2.8 11.5 + - - +
200A GLU* 1.3 72.9 - - - +
202A VAL* 1.3 65.1 + - - +
203A GLN 3.0 1.6 - - - -
204A SER* 3.0 6.4 + - - -
205A LEU* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.8 23.1 - - + -
198A GLY 2.9 17.7 + - - +
199A TYR* 3.8 14.8 - - + +
201A ALA* 1.3 74.6 - - - +
203A GLN* 1.3 63.6 + - - +
205A LEU* 3.0 13.0 + - - +
206A LEU* 2.7 49.8 + - + +
81C LEU* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A TYR* 3.0 53.0 + - + +
200A GLU* 3.5 10.5 - - - +
201A ALA 3.0 0.4 - - - -
202A VAL* 1.3 86.4 - - - +
204A SER* 1.3 56.3 + - - +
206A LEU* 2.9 27.1 - - - +
208A ARG* 2.9 56.1 + - - +
62C TYR* 5.3 0.8 + - - -
71C HIS* 2.6 36.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS* 3.4 22.6 - - - +
80A SER* 3.7 15.7 - - - -
145A GLN* 2.7 18.4 + - - -
200A GLU 2.6 23.4 + - - -
201A ALA 3.1 3.4 + - - -
203A GLN* 1.3 71.8 - - - +
205A LEU* 1.3 59.8 + - - +
206A LEU 3.0 13.4 - - - +
207A ASP* 4.0 2.3 - - - +
208A ARG* 4.9 3.1 - - - +
238A GLN* 4.4 15.0 - - - +
239A SER* 6.3 0.2 - - - -
240A GLY 6.2 0.9 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
77A LYS* 4.0 22.6 + - + +
80A SER* 3.8 25.8 - - - +
81A LEU* 3.5 36.3 - - + -
84A LEU* 4.0 20.9 - - + -
201A ALA 2.9 15.7 + - - +
202A VAL* 3.4 9.2 - - - +
204A SER* 1.3 76.5 - - - +
206A LEU* 1.3 62.7 + - - +
77C LYS* 3.4 31.8 + - - +
81C LEU* 3.8 27.1 - - + -
205C LEU* 4.4 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A VAL* 2.7 27.8 + - + +
203A GLN* 2.9 42.8 - - - +
204A SER 3.0 9.9 - - - -
205A LEU* 1.3 71.0 - - - +
207A ASP* 1.3 62.4 + - - +
208A ARG 2.7 9.0 + - - -
62C TYR* 4.2 21.5 - - + +
71C HIS* 4.1 17.5 - - + +
74C GLY 5.8 1.3 - - - +
75C HIS* 5.0 7.2 - - - +
77C LYS* 4.1 6.5 - - + -
78C ALA* 3.9 26.0 - - + +
81C LEU* 3.6 25.8 - - + -
----------------------------------------------------------
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