Contacts of the helix formed by residues 180 - 197 (chain A) in PDB entry 1V0O
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 180 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A HIS* 3.3 54.7 - - + +
122A LEU* 3.5 19.0 - - + +
179A SER* 1.3 71.7 - - - +
181A THR* 1.3 67.2 + - - +
182A ILE 3.1 0.4 - - - -
183A ASP 3.1 12.6 + - - -
184A ILE* 3.4 9.6 + - - +
274A THR* 6.0 2.4 - - - +
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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
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170A ASP* 4.4 5.2 + - - -
177A LYS 5.4 0.2 + - - -
179A SER* 3.0 24.4 - - - +
180A THR* 1.3 83.4 + - - +
182A ILE* 1.3 64.4 + - - +
184A ILE* 3.2 12.0 + - - +
185A TRP 3.2 13.9 + - - -
269A PRO* 3.4 39.2 - - + +
270A ASN* 5.5 1.1 - - - +
272A ARG* 3.0 32.1 + - + +
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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
----------------------------------------------------------
122A LEU* 4.5 5.2 - - + -
124A ARG* 4.4 26.5 - - + +
157A TYR* 3.6 37.7 - - + +
166A TYR 4.9 0.9 - - - +
167A ARG* 6.1 1.1 - - + -
168A ALA* 4.8 9.9 - - + +
170A ASP* 6.0 0.7 - - - -
171A VAL* 3.9 24.5 - - + -
179A SER* 3.1 20.3 + - - +
181A THR* 1.3 83.4 + - - +
183A ASP* 1.3 79.2 + - - +
185A TRP* 3.6 5.7 + - - +
186A SER* 3.4 20.3 + - - +
272A ARG* 4.4 4.5 - - - +
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Residues in contact with ASP 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 4.2 5.0 - - + +
116A CYS* 5.9 0.2 - - - +
117A HIS* 2.6 38.8 + - + +
122A LEU* 3.6 3.1 - - - +
123A HIS* 3.0 29.1 + - - +
124A ARG* 2.9 29.9 + - - -
126A LEU* 4.0 14.9 + - + +
180A THR 3.1 1.2 + - - -
182A ILE* 1.3 85.6 - - - +
184A ILE* 1.3 67.3 + - - +
186A SER* 3.1 9.7 + - - -
187A VAL* 3.0 25.7 + - - +
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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
----------------------------------------------------------
110A LEU* 5.4 3.4 - - + -
113A ILE* 4.8 3.6 - - + -
117A HIS* 4.1 15.9 - - + +
180A THR* 3.6 15.9 - - - +
181A THR* 3.2 12.2 + - - +
183A ASP* 1.3 77.9 - - - +
185A TRP* 1.3 62.9 + - - +
187A VAL* 3.2 9.3 + - + +
188A GLY 3.1 17.7 + - - -
264A MET* 3.9 37.6 - - + +
272A ARG* 4.5 5.6 - - + -
273A ILE* 3.3 28.7 - - + +
274A THR* 4.6 2.2 - - - -
275A ALA* 3.7 30.3 - - + +
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Residues in contact with TRP 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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165A TRP 5.1 0.4 + - - -
166A TYR 3.5 20.1 + - - -
167A ARG 3.4 11.1 + - - -
168A ALA* 3.6 25.4 - - + -
169A PRO* 3.6 32.8 - - + -
181A THR 3.2 5.9 + - - -
182A ILE 3.7 5.2 - - - +
184A ILE* 1.3 76.9 - - - +
186A SER* 1.3 60.5 + - - +
188A GLY 3.2 1.9 + - - -
189A CYS* 3.1 31.6 + - - -
201A PHE* 3.9 21.2 - + - -
213A ILE* 3.8 18.7 - - + +
217A LEU* 3.7 22.9 - - + -
264A MET 4.1 6.9 + - - -
265A LEU* 3.5 30.4 - - + +
266A LYS 3.6 17.9 - - - -
267A LEU* 4.1 2.0 - - + -
272A ARG* 3.7 23.2 - - - +
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Residues in contact with SER 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG 5.7 2.9 - - - -
126A LEU* 3.8 35.5 + - - +
166A TYR* 2.9 28.7 + - - +
182A ILE* 3.4 11.1 + - - +
183A ASP* 3.1 12.1 + - - -
185A TRP* 1.3 77.0 - - - +
187A VAL* 1.3 64.3 + - - +
189A CYS* 3.2 3.8 + - - +
190A ILE* 3.0 29.6 + - - +
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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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106A LEU* 3.5 27.7 - - + +
109A LEU* 4.0 11.7 - - + -
110A LEU* 4.1 12.1 - - + -
113A ILE* 3.2 35.7 - - + -
126A LEU* 4.1 2.5 - - + -
183A ASP 3.0 17.4 + - - +
184A ILE* 3.2 13.2 + - + +
186A SER* 1.3 74.6 - - - +
188A GLY* 1.3 51.6 + - - +
190A ILE* 3.2 6.5 + - - +
191A PHE* 2.7 32.7 + - - +
264A MET* 3.6 19.1 - - + -
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Residues in contact with GLY 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 3.1 10.7 + - - -
185A TRP 3.2 4.7 + - - -
186A SER 3.2 0.2 - - - -
187A VAL* 1.3 77.2 - - - +
189A CYS* 1.3 60.9 + - - +
191A PHE* 3.3 0.7 + - - -
192A ALA* 3.0 21.7 + - - +
261A LEU* 3.4 14.2 - - - +
264A MET* 3.9 23.5 - - - -
265A LEU* 3.8 16.6 - - - +
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Residues in contact with CYS 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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165A TRP 4.2 9.0 - - - +
166A TYR* 3.6 22.4 - - + -
185A TRP* 3.1 44.2 + - - -
186A SER 3.2 7.6 + - - +
188A GLY* 1.3 75.8 - - - +
190A ILE* 1.3 57.6 + - - +
192A ALA* 3.5 7.3 + - - +
193A GLU* 3.1 27.5 + - - +
200A LEU* 4.8 9.1 + - + +
201A PHE* 3.8 27.6 - - + -
265A LEU* 4.0 3.6 - - - -
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Residues in contact with ILE 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 4.0 26.2 - - + -
109A LEU* 4.3 11.9 - - + -
126A LEU* 4.0 12.3 - - + +
127A LYS* 3.9 28.7 - - - +
128A PRO* 4.0 7.4 - - + -
131A LEU* 4.2 16.8 - - + -
166A TYR* 4.0 17.7 - - + -
186A SER 3.0 24.7 + - - +
187A VAL* 3.6 4.3 - - - +
189A CYS* 1.3 73.1 - - - +
191A PHE* 1.3 67.4 + - - +
193A GLU* 3.2 7.4 + - - +
194A MET* 3.0 34.3 + - + +
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Residues in contact with PHE 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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102A ALA* 5.3 6.3 - - + -
106A LEU* 3.6 39.0 - - + -
187A VAL 2.7 18.5 + - - +
188A GLY* 3.4 6.3 - - - +
190A ILE* 1.3 75.9 - - - +
192A ALA* 1.3 63.5 + - - +
194A MET* 3.1 25.4 + - + +
195A VAL* 3.3 27.1 + - + +
253A LEU* 4.1 8.7 - - + -
257A GLY 3.5 24.7 - - - -
260A LEU* 4.1 10.3 - - + -
261A LEU* 3.7 22.7 - - + -
264A MET* 4.2 8.7 - - - -
283A TYR* 3.7 31.0 - + - -
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Residues in contact with ALA 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 GLY 3.0 16.5 + - - +
189A CYS 3.7 5.6 - - - +
190A ILE 3.3 0.2 - - - -
191A PHE* 1.3 75.5 - - - +
193A GLU* 1.3 56.7 + - - +
195A VAL* 3.2 14.0 - - - +
196A ASN* 3.1 31.3 + - - +
198A THR 4.8 0.9 - - - -
200A LEU* 3.8 33.9 - - + -
250A LEU* 4.1 15.9 - - + -
261A LEU* 4.3 7.3 - - + +
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Residues in contact with GLU 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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90A LEU* 3.6 24.3 - - + +
128A PRO* 3.8 12.2 - - + +
165A TRP* 5.5 1.0 - - - -
166A TYR* 2.6 40.8 + - - -
189A CYS 3.1 15.2 + - - +
190A ILE* 3.2 6.7 + - - +
192A ALA* 1.3 73.6 - - - +
194A MET* 1.3 60.9 + - - +
197A GLY* 2.8 30.6 + - - +
198A THR* 3.5 25.1 - - - +
199A PRO* 3.7 25.7 - - + +
200A LEU 5.3 0.4 - - - +
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Residues in contact with MET 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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86A LEU* 4.1 21.8 - - + -
90A LEU* 4.0 7.6 - - + -
96A GLY* 3.3 2.3 - - - -
97A LEU* 2.9 54.0 + - + +
102A ALA* 3.9 28.4 - - + +
105A PHE* 3.7 25.1 - - + -
106A LEU* 4.0 21.5 - - + +
109A LEU* 5.5 2.0 - - + -
190A ILE* 3.0 29.5 + - + +
191A PHE* 3.1 18.4 + - + +
193A GLU* 1.3 77.2 - - - +
195A VAL* 1.3 60.8 + - - +
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Residues in contact with VAL 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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95A GLY 4.2 0.2 - - - +
96A GLY* 4.0 7.6 - - - -
97A LEU 5.0 4.0 - - - +
102A ALA* 5.0 8.7 - - + -
191A PHE* 3.3 34.7 + - + +
192A ALA* 3.2 13.0 - - - +
194A MET* 1.3 80.7 - - + +
196A ASN* 1.3 68.5 + - - +
250A LEU* 3.6 27.1 - - + -
251A LYS* 4.1 29.4 - - - +
252A GLY 5.0 3.3 - - - +
253A LEU* 4.1 20.4 - - + -
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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
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95A GLY* 3.4 11.1 - - - -
192A ALA 3.1 17.5 + - - +
195A VAL* 1.3 81.7 - - - +
197A GLY* 1.3 58.9 + - - +
198A THR* 3.3 25.8 + - + +
200A LEU* 4.6 12.5 - - - +
249A PHE 2.9 23.7 + - - +
250A LEU* 3.6 10.4 - - - +
251A LYS* 3.3 49.3 + - - +
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Residues in contact with GLY 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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90A LEU* 4.4 22.3 - - - +
93A CYS 5.4 0.3 - - - +
95A GLY* 3.6 5.2 - - - -
96A GLY* 3.1 26.0 - - - -
193A GLU* 2.8 20.2 + - - +
196A ASN* 1.3 75.9 - - - +
198A THR* 1.3 60.0 + - - +
199A PRO* 4.8 0.3 - - - +
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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