Contacts of the helix formed by residues 186 - 202 (chain A) in PDB entry 5W4A
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 186 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A TYR* 3.8 25.6 - - + -
157A PHE* 3.6 37.9 - - + -
181A LEU 2.7 27.0 + - - +
182A GLU* 3.3 3.8 - - - -
183A ASP* 2.9 19.0 + - - +
185A ASP* 1.3 80.1 - - - +
187A ALA* 1.3 65.9 + - - +
188A ASP 3.3 2.5 - - - -
189A GLU* 3.0 10.4 + - - +
190A VAL* 2.9 21.9 + - - +
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Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A GLU* 4.2 25.6 - - + +
183A ASP 2.9 18.5 + - - +
184A GLU* 4.1 7.8 + - - +
185A ASP 3.6 2.4 - - - -
186A THR* 1.3 76.5 - - - +
188A ASP* 1.3 67.6 + - - +
190A VAL* 3.3 2.1 + - - +
191A GLU* 2.9 23.7 + - - +
194A ARG* 4.9 0.3 + - - -
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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
----------------------------------------------------------
184A GLU 5.4 1.1 + - - -
185A ASP 5.3 1.1 + - - +
186A THR 3.3 1.0 - - - -
187A ALA* 1.3 79.9 - - - +
189A GLU* 1.3 62.6 + - + +
191A GLU* 3.3 16.3 + - - +
192A VAL* 3.3 24.8 + - - +
129C LYS* 4.2 28.8 + - + +
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Residues in contact with GLU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 4.6 1.1 + - - -
157A PHE* 3.4 21.8 - - + -
161A SER* 5.0 1.4 + - - -
185A ASP 4.5 10.6 - - - +
186A THR* 3.0 8.9 + - - +
188A ASP* 1.3 75.3 - - + +
190A VAL* 1.3 66.6 + - - +
192A VAL* 3.1 6.9 + - - +
193A ILE* 3.0 25.5 + - - +
125C LEU* 4.5 12.6 - - - +
128C ARG* 3.0 57.3 + - + +
129C LYS* 4.1 19.0 - - + +
132C LEU* 3.8 18.6 - - + +
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Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PHE* 3.7 25.3 - - + -
173A TYR* 4.6 7.9 - - + -
176A THR* 3.7 24.0 - - + -
182A GLU* 3.7 32.1 - - + +
186A THR* 2.9 30.4 + - - +
187A ALA 3.6 4.7 - - - +
189A GLU* 1.3 75.8 - - - +
191A GLU* 1.3 58.9 + - - +
193A ILE* 3.2 6.6 + - + +
194A ARG* 2.8 41.4 + - - +
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Residues in contact with GLU 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 ALA 2.9 14.0 + - - +
188A ASP* 3.5 17.8 - - - +
189A GLU 3.2 0.2 - - - -
190A VAL* 1.3 77.2 - - - +
192A VAL* 1.3 58.5 + - + +
194A ARG* 3.6 21.1 - - - +
195A ASP* 2.9 50.9 + - - +
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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
----------------------------------------------------------
188A ASP 3.5 14.1 - - - +
189A GLU* 3.1 9.4 + - - +
191A GLU* 1.3 76.9 - - + +
193A ILE* 1.3 58.5 + - - +
195A ASP* 3.3 5.9 + - - +
196A ASN* 2.8 40.9 + - - +
129C LYS* 4.3 25.8 - - + +
132C LEU* 3.6 35.2 - - + +
133C GLN* 5.6 3.8 - - + -
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Residues in contact with ILE 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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157A PHE* 3.8 24.9 - - + -
161A SER* 3.8 22.0 - - - +
164A CYS* 3.7 23.8 - - - -
169A ASP* 3.6 23.1 - - - +
172A ALA* 3.9 12.6 - - + -
173A TYR* 3.9 18.4 - - + +
176A THR* 5.1 2.5 - - - +
189A GLU 3.0 9.9 + - - +
190A VAL* 3.7 7.4 - - - +
192A VAL* 1.3 73.7 - - - +
194A ARG* 1.3 65.4 + - - +
196A ASN* 3.3 9.6 + - - +
197A PHE* 3.1 21.8 + - - +
132C LEU* 4.1 12.3 - - + -
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Residues in contact with ARG 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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173A TYR* 3.2 52.5 + - + -
177A LYS* 5.5 1.4 - - - +
182A GLU* 4.1 23.2 + - - -
187A ALA 4.9 0.8 + - - -
190A VAL* 2.8 21.8 + - - +
191A GLU* 3.6 34.2 + - - +
193A ILE* 1.3 77.9 - - - +
195A ASP* 1.3 60.9 + - - +
197A PHE* 3.2 6.1 + - + +
198A LEU* 2.9 42.0 + - + +
212A ILE* 3.8 28.5 - - + -
213A ARG* 5.6 2.0 - - - +
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Residues in contact with ASP 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLU* 2.9 37.9 + - - +
192A VAL* 3.7 6.4 - - + +
194A ARG* 1.3 81.7 + - - +
196A ASN* 1.3 58.0 + - - +
198A LEU* 3.9 15.7 - - - +
199A ASN* 2.8 44.1 + - - +
213A ARG* 5.3 3.5 + - - +
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Residues in contact with ASN 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A CYS* 4.9 1.6 - - - +
169A ASP* 2.9 33.2 + - - +
192A VAL* 2.8 31.1 + - - +
193A ILE* 3.5 4.3 - - - +
195A ASP* 1.3 80.5 - - - +
197A PHE* 1.3 62.8 + - - +
199A ASN* 3.4 18.0 + - - +
200A ARG* 3.5 10.2 + - - +
132C LEU* 3.0 29.7 + - - +
133C GLN* 5.6 0.5 - - - -
134C LYS* 3.8 21.2 - - - +
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Residues in contact with PHE 197 (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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13A GLY 4.6 3.8 - - - -
14A ILE* 4.2 20.9 - - + -
15A ARG 5.9 0.2 - - - -
47A VAL* 6.3 0.2 - - + -
48A PHE* 4.4 3.6 - + - -
169A ASP* 4.0 14.1 - - + +
170A PHE* 3.3 57.4 - + + +
173A TYR* 4.7 14.8 - + + -
193A ILE 3.1 12.2 + - - +
194A ARG* 3.6 8.1 - - + +
196A ASN* 1.3 77.2 - - - +
198A LEU* 1.3 63.9 + - + +
200A ARG* 3.0 9.2 + - + +
201A LEU* 2.9 50.6 + - + +
212A ILE* 3.8 30.1 - - + -
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Residues in contact with LEU 198 (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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194A ARG* 2.9 37.8 + - + +
195A ASP* 3.3 14.1 + - - +
197A PHE* 1.3 82.0 - - + +
199A ASN* 1.3 57.7 + - - +
201A LEU* 4.2 4.3 - - + +
202A ASP* 2.7 36.6 + - - -
209A ALA* 3.9 18.4 - - + -
212A ILE* 3.8 38.1 - - + -
213A ARG* 3.6 47.1 - - + +
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Residues in contact with ASN 199 (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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195A ASP* 2.8 33.3 + - - +
196A ASN* 3.7 14.1 + - - +
197A PHE 3.2 0.2 - - - -
198A LEU* 1.3 77.8 - - - +
200A ARG* 1.3 58.3 + - - +
202A ASP* 4.1 12.5 - - - +
203A GLN* 3.5 21.7 + - - +
213A ARG* 4.7 5.0 + - - -
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Residues in contact with ARG 200 (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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10A GLU* 3.0 31.3 + - - -
13A GLY* 3.2 32.6 + - - +
15A ARG* 5.8 3.6 - - + +
196A ASN 3.5 7.0 + - - +
197A PHE* 3.0 11.9 + - + +
199A ASN* 1.3 78.0 - - - +
201A LEU* 1.3 66.1 + - - +
202A ASP 3.2 0.2 - - - -
203A GLN* 3.0 52.5 + - - +
204A THR* 3.9 15.2 + - - +
7B GLU* 5.0 4.8 + - - -
8B ILE 5.0 8.9 + - - -
9B VAL* 6.1 0.4 - - - +
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Residues in contact with LEU 201 (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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12A LEU 4.9 0.2 - - - +
13A GLY 4.5 3.5 + - - +
14A ILE* 3.8 32.1 - - + -
48A PHE* 4.2 7.9 - - + -
197A PHE* 2.9 40.8 + - + +
198A LEU* 4.0 7.0 - - + +
200A ARG* 1.3 76.5 - - - +
202A ASP* 1.3 56.3 + - - +
204A THR* 3.0 9.5 + - - +
205A LYS* 2.8 58.5 + - + +
208A LEU* 4.1 7.2 - - + -
209A ALA* 3.6 28.5 - - + +
212A ILE* 4.2 7.4 - - + -
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Residues in contact with ASP 202 (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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198A LEU 2.7 25.5 + - - +
199A ASN* 4.1 10.7 - - - +
200A ARG 3.2 0.2 - - - -
201A LEU* 1.3 71.8 - - - +
203A GLN* 1.3 61.1 + - + +
204A THR 3.5 0.3 + - - -
206A PRO* 3.6 32.9 - - + +
209A ALA* 3.1 12.3 - - - +
213A ARG* 2.7 43.1 + - - -
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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