Contacts of the helix formed by residues 172 - 192 (chain A) in PDB entry 2NL9
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 172 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ASP* 1.3 62.7 + - - +
174A LEU 3.5 2.4 + - - -
175A TYR* 3.0 28.1 + - + +
176A ARG* 2.9 30.0 + - - +
303A ARG* 2.7 45.8 + - - -
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Residues in contact with ASP 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP* 1.3 76.0 + - - +
174A LEU* 1.3 59.2 + - - +
176A ARG* 3.3 10.8 + - - +
177A GLN* 2.8 34.0 + - - +
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP* 3.3 1.6 + - - -
173A ASP* 1.3 79.4 - - - +
175A TYR* 1.3 55.3 + - - +
177A GLN* 4.1 18.4 - - - +
178A SER* 2.7 50.3 + - - +
299A VAL* 4.3 7.2 - - + -
303A ARG* 3.8 24.0 - - - +
306A LEU* 3.9 32.1 - - + -
307A VAL* 4.0 23.3 - - + +
311A GLY* 4.4 14.8 - - - -
312A TRP* 4.4 8.3 - - + +
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Residues in contact with TYR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP* 3.0 35.2 + - + +
174A LEU* 1.3 76.5 - - - +
176A ARG* 1.3 63.1 + - + +
178A SER* 3.2 2.1 + - - -
179A LEU* 2.8 60.1 + - + +
292A GLU* 3.9 22.0 + - - +
295A THR* 3.5 26.0 - - + -
296A ASP* 4.5 13.0 - - + -
299A VAL* 4.1 21.0 - - + +
303A ARG* 5.8 0.2 - - - -
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Residues in contact with ARG 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP 2.9 17.2 + - - +
173A ASP* 3.8 10.8 - - - +
175A TYR* 1.3 85.0 - - + +
177A GLN* 1.3 58.5 + - - +
179A LEU* 3.4 5.5 + - - +
180A GLU* 2.9 42.3 + - - +
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Residues in contact with GLN 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASP 2.8 20.0 + - - +
174A LEU* 3.8 16.0 - - - +
176A ARG* 1.3 73.9 - - - +
178A SER* 1.3 62.9 + - - +
180A GLU* 3.3 7.5 + - - +
181A ILE* 3.1 44.0 + - + +
203A GLY 5.0 5.2 + - - -
205A ALA* 4.4 9.4 - - - +
206A GLY* 4.1 19.3 + - - -
310A ARG 5.9 0.2 + - - -
311A GLY* 5.6 0.6 - - - -
312A TRP* 3.7 26.2 - - + +
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Residues in contact with SER 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 2.7 27.7 + - - +
175A TYR 3.6 1.8 - - - -
177A GLN* 1.3 73.8 - - - +
179A LEU* 1.3 61.7 + - - +
181A ILE* 3.3 1.4 + - - +
182A ILE* 2.9 36.5 + - - +
295A THR* 3.8 6.1 - - - -
298A LEU* 6.3 0.2 - - - -
299A VAL* 3.5 27.0 - - - +
306A LEU* 5.4 1.2 - - - +
312A TRP* 2.8 34.9 + - - +
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 2.8 44.1 + - + +
176A ARG* 3.7 5.6 - - - +
178A SER* 1.3 77.9 - - - +
180A GLU* 1.3 58.8 + - - +
183A SER* 2.8 56.3 + - - +
288A GLU* 3.6 11.2 - - - +
291A ALA* 3.9 1.1 - - + +
292A GLU* 3.8 31.0 - - + +
295A THR* 3.6 25.7 - - + +
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Residues in contact with GLU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ARG* 2.9 34.6 + - - +
177A GLN* 3.5 8.1 - - - +
179A LEU* 1.3 76.8 - - - +
181A ILE* 1.3 66.1 + - + +
183A SER* 4.0 3.0 - - - -
184A ARG* 2.9 51.0 + - + +
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Residues in contact with ILE 181 (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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177A GLN* 3.1 25.6 + - + +
178A SER 3.7 3.4 - - - +
180A GLU* 1.3 79.4 - - + +
182A ILE* 1.3 62.9 + - - +
184A ARG* 4.8 2.2 - - - -
185A TYR* 3.0 22.9 + - - +
206A GLY* 4.0 20.9 - - - +
209A ALA* 3.6 23.1 - - + -
210A LEU* 3.7 24.1 - - + +
213A LEU* 3.8 21.3 - - + -
312A TRP* 3.6 42.6 - - + -
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Residues in contact with ILE 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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178A SER* 2.9 18.7 + - - +
181A ILE* 1.3 78.1 - - + +
183A SER* 1.3 58.4 + - - +
185A TYR* 3.4 4.2 + - - +
186A LEU* 2.9 45.3 + - + +
213A LEU* 4.6 1.6 - - + -
268A ILE* 3.9 22.9 - - + -
291A ALA* 4.1 16.8 - - + +
294A ILE* 4.2 12.6 - - + -
295A THR* 3.5 31.6 - - + +
298A LEU* 3.9 28.0 - - + -
312A TRP* 4.2 16.2 - - + -
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Residues in contact with SER 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LEU* 2.8 32.4 + - - +
180A GLU* 4.0 3.4 - - - -
182A ILE* 1.3 74.8 - - - +
184A ARG* 1.3 58.1 + - - +
186A LEU 3.4 0.5 + - - -
187A ARG* 2.9 39.9 + - - +
287A ILE* 3.5 4.8 - - - +
288A GLU* 2.6 39.0 + - - -
291A ALA* 3.2 14.7 - - - +
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Residues in contact with ARG 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A GLU* 2.9 43.3 + - + +
181A ILE 3.9 0.4 - - - +
183A SER* 1.3 76.8 - - - +
185A TYR* 1.3 57.2 + - - +
187A ARG* 3.7 16.1 - - - +
188A GLU* 2.9 51.8 + - + +
207A ARG* 6.0 4.8 - - - +
210A LEU* 3.5 31.7 - - + +
214A ARG* 3.9 9.1 - - - +
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Residues in contact with TYR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE 3.0 10.8 + - - +
182A ILE 3.8 2.2 - - - +
184A ARG* 1.3 76.8 - - - +
186A LEU* 1.3 65.0 + - + +
188A GLU* 3.2 6.1 + - - +
189A GLN* 2.9 53.8 + - + +
210A LEU* 3.8 8.2 - - + +
213A LEU* 3.5 45.5 - - + -
214A ARG* 3.7 31.0 - - + -
217A GLY* 3.0 20.0 + - - -
218A ASP* 2.8 22.4 + - - -
221A GLN* 4.5 2.4 + - - -
268A ILE* 3.8 17.5 - - + -
269A SER* 4.3 10.7 + - - -
272A ALA* 3.7 20.9 - - + -
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ILE* 2.9 29.5 + - + +
183A SER 3.8 3.1 - - - +
185A TYR* 1.3 83.1 - - + +
187A ARG* 1.3 57.5 + - - +
189A GLN* 3.3 2.6 + - - +
190A ALA* 2.9 31.8 + - - +
268A ILE* 3.9 11.9 - - + +
271A GLY 4.1 6.5 - - - +
272A ALA* 3.8 34.5 - - + +
275A ALA* 4.2 6.3 - - + +
287A ILE* 4.0 15.3 - - + +
290A LEU* 4.2 10.1 - - + -
291A ALA* 3.8 34.1 - - + +
294A ILE* 4.0 14.4 - - + -
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Residues in contact with ARG 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A SER* 2.9 34.8 + - - +
184A ARG* 3.7 15.2 - - - +
186A LEU* 1.3 76.1 - - - +
188A GLU* 1.3 63.4 + - - +
190A ALA* 4.6 0.4 - - - -
191A THR* 2.8 48.5 + - + +
193A SER* 5.6 1.8 - - - +
279A LYS* 5.7 1.6 - - - -
286A CYS* 5.7 2.8 - - - -
287A ILE* 3.9 23.3 - - + +
288A GLU* 2.9 28.5 + - - +
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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 ARG* 2.9 36.2 + - - +
185A TYR* 3.6 7.7 - - + +
187A ARG* 1.3 74.5 - - + +
189A GLN* 1.3 63.2 + - + +
192A GLY* 2.8 35.2 + - - +
193A SER 3.3 24.9 - - - +
210A LEU* 3.9 5.2 - - - +
214A ARG* 2.6 55.5 + - - +
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Residues in contact with GLN 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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185A TYR* 2.9 37.8 + - + +
186A LEU 3.6 4.0 - - - +
188A GLU* 1.3 82.5 - - - +
190A ALA* 1.3 61.8 + - - +
191A THR 3.5 0.2 + - - -
192A GLY* 3.7 4.7 + - - -
214A ARG* 6.0 0.5 - - - +
218A ASP* 3.0 31.1 + - - +
221A GLN* 4.4 15.2 + - - +
272A ALA* 3.6 31.0 + - + +
276A LYS* 3.7 29.4 - - + +
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Residues in contact with ALA 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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186A LEU 2.9 18.1 + - - +
187A ARG 4.0 2.2 - - - +
189A GLN* 1.3 77.7 - - - +
191A THR* 1.3 59.6 - - - +
275A ALA 3.6 27.8 - - - +
276A LYS* 3.7 16.1 - - - +
279A LYS* 3.7 30.9 - - + +
283A GLN* 4.6 4.3 + - - -
287A ILE* 3.7 11.7 - - + -
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Residues in contact with THR 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 ARG* 2.8 36.6 + - + +
190A ALA* 1.3 79.4 - - + +
192A GLY* 1.3 54.0 + - - +
193A SER* 2.6 39.2 + - - +
279A LYS* 3.7 28.9 - - + +
283A GLN* 5.5 4.5 - - - +
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Residues in contact with GLY 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* 2.8 16.8 + - - +
189A GLN 3.7 5.0 + - - -
190A ALA 3.6 2.0 - - - -
191A THR* 1.3 75.8 - - - +
193A SER* 1.3 60.7 + - - +
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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
------------------------------------------------------------
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