Contacts of the helix formed by residues 177 - 194 (chain A) in PDB entry 3GNI
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 THR 177 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PRO* 6.2 4.5 - - + -
175A MET* 3.7 18.1 - - - +
176A SER* 1.3 73.8 + - - +
178A PHE* 1.3 60.6 + - - +
179A ASP* 3.4 15.3 - - - +
180A ILE* 3.3 22.3 + - + +
181A ALA 3.1 21.3 + - - -
64B PRO* 3.9 23.1 - - + -
135B ALA* 6.5 0.2 - - - -
136B THR* 3.6 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A MET 4.7 1.1 - - - -
176A SER 3.3 2.8 + - - +
177A THR* 1.3 70.2 - - - +
179A ASP* 1.3 60.6 + - - +
181A ALA* 4.3 10.5 - - + -
182A SER* 2.9 58.0 + - - -
222A ASN* 5.6 3.6 - - - -
224A VAL* 3.8 24.5 - - + -
228A GLN* 5.5 0.7 - - - -
104B LEU* 5.6 2.2 - - + -
112B VAL* 5.5 2.7 - - + -
116B GLN* 3.3 23.3 - - + -
119B LEU* 3.5 31.0 - - + -
136B THR* 2.9 19.2 + - - +
137B PHE* 3.8 13.9 - - - -
138B ILE* 3.7 27.4 - - + +
143B LEU* 3.5 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 5.0 11.4 - - + +
177A THR* 3.5 18.5 - - - -
178A PHE* 1.3 74.8 - - - +
180A ILE* 1.3 74.6 + - - +
182A SER* 3.8 3.5 - - - -
183A ASP* 3.2 22.9 + - - +
119B LEU* 4.2 29.4 - - + +
120B HIS* 5.9 0.2 - - - -
123B LYS* 3.5 33.8 + - + +
136B THR* 3.4 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TYR* 3.6 32.7 - - + +
137A PRO* 4.2 24.2 - - + +
140A ALA* 3.9 23.3 - - + -
141A LEU* 5.3 8.7 - - + +
175A MET* 3.5 25.6 - - + -
177A THR* 3.3 20.8 + - + +
178A PHE 3.3 0.2 - - - -
179A ASP* 1.3 94.1 + - - +
181A ALA* 1.3 59.2 + - - +
183A ASP* 3.2 7.8 + - + +
184A ALA* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A TYR 3.5 17.2 + - - +
173A VAL* 3.7 22.5 - - - +
174A GLU 4.7 0.2 - - - -
175A MET* 3.4 27.0 - - + +
177A THR 3.1 9.9 + - - +
178A PHE* 3.9 12.3 - - + +
180A ILE* 1.3 76.9 - - - +
182A SER* 1.3 56.0 + - - +
184A ALA* 3.4 1.9 + - - +
185A PHE* 2.9 29.7 + - - +
222A ASN* 6.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PHE* 2.9 54.3 + - - -
179A ASP* 3.8 6.3 - - - -
181A ALA* 1.3 72.4 - - - +
183A ASP* 1.3 60.7 + - - +
185A PHE* 3.4 7.2 + - - +
186A ALA* 3.0 28.8 + - - +
228A GLN* 5.2 3.9 + - - +
116B GLN* 3.2 27.2 + - - +
119B LEU* 5.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TYR* 2.7 33.7 + - + -
141A LEU* 4.4 19.6 - - + +
144A GLY* 3.4 8.1 - - - -
148A ARG* 2.9 37.8 + - - +
179A ASP 3.2 12.9 + - - +
180A ILE* 3.2 12.1 + - + +
182A SER* 1.3 78.9 - - - +
184A ALA* 1.3 59.5 + - - +
186A ALA* 3.3 7.1 + - - +
187A THR* 3.2 17.3 + - - -
120B HIS* 4.2 13.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
134A TYR* 3.5 25.3 + - + -
169A PHE* 3.6 9.3 - - + -
172A TYR* 3.8 34.1 - - + -
173A VAL* 4.0 4.0 - - + -
180A ILE 2.9 16.3 + - - +
181A ALA 3.7 4.3 - - - +
183A ASP* 1.3 72.1 - - - +
185A PHE* 1.3 61.5 + - - +
187A THR 3.3 0.9 + - - -
188A PHE* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A VAL* 3.6 28.8 - - + +
181A ALA 2.9 18.0 + - - +
182A SER* 3.9 4.5 - - - +
183A ASP 3.4 0.2 - - - -
184A ALA* 1.3 76.3 - - - +
186A ALA* 1.3 59.1 + - - +
188A PHE* 3.5 19.5 - + - +
189A LYS* 2.9 45.1 + - + +
214A TYR* 5.1 0.2 - - - -
217A LEU* 5.4 0.9 - - + -
225A THR* 6.2 1.1 - - + -
228A GLN* 3.6 62.4 - - + +
229A SER* 3.9 20.2 - - - -
232A LEU* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ARG* 4.5 17.0 - - - +
182A SER 3.0 14.2 + - - +
183A ASP* 3.4 13.2 - - - +
185A PHE* 1.3 79.4 - - - +
187A THR* 1.3 55.8 + - - +
189A LYS* 3.6 6.3 + - - +
190A ASP* 3.1 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TYR* 3.0 14.4 + - - -
144A GLY 4.3 1.0 + - - -
147A LEU* 3.8 19.3 - - + -
148A ARG* 2.8 36.2 + - - +
151A ILE* 3.6 19.5 - - + +
169A PHE* 3.7 22.2 - - + -
183A ASP 3.2 3.0 + - - -
184A ALA 3.7 7.4 - - - -
185A PHE 3.3 0.2 - - - -
186A ALA* 1.3 72.8 - - - +
188A PHE* 1.3 59.9 + - - +
190A ASP* 3.5 6.2 + - - +
191A LEU* 3.0 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A PHE* 3.8 26.0 - + - -
169A PHE* 3.7 33.0 - + + -
170A PHE* 4.0 34.8 - + - -
173A VAL* 4.4 6.3 - - + -
184A ALA 3.0 17.8 + - - +
185A PHE* 3.5 29.4 - + - +
187A THR* 1.3 77.9 - - - +
189A LYS* 1.3 62.3 + - - +
191A LEU* 3.4 8.5 + - - +
192A LEU* 3.2 48.0 + - + +
210A PHE* 4.1 3.6 - + - -
214A TYR* 4.1 11.7 - + - -
217A LEU* 4.6 5.6 - - + -
232A LEU* 3.9 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A PHE* 2.9 32.6 + - + +
186A ALA* 4.0 6.1 - - - +
188A PHE* 1.3 74.5 - - - +
190A ASP* 1.3 60.6 + - - +
192A LEU* 3.1 2.9 + - - +
193A THR* 2.6 42.3 + - - +
231A LYS* 5.5 6.3 - - - +
232A LEU* 3.8 34.5 - - + -
235A GLU* 4.2 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ARG* 5.0 11.4 - - + +
151A ILE* 3.4 21.9 - - + +
186A ALA 3.1 19.3 + - - +
187A THR* 3.6 6.1 - - - +
189A LYS* 1.3 76.7 - - - +
191A LEU* 1.3 57.5 + - - +
193A THR* 3.7 5.6 - - - -
194A ARG* 2.7 83.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
151A ILE* 3.7 33.0 - - + +
157A ALA* 4.0 28.9 - - + +
160A ILE* 3.8 15.9 - - + -
161A LEU* 3.6 32.3 - - + +
166A PHE* 4.0 12.1 - - + -
169A PHE* 3.6 33.9 - - + -
187A THR* 3.0 20.1 + - + +
188A PHE* 3.4 9.0 - - - +
190A ASP* 1.3 77.6 + - - +
192A LEU* 1.3 60.3 + - - +
194A ARG 4.6 1.9 + - - -
195A HIS* 4.9 5.0 + - - +
198A LEU* 5.7 0.5 - - - +
199A SER* 4.1 5.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 5.0 2.2 - - + -
166A PHE* 4.5 7.6 - - + -
188A PHE* 3.2 51.6 + - + +
189A LYS* 3.1 5.6 + - - +
191A LEU* 1.3 76.9 - - + +
193A THR* 1.3 60.1 + - + +
196A LYS* 5.5 0.5 - - - +
199A SER* 2.6 29.4 + - - +
202A PHE* 4.0 20.9 - - + -
203A LEU* 4.2 9.2 - - + -
210A PHE* 3.8 28.3 - - + -
232A LEU* 4.1 11.7 - - + -
236A LEU* 3.7 25.4 - - + +
242A ASN* 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LYS* 2.6 36.1 + - + +
190A ASP* 3.7 4.5 + - - -
192A LEU* 1.3 83.3 - - - +
194A ARG* 1.3 66.2 + - - +
195A HIS 3.8 0.7 - - - -
196A LYS* 3.1 39.1 + - - +
232A LEU* 3.8 25.6 - - + -
235A GLU* 5.9 4.3 - - + +
236A LEU* 4.1 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ARG* 5.6 0.8 + - - +
151A ILE 3.9 2.0 - - - +
152A ARG* 3.8 24.6 + - - +
190A ASP* 2.7 55.6 + - - +
191A LEU 4.6 0.6 + - - +
193A THR* 1.3 80.5 + - - +
195A HIS* 1.3 90.8 + - + +
196A LYS* 3.4 8.5 + - - +
342A CIT 3.3 53.8 + - - +
----------------------------------------------------------
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