Contacts of the helix formed by residues 184 - 196 (chain A) in PDB entry 1W31
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 GLY 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ARG* 3.6 10.2 + - - -
182A ILE 3.3 0.8 + - - -
183A ASP* 1.3 71.1 - - - +
185A ARG* 1.3 64.1 + - - +
186A ILE 3.3 3.4 + - - -
187A ARG* 3.4 14.3 + - - +
188A ASP* 3.2 16.5 + - - +
251A ARG* 4.1 10.3 - - - +
255A GLU* 3.5 25.1 + - - -
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Residues in contact with ARG 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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158A VAL* 3.8 24.9 - - + +
161A LEU* 4.5 5.6 - - + -
178A PRO* 2.7 38.8 + - + +
180A ASP* 2.7 35.6 + - - +
181A MET* 3.4 30.7 - - - +
182A ILE 3.2 16.0 + - - +
183A ASP 3.3 1.4 + - - -
184A GLY* 1.3 77.3 - - - +
186A ILE* 1.3 72.3 + - - +
188A ASP* 3.4 2.1 + - - +
189A ILE* 3.0 34.9 + - + +
206A SER* 3.8 7.9 + - - -
207A TYR* 3.2 23.2 + - - +
251A ARG* 4.1 15.4 - - - +
252A ASP* 3.3 21.6 + - - -
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Residues in contact with ILE 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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178A PRO* 3.7 25.1 - - + -
184A GLY 3.3 0.8 - - - -
185A ARG* 1.3 89.7 - - - +
187A ARG* 1.3 57.1 + - - +
189A ILE* 3.3 3.8 + - - +
190A LYS* 2.9 28.9 + - + +
204A VAL* 4.4 10.3 - - + +
206A SER* 3.3 36.3 - - - +
252A ASP* 3.7 25.4 - - - +
255A GLU* 3.4 35.2 + - + +
256A GLY 4.2 1.8 - - - -
257A ALA* 3.8 12.1 - - - +
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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
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154A ARG* 4.5 11.9 - - - +
184A GLY* 3.7 7.0 + - - +
185A ARG 3.3 0.4 - - - -
186A ILE* 1.3 75.8 - - - +
188A ASP* 1.3 83.4 + - - +
190A LYS* 3.3 3.3 + - - +
191A ARG* 2.9 31.6 + - + +
255A GLU* 3.1 44.2 + - + +
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Residues in contact with ASP 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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154A ARG* 3.8 8.3 + - - -
158A VAL* 3.4 33.1 - - + +
159A SER* 5.8 1.1 - - - -
162A ALA* 3.7 18.4 - - + +
184A GLY 3.2 16.0 + - - +
185A ARG 3.4 5.3 + - - +
186A ILE 3.3 0.4 - - - -
187A ARG* 1.3 103.9 + - - +
189A ILE* 1.3 57.4 + - - +
191A ARG* 3.4 6.3 + - - +
192A GLY* 2.9 25.8 + - - -
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Residues in contact with ILE 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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132A VAL* 4.5 4.0 - - + -
158A VAL 5.6 0.2 - - - +
161A LEU* 4.5 7.4 - - + +
162A ALA* 3.9 24.5 - - + +
165A ALA* 3.9 28.0 - - + -
166A VAL* 4.6 0.9 - - - +
176A VAL* 4.4 8.1 - - + -
178A PRO* 3.3 35.9 - - + -
185A ARG* 3.0 28.6 + - + +
186A ILE* 3.6 5.8 - - + +
188A ASP* 1.3 74.0 - - - +
190A LYS* 1.3 60.9 + - - +
192A GLY* 3.4 1.2 + - - -
193A LEU* 2.9 42.6 + - + +
204A VAL* 4.8 9.2 - - + -
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Residues in contact with LYS 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 ILE* 2.9 17.5 + - + +
187A ARG* 3.6 4.0 - - - +
189A ILE* 1.3 77.8 - - - +
191A ARG* 1.3 56.3 + - - +
193A LEU* 3.3 8.8 + - + +
194A ILE* 2.9 45.2 + - + +
199A ALA* 4.7 18.0 + - + +
202A THR 4.7 4.0 + - - -
204A VAL* 4.0 15.9 - - + +
255A GLU 3.7 12.8 - - - +
256A GLY* 2.9 35.4 + - - +
258A ASP* 3.0 27.9 + - - -
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Residues in contact with ARG 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* 2.9 18.4 + - + +
188A ASP* 3.7 8.5 - - - +
190A LYS* 1.3 74.9 - - - +
192A GLY* 1.3 60.7 + - - +
194A ILE* 3.2 41.3 + - - +
195A ASN* 2.8 50.4 + - - +
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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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162A ALA* 5.4 4.0 - - - -
166A VAL* 3.5 16.6 - - - +
188A ASP 2.9 17.8 + - - -
189A ILE 3.8 1.6 - - - -
191A ARG* 1.3 76.2 - - - +
193A LEU* 1.3 56.3 + - - +
195A ASN* 3.2 9.0 + - - +
196A ALA* 2.8 30.5 + - - +
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Residues in contact with LEU 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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165A ALA 4.6 2.2 - - - +
166A VAL* 3.7 18.1 - - + +
169A ALA* 3.9 28.5 - - + -
176A VAL* 4.6 2.9 - - + -
189A ILE* 2.9 31.7 + - + +
190A LYS* 3.6 7.9 - - + +
192A GLY* 1.3 77.3 - - - +
194A ILE* 1.3 61.0 + - - +
196A ALA* 3.1 3.2 + - - -
197A ASN 3.0 4.5 + - - -
198A LEU* 2.8 33.2 + - + -
199A ALA* 3.7 15.7 - - + +
202A THR* 4.0 23.8 - - + +
204A VAL* 3.7 30.7 - - + -
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Residues in contact with ILE 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 LYS* 2.9 34.2 + - + +
191A ARG* 3.2 43.9 + - - +
193A LEU* 1.3 76.6 - - - +
195A ASN* 1.3 66.3 + - - +
197A ASN* 3.1 23.8 + - - +
199A ALA* 3.6 22.4 - - + +
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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
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191A ARG* 2.8 43.8 + - - +
192A GLY* 3.7 7.0 - - - +
194A ILE* 1.3 82.1 - - - +
196A ALA* 1.3 59.6 + - - +
197A ASN* 3.2 5.7 + - - -
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Residues in contact with ALA 196 (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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166A VAL* 3.7 24.9 - - + -
170A LYS* 4.5 12.3 - - - +
192A GLY 2.8 16.9 + - - +
193A LEU 3.1 3.5 + - - +
195A ASN* 1.3 76.0 - - - +
197A ASN* 1.3 70.3 - - - +
198A LEU* 3.3 21.9 + - + +
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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