Contacts of the helix formed by residues 186 - 201 (chain A) in PDB entry 5VGR
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 LEU 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A PHE* 3.9 27.1 - - + -
172A TYR* 4.5 5.2 - - + -
182A ASP 4.4 5.4 - - - +
183A LEU* 2.9 26.2 + - + +
185A GLN* 1.3 73.9 - - - +
187A GLN* 1.3 63.5 + - - +
188A LEU 3.1 2.7 - - - -
189A PHE* 3.1 34.0 + - + +
190A THR* 3.7 8.9 + - + +
208A LEU* 4.1 16.4 - - + -
210A PHE* 4.0 21.5 - - + -
249A VAL* 4.2 10.8 - - + -
253A ILE* 3.9 29.6 - - + -
257A PHE* 4.7 5.2 - - + -
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Residues in contact with GLN 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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184A GLN* 2.9 46.0 + - - +
186A LEU* 1.3 77.2 - - - +
188A LEU* 1.3 73.7 + - + +
189A PHE 3.0 0.2 - - - -
190A THR* 2.5 29.3 + - - +
191A GLU* 4.5 1.2 + - - +
245A GLU* 4.3 16.2 - - + +
249A VAL* 3.8 17.4 - - + +
337A LEU* 6.2 1.2 - - - +
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Residues in contact with LEU 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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157A ALA* 3.4 50.3 - - + +
160A PHE* 4.2 8.5 - - + -
161A ALA* 4.2 15.9 - - + +
185A GLN* 3.8 22.2 - - + +
187A GLN* 1.3 90.6 - - + +
189A PHE* 1.3 76.8 + - + +
191A GLU 5.3 0.3 + - - -
192A TYR* 4.8 1.7 + - - +
337A LEU* 4.1 22.4 - - + -
343A MET* 4.3 15.9 - - - +
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Residues in contact with PHE 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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160A PHE* 4.0 12.6 - + - -
161A ALA* 3.6 31.9 - - + -
164A THR* 3.3 35.4 - - + -
165A MET* 5.0 1.3 - - + -
186A LEU* 3.1 37.2 + - + +
187A GLN 3.0 1.0 - - - -
188A LEU* 1.3 95.9 - - + +
190A THR* 1.3 55.6 + - - +
191A GLU 3.5 1.8 - - - -
192A TYR* 3.1 10.2 + - - +
193A GLY 2.8 31.4 + - - -
205A PHE* 3.8 28.9 - + + -
256A CYS* 3.3 13.0 - - + -
257A PHE* 4.4 12.3 - + - -
343A MET* 4.9 6.5 - - + -
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Residues in contact with THR 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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186A LEU* 3.9 12.6 - - + +
187A GLN* 2.5 32.3 + - - +
189A PHE* 1.3 75.3 - - - +
191A GLU* 1.3 80.9 + - - +
193A GLY* 3.2 1.4 + - - -
194A ARG* 3.0 27.3 + - - +
248A ASN* 4.3 8.7 - - + +
249A VAL* 3.9 30.7 - - + +
252A HIS* 4.4 13.4 - - + +
253A ILE* 5.3 1.3 - - - +
256A CYS* 3.8 12.3 - - - -
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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 GLN 4.5 2.1 + - - +
188A LEU 5.3 0.6 + - - -
190A THR* 1.3 90.2 + - - +
192A TYR* 1.3 51.6 + - - +
194A ARG* 3.2 39.8 + - + +
195A LEU* 2.8 37.1 + - - +
248A ASN* 5.4 4.4 - - - +
252A HIS* 5.1 1.9 + - - -
340A PRO* 4.0 21.7 - - + +
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Residues in contact with TYR 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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165A MET* 4.1 10.8 - - + +
188A LEU 4.8 1.3 + - - +
189A PHE* 3.1 13.2 + - - +
191A GLU* 1.3 77.8 - - - +
193A GLY* 1.3 56.8 + - - +
195A LEU* 3.3 3.2 + - + +
196A ALA* 2.9 30.0 + - + +
204A PRO* 3.8 17.6 - - + +
205A PHE* 3.5 42.5 - + - -
328A TYR* 4.4 1.0 + - - -
340A PRO* 4.1 16.9 - - - +
343A MET* 3.7 36.8 - - + -
344A LEU* 3.7 34.7 - - + +
347A THR* 2.9 32.2 + - - +
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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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189A PHE 2.8 17.3 + - - -
190A THR 3.7 3.1 - - - -
192A TYR* 1.3 73.6 - - - +
194A ARG* 1.3 61.8 + - - +
196A ALA* 3.6 1.0 + - - +
197A MET* 3.2 30.3 + - - +
204A PRO* 3.8 14.8 - - - +
255A SER* 3.6 20.5 - - - +
256A CYS* 3.9 7.4 - - - -
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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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190A THR 3.0 13.3 + - - +
191A GLU* 3.2 37.7 + - + +
193A GLY* 1.3 74.4 - - - +
195A LEU* 1.3 64.8 + - - +
197A MET* 3.6 4.1 + - - +
198A ASP* 3.2 31.2 + - - +
252A HIS* 2.9 55.4 + - + -
255A SER* 4.8 5.6 - - - +
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Residues in contact with LEU 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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191A GLU 2.8 21.3 + - - +
192A TYR* 3.3 5.6 + - + +
194A ARG* 1.3 71.4 - - - +
196A ALA* 1.3 60.3 + - - +
198A ASP* 3.2 4.3 + - + -
199A GLU* 2.9 64.1 + - + +
339A HIS* 5.9 0.2 - - + -
340A PRO* 3.2 41.5 - - + +
341A LYS* 3.7 23.1 - - + +
344A LEU* 4.1 20.2 - - + -
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Residues in contact with ALA 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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192A TYR* 2.9 19.6 + - + +
193A GLY 4.1 2.9 - - - +
194A ARG 3.4 0.2 - - - -
195A LEU* 1.3 78.2 - - - +
197A MET* 1.3 57.7 + - - +
199A GLU* 5.3 0.7 - - - -
200A ILE* 2.7 46.6 + - + +
201A PHE 3.1 4.3 + - - -
202A GLN 3.6 13.5 - - - +
204A PRO* 4.2 19.1 - - + -
344A LEU* 4.6 13.5 - - + -
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Residues in contact with MET 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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193A GLY 3.2 17.5 + - - +
194A ARG* 4.1 5.2 - - - +
196A ALA* 1.3 76.0 - - - +
198A ASP* 1.3 65.9 + - - +
201A PHE* 3.3 26.4 + - - -
202A GLN* 3.8 21.8 - - - +
203A LYS* 4.1 25.4 - - + +
255A SER* 3.7 38.4 - - - +
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Residues in contact with ASP 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* 3.2 17.9 + - - +
195A LEU* 3.2 6.3 + - + +
197A MET* 1.3 83.4 - - - +
199A GLU* 1.3 66.5 + - + +
201A PHE* 3.6 15.8 - - - -
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Residues in contact with GLU 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 LEU* 2.9 39.8 + - + +
198A ASP* 1.3 86.5 - - + +
200A ILE* 1.3 68.8 + - + +
201A PHE* 3.6 13.5 - - - -
341A LYS* 5.4 7.9 - - - -
344A LEU* 4.7 13.0 - - + +
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Residues in contact with ILE 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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196A ALA* 2.7 32.8 + - + +
199A GLU* 1.3 82.8 - - + +
201A PHE* 1.3 70.4 + - - +
202A GLN* 3.2 31.8 + - + +
204A PRO* 6.4 1.1 - - + -
312A ASN* 4.0 20.2 - - + +
344A LEU* 4.2 19.1 - - + -
404A MET* 3.8 31.9 - - + -
405A GLY 6.3 0.4 - - - +
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Residues in contact with PHE 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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196A ALA 3.1 3.8 + - - -
197A MET* 3.3 25.2 + - - +
198A ASP* 3.6 19.7 - - - -
199A GLU* 4.3 9.4 - - - -
200A ILE* 1.3 80.3 - - - +
202A GLN* 1.3 62.8 + - + +
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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