Contacts of the helix formed by residues 191 - 207 (chain A) in PDB entry 1VPW
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 ASN 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A SER 4.7 3.0 + - - -
146A ASP 3.6 21.4 + - - +
147A TRP* 3.8 7.6 + - - -
148A GLY* 3.3 27.8 - - - +
149A GLU* 5.2 0.5 - - - +
160A ASP* 3.0 38.8 + - - -
162A ALA* 3.6 8.7 - - - +
190A ARG* 1.3 68.0 - - - +
192A THR* 1.3 56.2 + - + +
193A GLY 2.8 9.8 + - - -
194A ALA* 5.5 0.4 - - - -
195A GLY* 2.7 41.3 + - - +
196A ARG 3.6 0.3 + - - -
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Residues in contact with THR 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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73A TYR* 3.8 11.9 - - + +
146A ASP* 6.4 2.0 - - + -
160A ASP* 3.9 13.7 - - - +
162A ALA* 4.7 0.4 - - - -
186A GLY 5.2 1.0 + - - -
190A ARG* 4.2 5.7 - - - +
191A ASN* 1.3 79.1 - - + +
193A GLY* 1.3 56.5 + - - +
196A ARG* 2.8 59.8 - - - +
221A PHE* 3.4 14.8 - - - -
246A GLY* 4.5 2.3 - - - +
599A HPA 2.7 40.1 + - + +
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Residues in contact with GLY 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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185A PRO* 5.0 2.1 - - - +
186A GLY* 3.7 23.3 - - - -
187A PRO 3.3 18.6 + - - -
188A LEU* 4.4 2.2 - - - -
190A ARG* 3.1 4.0 + - - +
191A ASN 2.8 2.0 + - - -
192A THR* 1.3 80.2 + - - +
194A ALA* 1.3 66.0 + - - -
195A GLY 3.0 1.4 + - - -
196A ARG* 3.1 11.6 + - - +
197A LEU* 3.1 11.8 + - - +
221A PHE* 4.6 1.1 - - - -
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Residues in contact with ALA 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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187A PRO 3.8 4.4 + - - -
188A LEU* 3.4 42.3 - - + +
190A ARG 3.0 9.2 + - - +
191A ASN* 5.5 0.2 - - - -
193A GLY* 1.3 70.8 - - - -
195A GLY* 1.3 61.6 + - - +
197A LEU* 3.3 4.6 + - - +
198A ALA* 3.0 26.0 + - - +
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Residues in contact with GLY 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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162A ALA* 3.8 8.5 - - - -
163A PHE* 3.3 27.0 - - - +
191A ASN* 2.7 32.2 + - - +
194A ALA* 1.3 73.4 - - - +
196A ARG* 1.3 62.8 + - - +
198A ALA* 3.8 2.6 + - - +
199A GLY 3.5 8.1 + - - -
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Residues in contact with ARG 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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73A TYR* 4.0 1.0 - - - -
162A ALA* 3.3 21.2 - - + +
166A GLY* 3.1 23.5 - - - -
191A ASN 3.6 1.0 + - - -
192A THR* 2.8 55.4 + - - +
193A GLY 3.1 3.0 + - - +
195A GLY* 1.3 73.8 - - - +
197A LEU* 1.3 66.8 + - - +
199A GLY 3.3 0.5 + - - -
200A PHE* 3.1 8.4 + - - +
221A PHE* 4.4 0.2 - - - -
244A PHE* 4.3 8.9 - - + -
246A GLY* 2.8 35.3 + - - +
274A TYR* 3.3 53.9 + - + -
275A ASP* 2.6 31.6 + - - -
292A GLN* 3.7 15.6 + - - +
599A HPA 3.5 10.5 + - - -
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Residues in contact with LEU 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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183A VAL* 3.7 27.8 - - + -
185A PRO* 4.1 20.2 - - + -
188A LEU* 4.2 22.4 - - + -
193A GLY 3.1 12.0 + - - +
194A ALA* 3.5 10.1 - - - +
196A ARG* 1.3 79.0 - - - +
198A ALA* 1.3 58.6 + - - +
200A PHE* 3.2 7.1 - - + +
201A MET* 2.7 47.5 + - + +
216A ILE* 5.8 5.6 - - + -
244A PHE* 5.2 2.9 - - - -
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Residues in contact with ALA 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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163A PHE* 3.9 14.8 - - + -
194A ALA 3.0 13.8 + - - +
195A GLY* 4.3 4.3 - - - +
196A ARG 3.2 0.2 - - - -
197A LEU* 1.3 78.4 - - + +
199A GLY* 1.3 66.1 + - - +
200A PHE 3.0 1.6 - - - -
201A MET* 3.6 7.8 - - - +
202A LYS* 2.9 24.8 + - - +
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Residues in contact with GLY 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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163A PHE* 3.1 43.0 - - - -
167A TYR* 3.1 22.6 - - - +
195A GLY 3.5 5.9 + - - -
196A ARG 3.3 5.1 + - - -
198A ALA* 1.3 78.4 - - - +
200A PHE* 1.3 61.2 + - - +
202A LYS* 3.4 8.5 + - - +
203A ALA 3.4 7.3 + - - -
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Residues in contact with PHE 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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166A GLY 3.2 13.3 - - - +
167A TYR* 4.5 0.4 - - - +
170A GLY* 3.7 21.1 - - - -
173A LEU* 4.2 2.9 - - + -
181A ILE* 3.3 24.0 - - + -
183A VAL* 3.8 20.9 - - + -
196A ARG 3.1 12.6 + - - +
197A LEU* 3.2 9.0 - - - +
199A GLY* 1.3 74.5 - - - +
201A MET* 1.3 95.9 + - + +
202A LYS 3.2 0.5 + - - -
203A ALA* 3.3 6.0 + - - +
204A MET* 3.0 55.6 + - + +
211A VAL* 4.2 5.8 - - + -
244A PHE* 3.3 42.6 - + + -
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Residues in contact with MET 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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183A VAL* 4.5 3.8 - - + -
197A LEU* 2.7 44.3 + - + +
198A ALA* 3.1 8.7 + - - +
200A PHE* 1.3 115.0 - - + +
202A LYS* 1.3 59.9 + - - +
204A MET* 3.2 9.1 + - + +
205A GLU* 3.1 38.0 + - + +
211A VAL* 4.3 20.0 - - - -
216A ILE* 6.0 2.2 - - - -
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Residues in contact with LYS 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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163A PHE* 4.2 22.4 - - + -
167A TYR* 2.9 28.7 - - + -
198A ALA 2.9 14.5 + - - +
199A GLY 3.5 3.1 - - - +
200A PHE 3.2 0.2 - - - -
201A MET* 1.3 73.7 - - - +
203A ALA* 1.3 65.8 + - - +
204A MET 3.2 0.2 + - - -
205A GLU* 3.2 13.7 + - - +
206A GLU* 2.7 64.8 + - - +
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Residues in contact with ALA 203 (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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167A TYR* 3.5 33.4 - - + +
170A GLY* 4.4 5.2 - - - -
171A ARG* 4.0 31.4 + - - +
174A ILE* 4.3 3.7 - - + +
199A GLY 3.4 2.4 + - - +
200A PHE 3.3 9.2 + - - +
202A LYS* 1.3 81.8 - - - +
204A MET* 1.3 57.2 + - + +
206A GLU* 3.1 6.4 - - - +
207A ALA* 2.9 29.3 + - - +
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Residues in contact with MET 204 (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 GLY* 3.8 18.6 - - - +
174A ILE* 4.8 4.9 - - + -
181A ILE* 3.9 22.0 - - + -
200A PHE* 3.0 63.9 + - + +
201A MET* 3.2 12.8 + - + +
202A LYS 3.1 0.6 - - - -
203A ALA* 1.3 73.9 - - - +
205A GLU* 1.3 59.3 + - + +
207A ALA* 2.7 22.7 + - - +
209A ILE* 2.8 57.6 + - + +
211A VAL* 4.2 11.0 - - + -
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Residues in contact with GLU 205 (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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201A MET* 3.1 26.6 + - + +
202A LYS* 3.6 12.7 + - - +
204A MET* 1.3 75.7 - - + +
206A GLU* 1.3 64.0 + - - +
208A MET* 2.8 19.2 + - - +
209A ILE 4.0 6.0 + - - +
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Residues in contact with GLU 206 (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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167A TYR* 2.6 46.8 + - - -
171A ARG* 4.1 12.7 + - - +
202A LYS* 2.7 30.7 + - - +
203A ALA* 3.1 10.4 - - - +
205A GLU* 1.3 77.8 - - - +
207A ALA* 1.3 59.2 + - + +
208A MET* 3.3 4.4 + - - +
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Residues in contact with ALA 207 (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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171A ARG* 5.0 5.2 - - - +
174A ILE* 3.1 38.8 - - + -
179A ARG* 2.6 33.9 + - - +
203A ALA 2.9 4.9 + - - +
204A MET 2.7 7.9 + - - +
206A GLU* 1.3 77.8 - - - +
208A MET* 1.3 58.2 + - - +
209A ILE* 3.1 5.2 - - + -
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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