Contacts of the helix formed by residues 182 - 191 (chain A) in PDB entry 1V72
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 ARG 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A SER* 3.9 7.9 + - - -
15A ASP* 2.8 41.2 + - - +
149A GLN 3.7 5.4 + - - -
150A ALA* 3.5 27.5 + - + +
151A THR 4.5 10.0 + - - -
152A GLU* 4.5 10.5 + - - +
154A GLY* 6.3 0.2 - - - -
180A GLY* 3.0 0.4 - - - -
181A SER* 1.3 85.7 - - - +
183A PHE* 1.3 65.7 + - - +
184A ALA 3.3 2.7 - - - -
185A ASN* 3.2 29.7 + - + +
186A ALA 3.5 3.5 + - - -
212A LYS* 3.7 15.5 - - + +
213A ASN* 6.4 1.1 - - - -
295A ASN* 3.8 16.2 - - - +
296A ILE* 3.8 27.9 - - - +
327A ARG* 5.4 7.5 - - - +
329A VAL* 4.6 3.8 - - - +
513A PLP 3.1 23.1 + - - +
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Residues in contact with PHE 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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56A PHE* 4.0 15.7 - + - -
149A GLN 3.5 8.1 - - - -
178A MET* 4.0 9.0 - - - -
180A GLY* 3.0 19.5 + - - +
181A SER 3.5 0.8 + - - -
182A ARG* 1.3 74.9 - - - +
184A ALA* 1.3 67.3 + - - +
186A ALA* 3.2 6.2 + - - +
187A LEU* 3.0 31.9 + - + +
194A PRO* 4.3 11.2 - - + -
197A MET* 3.3 28.4 - - + +
198A THR* 3.5 31.0 - - + -
206A LEU* 3.8 18.6 - - + -
208A PHE* 3.6 33.2 - + + -
209A GLY 4.4 10.4 + - - +
262A TRP* 4.2 11.7 - + - -
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Residues in contact with ALA 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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182A ARG 3.3 0.6 - - - -
183A PHE* 1.3 82.7 - - - +
185A ASN* 1.3 57.1 + - - +
187A LEU* 3.5 8.7 - - - +
188A VAL* 3.0 34.7 + - - +
209A GLY 5.1 2.4 + - - +
213A ASN* 3.5 31.0 - - + +
256A TYR* 4.0 9.9 - - - +
262A TRP* 4.2 17.5 - - + +
263A LEU* 5.2 1.6 - - + -
266A ALA* 3.6 9.6 - - + -
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Residues in contact with ASN 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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15A ASP* 4.8 1.6 + - - -
150A ALA* 5.0 0.7 - - + -
182A ARG* 3.2 36.4 + - + +
184A ALA* 1.3 77.3 - - - +
186A ALA* 1.3 60.1 + - - +
188A VAL* 3.6 2.2 - - - +
189A SER* 3.4 12.1 + - - -
212A LYS* 5.9 1.4 + - - +
213A ASN* 4.8 13.7 + - - +
266A ALA* 3.8 8.7 - - - +
269A ALA* 3.7 12.3 - - - +
270A ASN* 2.8 49.1 + - - +
294A ALA* 4.0 10.5 - - + +
295A ASN* 3.6 27.0 + - - +
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Residues in contact with ALA 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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149A GLN* 3.5 38.6 - - + +
150A ALA* 3.5 21.3 - - + +
156A ILE* 3.6 15.5 - - + -
182A ARG 3.5 1.4 + - - -
183A PHE 3.2 5.4 + - - +
185A ASN* 1.3 76.6 - - - +
187A LEU* 1.3 67.2 + - - +
189A SER* 3.3 1.7 + - - -
190A LEU* 3.1 28.8 + - - +
197A MET* 4.2 2.7 - - - -
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Residues in contact with LEU 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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183A PHE* 3.0 16.7 + - + +
184A ALA* 3.5 8.1 - - - +
186A ALA* 1.3 79.4 - - - +
188A VAL* 1.3 57.3 + - + +
190A LEU* 3.4 0.9 + - - +
191A GLY* 2.8 26.9 + - - -
192A CYS* 3.3 35.0 + - - +
193A SER 3.7 20.4 - - - +
194A PRO* 3.8 15.3 - - + -
197A MET* 3.9 17.0 - - + +
262A TRP* 3.8 24.2 - - + -
263A LEU* 3.6 28.7 - - + -
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Residues in contact with VAL 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 ALA 3.0 20.2 + - - +
185A ASN 3.6 0.4 - - - +
187A LEU* 1.3 73.7 - - + +
189A SER* 1.3 67.1 + - - +
191A GLY* 3.8 9.0 + - - +
263A LEU* 3.9 40.8 - - + +
266A ALA* 3.9 16.6 - - + -
267A ARG* 4.0 27.6 - - + +
270A ASN* 3.4 24.0 - - + +
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Residues in contact with SER 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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156A ILE* 3.3 22.9 - - - +
185A ASN 3.4 8.9 + - - -
186A ALA 3.3 0.6 + - - -
187A LEU 3.2 0.6 - - - -
188A VAL* 1.3 83.1 - - - +
190A LEU* 1.3 61.9 + - - +
270A ASN* 4.0 3.1 - - - -
293A GLU* 2.7 33.9 + - - +
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Residues in contact with LEU 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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149A GLN* 4.0 2.0 - - - +
156A ILE* 4.0 17.3 - - + -
157A TYR 3.9 17.5 - - - +
158A THR* 4.6 14.1 - - + -
159A LEU* 4.1 17.5 - - + +
186A ALA 3.1 14.4 + - - +
187A LEU 3.9 0.2 - - - +
189A SER* 1.3 80.7 - - - +
191A GLY* 1.3 62.4 + - - +
192A CYS* 3.3 21.5 + - + +
197A MET* 3.6 29.8 - - - -
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Residues in contact with GLY 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 LEU 2.8 10.8 + - - -
188A VAL* 3.8 8.7 + - - -
189A SER 3.4 2.4 - - - -
190A LEU* 1.3 79.3 - - - +
192A CYS* 1.3 61.7 + - - +
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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