Contacts of the helix formed by residues 176 - 194 (chain A) in PDB entry 3O2T
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 ASN 176 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A VAL* 3.7 34.3 - - + +
127A LYS* 3.5 13.3 + - - +
174A SER* 2.9 10.9 + - - +
175A ASP* 1.3 78.4 - - - +
177A ASP* 1.3 65.5 + - - +
178A GLY 3.0 8.2 + - - -
179A ILE* 2.9 36.5 + - + +
180A ARG* 3.0 25.2 + - - +
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Residues in contact with ASP 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ASP 3.8 3.4 + - - -
176A ASN* 1.3 72.7 - - - +
178A GLY* 1.3 58.2 + - - +
180A ARG* 3.0 21.7 + - - +
181A THR* 3.0 23.4 + - - -
249A SER* 2.6 29.0 + - - -
251A ILE* 3.5 20.1 - - - +
252A ASN* 3.0 26.6 + - - +
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Residues in contact with GLY 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LYS* 4.0 14.6 - - - -
176A ASN* 3.0 9.5 + - - -
177A ASP* 1.3 76.5 + - - +
179A ILE* 1.3 64.2 + - - +
181A THR* 3.2 7.3 + - - -
182A HIS* 2.8 36.1 + - - -
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Residues in contact with ILE 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A VAL* 3.7 31.9 - - + +
126A VAL* 3.9 23.1 - - + -
127A LYS* 4.0 20.0 - - + -
130A ILE* 4.0 10.5 - - + +
171A LEU* 3.8 25.6 - - + -
174A SER* 3.6 33.9 - - - +
176A ASN* 2.9 17.0 + - + +
178A GLY* 1.3 75.2 - - - +
180A ARG* 1.3 58.8 + - - +
182A HIS* 3.2 4.2 + - - +
183A ALA* 2.8 27.0 + - - +
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Residues in contact with ARG 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU 3.8 11.2 - - - +
172A LEU* 3.4 25.4 - - - +
173A ASP 4.8 0.2 - - - -
174A SER 2.9 41.3 + - - +
175A ASP* 3.5 20.4 + - - +
176A ASN 3.0 10.3 + - - +
177A ASP* 3.0 40.7 + - - +
178A GLY 3.2 0.2 - - - -
179A ILE* 1.3 75.6 - - - +
181A THR* 1.3 64.0 + - - +
183A ALA* 3.2 4.0 + - - +
184A ILE* 2.9 27.8 + - - +
242A PHE* 4.1 10.5 - - + -
245A HIS* 5.6 1.6 - - - -
248A ILE* 4.6 10.8 - - - +
249A SER* 4.3 8.3 - - - +
252A ASN* 2.8 27.2 + - - +
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Residues in contact with THR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ASP* 3.0 8.9 + - - -
178A GLY* 3.2 10.4 + - - -
180A ARG* 1.3 76.0 - - - +
182A HIS* 1.3 68.3 + - + +
184A ILE* 3.3 19.8 + - - +
185A LYS* 3.4 16.4 + - + +
251A ILE* 4.4 18.7 - - + +
252A ASN* 2.9 25.7 + - - +
255A THR* 3.8 23.7 - - + +
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Residues in contact with HIS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LYS* 3.5 47.2 - - + +
130A ILE* 3.5 25.9 - - + +
131A LEU* 3.6 33.2 - - + +
134A THR* 4.8 0.3 + - - -
178A GLY* 2.8 29.6 + - - +
179A ILE* 3.7 7.0 - - - +
181A THR* 1.3 82.7 - - + +
183A ALA* 1.3 62.7 + - - +
185A LYS* 3.2 9.3 + - - +
186A PHE 3.1 17.3 + - - -
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Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ILE* 4.1 1.9 - - + +
168A ILE* 3.7 35.7 - - + +
171A LEU* 3.8 20.4 - - + -
172A LEU* 3.9 8.1 - - + +
179A ILE 2.8 17.0 + - - +
180A ARG 3.6 4.9 - - - +
182A HIS* 1.3 73.9 - - - +
184A ILE* 1.3 66.5 + - - +
186A PHE* 3.2 1.6 + - - +
187A VAL* 2.9 27.9 + - - +
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LEU* 3.7 19.7 - - + +
180A ARG 2.9 20.6 + - - +
181A THR* 3.5 16.4 - - - +
182A HIS 3.3 0.4 - - - -
183A ALA* 1.3 75.6 - - - +
185A LYS* 1.3 58.8 + - - +
187A VAL* 3.2 4.2 + - - +
188A GLU* 2.8 26.5 + - - +
239A LEU* 4.1 11.0 - - + +
242A PHE* 3.4 23.3 - - + -
252A ASN* 3.4 30.1 - - + +
255A THR* 3.9 14.1 - - + -
256A ALA* 3.9 13.7 - - + +
259A SER* 3.4 22.0 - - - +
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Residues in contact with LYS 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 6.4 2.0 - - + -
134A THR* 4.1 12.9 - - + +
181A THR* 3.4 14.6 + - + +
182A HIS* 3.2 9.4 + - - +
183A ALA 3.2 0.4 - - - -
184A ILE* 1.3 74.4 - - - +
186A PHE* 1.3 64.6 + - - +
188A GLU* 2.7 32.3 + - - +
189A GLY* 3.1 17.5 + - - -
255A THR* 3.9 18.1 + - + -
258A GLY 5.4 0.8 - - - -
259A SER* 3.7 15.3 + - - +
262A ASN* 3.8 12.5 - - - +
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Residues in contact with PHE 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A EDO 3.0 29.7 + - - -
130A ILE* 4.0 2.9 - - + -
133A MET* 3.5 30.5 - - + -
134A THR* 3.4 29.7 + - - +
137A TYR* 4.1 6.7 - + + -
165A ALA* 3.6 46.9 - - + -
168A ILE* 3.4 34.1 - - + -
182A HIS 3.1 11.0 + - - +
183A ALA 3.6 7.0 - - - +
185A LYS* 1.3 75.6 - - - +
187A VAL* 1.3 65.9 + - + +
189A GLY 3.1 0.5 + - - -
190A LEU* 2.9 36.2 + - + -
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Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ILE 4.6 0.7 - - - +
169A ILE* 4.0 34.8 - - + +
172A LEU* 4.2 16.2 - - + -
183A ALA 2.9 20.7 + - - +
184A ILE* 3.7 5.8 - - - +
186A PHE* 1.3 81.3 - - + +
188A GLU* 1.3 67.2 + - - +
190A LEU* 3.1 5.3 + - - +
191A ILE* 2.9 40.6 + - + +
235A ALA* 3.8 22.9 - - + +
239A LEU* 4.4 12.8 - - + -
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Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ILE 2.8 16.9 + - - +
185A LYS* 2.7 36.6 + - - +
186A PHE 3.3 0.2 - - - -
187A VAL* 1.3 76.8 - - - +
189A GLY* 1.3 63.1 + - - +
191A ILE* 3.3 2.6 + - - +
192A VAL* 3.1 27.0 + - + +
207A GLN* 5.8 0.7 + - - -
239A LEU* 5.0 1.3 - - - +
259A SER* 2.8 37.8 + - - +
262A ASN* 2.9 31.5 + - + +
263A ILE* 4.1 17.5 - - + -
266A GLN* 4.4 6.4 + - - +
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Residues in contact with GLY 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A EDO 3.4 20.9 - - - -
134A THR* 5.5 2.2 - - - -
185A LYS 3.1 6.5 + - - -
186A PHE 3.1 4.4 + - - -
188A GLU* 1.3 80.4 - - - +
190A LEU* 1.3 54.6 + - - +
192A VAL* 3.9 4.6 - - - +
193A THR* 2.7 37.2 + - - -
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A EDO 3.5 4.0 - - - -
137A TYR* 3.5 44.2 - - + +
165A ALA* 4.3 9.6 - - + -
169A ILE* 3.7 35.0 - - + -
186A PHE* 2.9 25.5 + - + +
187A VAL* 3.1 8.7 + - - +
189A GLY* 1.3 73.9 - - - +
191A ILE* 1.3 66.0 + - - +
193A THR* 3.3 1.9 + - - -
194A LEU* 2.9 46.3 + - + +
231A GLU* 4.5 10.5 - - + +
232A GLY* 5.4 0.4 - - - -
235A ALA* 4.0 13.2 - - + -
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Residues in contact with ILE 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A VAL* 2.9 34.2 + - + +
188A GLU 3.3 4.2 + - - +
190A LEU* 1.3 78.3 - - - +
192A VAL* 1.3 61.1 + - - +
194A LEU 3.6 1.6 - - - -
195A SER* 2.8 26.9 + - - -
232A GLY* 3.8 12.1 - - - +
235A ALA* 3.7 9.0 - - + +
236A LEU* 3.5 44.6 - - + +
239A LEU* 4.1 7.6 - - + -
263A ILE* 3.8 35.7 - - + -
267A ARG* 5.8 0.2 - - + -
270A PHE* 4.0 22.9 - - + -
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A GLU* 3.1 20.3 + - + +
189A GLY* 4.1 4.7 - - - +
191A ILE* 1.3 73.4 - - + +
193A THR* 1.3 67.0 + - - +
195A SER* 3.2 10.2 - - - +
207A GLN* 4.9 7.0 - - - +
263A ILE* 4.1 20.2 - - + +
266A GLN* 3.5 31.4 - - + +
267A ARG* 2.8 63.0 + - + +
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Residues in contact with THR 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A EDO 3.5 14.5 - - - -
137A TYR* 4.1 13.9 - - + -
138A LYS* 4.0 13.0 - - + +
141A LEU* 3.8 27.6 - - + +
189A GLY 2.7 22.5 + - - -
190A LEU* 3.8 5.2 - - - -
192A VAL* 1.3 78.3 - - - +
194A LEU* 1.3 59.2 + - + +
195A SER 3.3 0.2 - - - -
210A ASP* 6.1 0.3 - - - +
211A ILE* 4.0 27.6 + - + +
212A SER* 3.4 3.3 - - - -
213A LEU* 3.3 23.4 + - - -
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Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A TYR* 3.6 26.7 - - + +
141A LEU* 3.9 23.6 - - + -
190A LEU* 2.9 32.1 + - + +
191A ILE 3.6 2.5 - - - -
192A VAL 3.2 0.2 - - - -
193A THR* 1.3 79.0 - - + +
195A SER* 1.3 59.3 + - - +
213A LEU* 3.7 20.6 - - + +
228A LEU* 3.6 37.9 - - + +
229A TRP* 4.1 4.0 - - - +
231A GLU* 3.6 37.0 - - + -
232A GLY* 3.8 14.6 - - - +
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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
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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) + - + + + + + -
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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