Contacts of the helix formed by residues 177 - 196 (chain A) in PDB entry 1WYI
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).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A THR* 4.6 8.7 - - - +
176A ALA* 1.3 76.8 - - - +
178A PRO* 1.3 75.5 - - - +
179A GLN* 3.3 15.1 + - - +
180A GLN* 2.8 39.0 + - - +
181A ALA* 3.0 18.9 + - - +
208A TYR* 5.1 0.6 + - - -
220A LEU* 4.9 1.6 - - - -
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Residues in contact with PRO 178 (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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176A ALA 4.6 0.7 - - - +
177A THR* 1.3 88.3 - - - +
179A GLN* 1.3 77.9 + - - +
181A ALA* 3.1 3.3 - - + +
182A GLN* 3.0 21.5 + - - +
219A GLU* 4.5 20.6 - - + +
220A LEU* 3.5 44.4 - - + +
223A GLN* 3.6 22.8 - - - +
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Residues in contact with GLN 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A THR* 3.3 15.7 + - - +
178A PRO* 1.3 94.9 - - - +
180A GLN* 1.3 57.5 + - - +
181A ALA 2.9 4.7 + - - -
182A GLN* 3.1 5.7 + - - +
183A GLU* 2.9 27.1 + - - +
223A GLN* 4.4 14.5 + - - +
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Residues in contact with GLN 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ARG* 3.8 21.9 + - - +
164A TYR* 5.3 0.5 - - - -
168A TRP* 3.1 19.2 - - + -
175A THR 3.1 9.7 - - - +
176A ALA* 2.9 14.7 - - + -
177A THR* 2.8 45.4 + - - +
179A GLN* 1.3 79.2 - - - +
181A ALA* 1.3 62.4 + - - +
183A GLU* 3.5 17.9 - - - +
184A VAL* 3.5 23.9 + - - +
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TYR* 5.3 2.9 - - - -
176A ALA* 6.2 0.9 - - + -
177A THR 3.0 12.8 + - - +
178A PRO* 3.1 17.5 - - + +
179A GLN 2.9 0.2 - - - -
180A GLN* 1.3 78.9 - - - +
182A GLN* 1.3 63.4 + - - +
184A VAL* 3.2 6.7 + - - +
185A HIS* 3.0 29.4 + - - -
208A TYR* 3.8 33.7 - - + -
220A LEU* 4.3 6.5 - - + -
226A VAL* 4.7 6.7 - - + -
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Residues in contact with GLN 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PRO 3.0 5.8 + - - +
179A GLN* 3.4 7.9 - - - +
181A ALA* 1.3 74.2 - - - +
183A GLU* 1.3 54.8 + - - +
185A HIS* 3.0 1.6 + - - +
186A GLU* 2.7 63.8 + - - +
223A GLN* 3.3 27.9 - - + +
224A PRO* 3.1 23.5 - - + +
225A ASP* 2.5 56.3 + - - +
226A VAL* 4.0 8.2 + - - +
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Residues in contact with GLU 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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134A ARG* 3.8 21.3 + - - -
139A THR* 5.5 3.3 - - - +
140A GLU* 5.7 1.8 - - - +
179A GLN 2.9 17.2 + - - +
180A GLN* 3.5 19.5 - - - +
182A GLN* 1.3 76.3 - - - +
184A VAL* 1.3 61.2 + - + +
186A GLU* 3.2 30.8 - - - +
187A LYS* 3.3 25.2 - - + +
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Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ARG* 3.9 13.9 - - - +
139A THR* 4.1 15.3 - - + -
143A VAL* 5.1 0.9 - - + -
164A TYR* 3.5 56.3 - - + +
180A GLN 3.5 13.2 - - - +
181A ALA 3.2 8.4 + - - +
182A GLN 3.1 0.4 - - - -
183A GLU* 1.3 79.0 - - - +
185A HIS* 1.3 66.3 + - - +
186A GLU 3.1 1.7 + - - -
187A LYS* 3.4 6.7 + - - +
188A LEU* 2.9 43.5 + - + +
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Residues in contact with HIS 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TYR* 3.8 19.2 - + + +
181A ALA 3.0 31.0 + - - +
182A GLN 3.0 4.9 + - - +
184A VAL* 1.3 76.7 - - - +
186A GLU* 1.3 56.7 + - - +
188A LEU* 3.3 7.9 + - - +
189A ARG* 2.9 30.0 + - - +
206A ILE* 2.9 46.0 + - + +
207A ILE 3.3 23.8 - - - -
208A TYR* 3.4 24.0 - + - +
225A ASP* 3.2 29.1 + - + +
226A VAL* 3.8 13.1 - - + +
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Residues in contact with GLU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A GLN* 2.7 40.8 + - - +
183A GLU* 3.2 19.0 - - - +
185A HIS* 1.3 76.9 - - - +
187A LYS* 1.3 59.8 + - + +
189A ARG* 3.1 5.5 + - - +
190A GLY* 2.8 31.4 + - - -
225A ASP* 3.2 13.2 + - - +
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Residues in contact with LYS 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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140A GLU* 3.2 36.6 + - + +
144A PHE* 3.8 24.7 - - + -
183A GLU* 3.3 25.4 - - + +
184A VAL* 3.4 7.8 + - - +
186A GLU* 1.3 83.3 + - + +
188A LEU* 1.3 53.6 + - + +
190A GLY* 3.0 3.5 + - - +
191A TRP* 2.6 36.4 + - - +
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Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 3.5 29.2 - - + -
143A VAL* 3.3 27.6 - - + -
144A PHE* 4.6 4.5 - - + -
147A THR* 4.4 7.9 - - + +
162A LEU* 3.7 22.1 - - + +
164A TYR* 4.3 5.4 - - + -
184A VAL* 2.9 39.5 + - + +
185A HIS 3.6 4.9 - - - +
186A GLU 3.2 0.2 - - - -
187A LYS* 1.3 81.8 - - + +
189A ARG* 1.3 59.8 + - - +
191A TRP* 3.5 7.4 + - - +
192A LEU* 3.1 27.7 + - - +
206A ILE* 3.6 24.0 - - + -
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Residues in contact with ARG 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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4A ARG* 3.3 22.9 - - - +
185A HIS 2.9 14.7 + - - +
186A GLU 3.6 3.6 - - - +
188A LEU* 1.3 77.0 - - - +
190A GLY* 1.3 58.9 + - - +
192A LEU* 3.3 3.6 + - + +
193A LYS* 3.0 27.1 + - + +
201A ALA* 2.8 55.5 + - + +
202A GLN* 4.9 1.8 - - - +
204A THR* 2.7 25.7 + - - -
206A ILE* 3.7 15.9 - - + +
225A ASP* 3.1 37.1 + - - +
227A ASP* 3.0 36.6 + - - -
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Residues in contact with GLY 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLU 2.8 14.6 + - - -
187A LYS* 3.0 5.6 + - - -
189A ARG* 1.3 76.4 - - - +
191A TRP* 1.3 62.6 + - - +
193A LYS* 4.1 9.0 - - - +
194A SER* 3.2 26.7 + - - -
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Residues in contact with TRP 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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144A PHE* 3.3 56.3 + + + +
147A THR* 3.5 22.4 - - + -
148A LYS* 3.5 42.4 - - + +
151A ALA* 3.6 24.9 - - + -
152A ASP* 5.3 0.9 - - - -
187A LYS 2.6 19.5 + - - +
188A LEU* 3.6 8.3 - - + +
190A GLY* 1.3 72.7 - - - +
192A LEU* 1.3 66.8 + - + +
194A SER* 4.8 0.2 - - - -
195A ASN* 2.7 80.5 + - + +
196A VAL* 4.0 4.5 - - + -
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Residues in contact with LEU 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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147A THR* 4.2 6.1 - - + -
157A TRP* 3.8 23.6 - - + -
162A LEU* 5.1 5.2 - - + -
188A LEU 3.1 15.8 + - - +
189A ARG* 3.6 6.3 - - - +
190A GLY 3.3 0.2 - - - -
191A TRP* 1.3 93.5 - - + +
193A LYS* 1.3 62.8 + - - +
196A VAL* 2.4 53.7 + - + +
197A SER 3.1 0.2 + - - -
200A VAL* 4.8 0.9 - - + -
201A ALA* 3.5 20.6 - - + +
204A THR* 3.7 39.0 - - + +
206A ILE* 4.6 8.1 - - + -
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Residues in contact with LYS 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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189A ARG* 3.0 10.9 + - + +
190A GLY* 4.1 7.4 - - - +
192A LEU* 1.3 79.4 - - - +
194A SER* 1.3 62.6 + - - +
196A VAL 4.2 0.2 - - - -
197A SER* 3.4 21.5 + - - -
198A ASP* 3.3 42.5 + - + +
201A ALA* 3.0 19.7 - - + +
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Residues in contact with SER 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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190A GLY 3.2 17.2 + - - -
191A TRP* 4.0 1.3 - - - -
192A LEU 3.1 0.6 - - - -
193A LYS* 1.3 84.8 - - - +
195A ASN* 1.3 70.5 + - - +
196A VAL 5.1 0.5 - - - -
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Residues in contact with ASN 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A TRP* 2.7 85.3 + - + +
194A SER* 1.3 82.3 + - - +
196A VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ALA* 4.7 4.5 - - + -
157A TRP* 3.8 21.5 - - + +
191A TRP* 4.0 10.3 - - + -
192A LEU* 2.4 56.3 + - + +
193A LYS 4.2 2.0 - - - -
194A SER 5.0 0.8 - - - +
195A ASN* 1.3 74.0 - - - +
197A SER* 1.3 65.0 + - - +
200A VAL* 3.6 33.0 - - + -
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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
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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