Contacts of the helix formed by residues 188 - 196 (chain A) in PDB entry 2VGL
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 TRP 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A PRO* 3.8 33.7 - - + +
155A LEU* 5.5 0.4 - - + -
156A VAL* 3.7 22.9 - - + -
172A LEU* 4.2 18.4 - - + -
183A VAL* 4.3 15.7 - - + -
184A PRO 3.3 24.1 + - - -
185A MET* 3.9 19.7 - - + -
186A GLY* 3.4 16.9 - - - +
187A ASP* 1.3 94.4 + - - +
189A THR* 1.3 73.0 + - - +
190A SER 3.0 3.5 + - - -
191A ARG* 3.1 13.2 + - - +
192A VAL* 3.0 43.3 + - + +
210A LEU* 5.0 0.4 - - + -
214A LEU* 4.0 24.7 - - + -
222A PHE* 4.7 3.1 - + - -
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Residues in contact with THR 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 MET* 3.7 15.9 - - - +
186A GLY 4.3 8.1 + - - -
187A ASP 3.4 1.8 - - - -
188A TRP* 1.3 88.9 - - - +
190A SER* 1.3 66.9 + - - +
192A VAL* 3.1 10.2 + - - +
193A VAL* 3.2 15.7 + - + +
221A GLU* 3.1 57.4 + - + +
222A PHE* 4.2 12.9 - - + -
224A THR* 6.0 0.4 - - - +
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Residues in contact with SER 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ASP 4.8 3.5 + - - -
188A TRP 3.2 0.8 - - - -
189A THR* 1.3 82.3 - - - +
191A ARG* 1.3 59.9 + - - +
193A VAL* 3.5 9.5 - - - +
194A HIS* 2.7 34.9 + - - +
224A THR* 5.8 1.6 - - - -
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Residues in contact with ARG 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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156A VAL* 3.6 55.3 + - + +
157A ALA* 6.0 0.6 - - - +
187A ASP* 3.1 47.5 + - - -
188A TRP* 3.1 4.8 + - - +
190A SER* 1.3 84.1 + - - +
192A VAL* 1.3 64.4 + - - +
194A HIS* 3.6 14.9 - - + +
195A LEU* 3.4 22.3 + - - +
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Residues in contact with VAL 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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155A LEU* 3.9 22.4 - - + -
156A VAL* 4.2 8.5 - - + -
188A TRP* 3.0 42.5 + - + +
189A THR* 3.6 6.7 - - - +
191A ARG* 1.3 72.8 - - - +
193A VAL* 1.3 59.0 + - - +
195A LEU* 2.8 37.0 + - + +
196A LEU 3.9 1.6 + - - -
207A ALA* 4.3 6.2 - - + +
210A LEU* 3.9 18.8 - - + -
211A ILE* 3.7 30.0 - - + +
222A PHE* 4.8 5.6 - - + -
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Residues in contact with VAL 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 THR* 3.2 16.7 + - + +
190A SER* 3.5 10.5 - - - +
192A VAL* 1.3 76.7 - - - +
194A HIS* 1.3 63.8 + - - +
196A LEU* 2.9 21.2 + - + +
211A ILE* 4.1 9.6 - - + -
222A PHE* 3.9 26.9 - - + -
224A THR* 3.4 27.8 - - - +
225A SER* 4.0 22.4 - - - +
228A LEU* 3.5 21.7 - - + +
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Residues in contact with HIS 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 SER 2.7 21.7 + - - +
191A ARG* 3.7 18.2 - - + +
192A VAL 3.1 1.0 - - - -
193A VAL* 1.3 74.8 - - - +
195A LEU* 1.3 68.0 + - + +
197A ASN* 2.8 35.6 + - + +
198A ASP 4.0 1.0 + - - -
228A LEU* 4.6 5.8 - - - +
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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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155A LEU* 4.0 37.9 - - + +
156A VAL* 6.0 0.7 - - - -
165A LYS* 3.9 26.9 - - + +
169A ALA* 5.7 0.4 - - + -
191A ARG 3.4 14.4 + - - +
192A VAL* 2.8 19.2 + - + +
194A HIS* 1.3 81.8 - - + +
196A LEU* 1.3 56.7 + - - +
197A ASN 3.0 0.4 - - - -
198A ASP* 2.8 31.9 + - - +
203A VAL* 3.9 25.6 - - + -
204A VAL* 4.0 6.9 - - - +
207A ALA* 3.9 19.7 - - + -
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Residues in contact with LEU 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 VAL 3.9 0.6 + - - -
193A VAL* 2.9 15.8 + - + +
194A HIS 2.9 0.6 + - - -
195A LEU* 1.3 77.0 - - - +
197A ASN* 1.3 58.4 + - - +
198A ASP 3.5 0.4 - - - -
204A VAL* 4.1 20.5 - - + +
207A ALA* 4.5 1.8 - - + -
208A THR* 3.1 32.5 - - - +
211A ILE* 4.1 18.2 - - + -
225A SER* 4.0 37.5 - - - +
228A LEU* 4.0 17.9 - - + -
229A ALA* 4.2 7.0 - - - +
232A ARG* 3.0 30.4 + - + +
261A LEU* 4.5 6.1 - - + -
264A LEU* 4.2 10.3 - - + -
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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