Contacts of the helix formed by residues 181 - 195 (chain A) in PDB entry 2V3V
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 HIS 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A CYS* 4.0 3.1 - - + -
17A GLY 4.7 0.4 - - - -
18A THR* 3.5 33.2 - - - +
161A TYR* 5.9 0.7 - - - -
177A THR* 2.8 21.3 + - + +
180A ALA* 1.3 98.6 + - + +
182A PRO* 1.3 66.6 - - - -
183A VAL 3.3 1.8 - - - -
184A LEU* 2.9 23.9 + - + -
185A PHE 3.1 8.0 + - - -
307A CYS* 3.9 26.5 - - - -
343A LEU* 4.0 29.7 - - + +
344A THR 3.2 25.6 + - - -
345A GLY* 4.2 4.0 - - - -
812A MGD 4.1 7.6 + - - -
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Residues in contact with PRO 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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16A CYS* 4.4 2.0 - - - -
47A CYS* 3.5 31.6 - - + -
49A LYS* 4.3 4.7 - - - +
177A THR 4.0 1.1 - - - +
178A SER 3.5 24.0 - - - +
179A GLU 3.7 11.2 - - - +
180A ALA 3.5 7.0 - - - +
181A HIS* 1.3 86.2 - - - +
183A VAL* 1.3 61.0 + - - +
185A PHE* 3.4 6.5 + - + +
186A ARG* 3.1 21.0 + - - +
619A ILE* 3.8 17.0 - - + -
800A SF4 3.8 12.6 - - - -
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Residues in contact with VAL 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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18A THR* 4.4 2.9 - - + -
20A CYS* 3.9 15.7 - - - -
42A ASN* 4.2 18.6 - - + +
45A LEU* 4.1 17.3 - - + +
46A LEU* 3.7 9.4 - - - +
47A CYS* 3.5 30.3 - - + +
181A HIS 3.0 1.0 + - - -
182A PRO* 1.3 74.4 - - - +
184A LEU* 1.3 57.7 + - - +
186A ARG* 3.5 13.6 + - + +
187A ARG* 3.2 23.9 + - - +
800A SF4 3.5 22.4 - - - -
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Residues in contact with LEU 184 (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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18A THR* 3.9 18.4 - - + +
41A HIS* 5.3 1.3 - - + +
161A TYR* 3.6 44.6 - - + -
164A ILE* 3.6 25.4 - - + -
177A THR* 4.5 2.9 - - + -
181A HIS* 3.2 16.6 - - + +
183A VAL* 1.3 77.6 - - - +
185A PHE* 1.3 65.8 + - - +
187A ARG* 3.0 19.1 + - - +
188A ILE* 3.0 22.3 + - + +
305A LEU* 4.3 8.3 - - + -
343A LEU* 4.0 28.0 - - + -
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Residues in contact with PHE 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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172A ILE* 5.8 1.1 - - + -
177A THR* 3.6 31.4 - - + +
178A SER* 3.7 31.6 - - - -
181A HIS 3.1 5.5 + - - -
182A PRO* 3.6 8.5 - - + +
184A LEU* 1.3 75.9 - - - +
186A ARG* 1.3 59.2 + - + +
188A ILE* 3.1 12.3 + - + +
189A ALA* 2.9 32.1 + - + +
209A ASN* 4.0 14.8 - - - -
210A THR* 3.7 38.1 - - + -
213A ILE* 3.6 43.7 - - + -
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Residues in contact with ARG 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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45A LEU* 3.4 37.7 - - - +
182A PRO 3.1 13.3 + - - +
183A VAL* 3.6 16.1 + - - +
184A LEU 3.2 0.2 - - - -
185A PHE* 1.3 78.7 - - + +
187A ARG* 1.3 64.5 + - - +
189A ALA* 3.8 7.1 - - + +
190A ARG* 2.8 72.0 + - + +
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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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41A HIS* 4.0 27.4 + - - +
161A TYR* 3.6 36.7 + - - +
162A ALA* 3.7 16.0 - - - +
164A ILE* 3.6 22.6 - - + +
165A ASP* 2.8 43.4 + - - +
183A VAL 3.2 12.7 + - - +
184A LEU* 3.0 15.6 + - - +
186A ARG* 1.3 85.9 - - - +
188A ILE* 1.3 59.4 + - - +
190A ARG* 3.5 8.1 - - + +
191A ARG* 3.1 17.5 + - - +
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Residues in contact with ILE 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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164A ILE* 3.8 22.2 - - + -
170A PHE* 4.1 29.5 - - + -
172A ILE* 4.2 22.7 - - + -
177A THR* 4.3 20.6 - - + +
184A LEU* 3.0 24.2 + - + +
185A PHE* 3.1 9.8 + - + +
187A ARG* 1.3 73.2 - - - +
189A ALA* 1.3 64.9 + - - +
191A ARG* 3.0 16.0 + - - +
192A LYS* 3.1 11.6 + - - +
200A ILE* 4.1 14.8 - - + -
213A ILE* 4.2 7.4 - - + -
305A LEU* 4.3 17.7 - - + -
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Residues in contact with ALA 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 PHE* 2.9 24.5 + - + +
186A ARG* 3.8 8.1 - - + +
188A ILE* 1.3 70.6 - - - +
190A ARG* 1.3 57.3 + - - +
192A LYS* 3.2 8.0 + - - +
193A GLN* 3.0 43.4 + - - +
213A ILE* 3.9 30.4 - - + +
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Residues in contact with ARG 190 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A ARG* 2.8 53.8 + - + +
187A ARG* 3.5 10.3 - - + +
189A ALA* 1.3 76.1 - - - +
191A ARG* 1.3 56.3 + - - +
193A GLN* 3.2 24.9 + - - +
194A VAL* 3.0 44.5 + - + +
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Residues in contact with ARG 191 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A ILE* 3.3 21.1 - - + +
165A ASP* 3.4 31.9 + - - +
166A GLN* 3.8 10.9 + - - +
167A ALA 2.7 23.4 + - - +
168A THR* 3.9 11.9 + - - -
170A PHE* 3.7 19.1 - - + -
187A ARG 3.1 11.6 + - - +
188A ILE 3.0 12.0 + - - +
190A ARG* 1.3 75.1 - - - +
192A LYS* 1.3 57.6 + - - +
194A VAL* 3.4 18.9 + - - +
195A GLU* 3.0 46.8 + - - +
198A VAL* 3.6 15.3 - - + +
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Residues in contact with LYS 192 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A ILE 3.1 7.2 + - - +
189A ALA* 3.2 11.6 + - - +
191A ARG* 1.3 77.8 - - - +
193A GLN* 1.3 58.4 + - + +
195A GLU 3.0 17.2 - - - +
196A PRO* 3.2 29.6 - - - +
198A VAL* 3.1 34.3 - - + +
200A ILE* 3.9 20.7 - - + +
213A ILE* 3.0 29.3 + - + +
214A ALA 4.5 0.6 - - - -
215A ASP* 3.0 32.4 + - - +
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Residues in contact with GLN 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 ALA* 3.0 33.0 + - - +
190A ARG* 3.2 26.9 + - + +
192A LYS* 1.3 75.9 - - + +
194A VAL* 1.3 67.4 + - + +
196A PRO* 4.1 10.3 - - - +
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Residues in contact with VAL 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 ARG* 3.0 39.2 + - + +
191A ARG* 3.7 21.8 - - - +
193A GLN* 1.3 79.5 - - + +
195A GLU* 1.3 61.2 - - + +
196A PRO* 3.7 5.7 - - - +
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Residues in contact with GLU 195 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A THR* 5.8 1.8 - - - +
191A ARG* 3.0 27.3 + - - +
192A LYS 3.0 9.8 - - - +
194A VAL* 1.3 80.4 - - + +
196A PRO* 1.4 69.4 - - - +
197A GLY* 3.1 27.4 + - - +
198A VAL* 3.1 37.3 + - + +
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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
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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