Contacts of the helix formed by residues 194 - 203 (chain A) in PDB entry 2VES
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 MET 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A PHE* 1.3 71.8 - - - +
195A ARG* 1.3 57.5 + - - +
197A ILE* 3.1 21.6 + - + +
198A GLU* 2.9 56.3 + - + +
211A VAL* 6.2 1.6 - - - -
216A VAL* 3.7 25.8 - - + +
217A VAL 2.9 10.5 + - - +
218A ASP* 5.1 4.0 - - + +
223A LEU* 3.8 20.2 - - + -
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Residues in contact with ARG 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 HIS* 4.3 2.6 - - - -
193A PHE* 3.7 44.8 - - + -
194A MET* 1.3 78.4 - - - +
196A ASP* 1.3 71.3 + - - +
198A GLU* 3.5 15.6 + - - +
199A TYR* 3.1 26.5 + - - +
219A GLU* 3.2 20.8 + - - +
143C ARG* 4.9 0.7 + - - +
157C GLU* 3.0 44.8 + - - +
158C ILE 4.8 0.4 + - - -
159C ASP* 3.1 24.9 + - - +
260C PHE* 3.6 37.3 - - + -
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Residues in contact with ASP 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 GLY* 5.5 0.2 - - - -
193A PHE* 3.1 32.2 + - - +
195A ARG* 1.3 87.0 + - - +
197A ILE* 1.3 59.7 + - - +
199A TYR* 3.3 1.4 + - - +
200A LEU* 2.8 39.7 + - + +
1296A GVR 3.9 19.6 - - + -
143C ARG* 3.0 30.1 + - - +
260C PHE* 5.7 2.8 - - - -
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Residues in contact with ILE 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 PHE 3.2 10.3 + - - +
194A MET* 3.1 20.8 + - + +
196A ASP* 1.3 75.4 - - - +
198A GLU* 1.3 58.4 + - - +
200A LEU* 3.8 5.3 - - - +
201A ARG* 2.8 49.4 + - + +
206A ALA* 5.3 1.3 - - + +
209A GLY 3.9 19.1 - - - +
210A SER* 4.7 8.7 - - - -
216A VAL* 3.8 39.3 - - + -
1296A GVR 3.7 37.9 - - + -
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Residues in contact with GLU 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 MET* 2.9 46.4 + - + +
195A ARG* 3.5 20.0 + - - +
197A ILE* 1.3 76.9 - - - +
199A TYR* 1.3 62.6 + - - +
201A ARG* 3.7 4.9 - - - +
202A SER* 3.0 23.9 + - - -
258C ARG* 4.6 18.6 + - - +
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Residues in contact with TYR 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 ARG 3.1 13.9 + - - +
196A ASP 3.6 3.6 - - - +
198A GLU* 1.3 80.7 - - - +
200A LEU* 1.3 77.7 + - + +
202A SER* 2.6 24.3 + - - -
203A GLN* 3.2 34.0 + - + +
205A LEU* 6.2 0.7 - - + -
136C SER* 4.1 12.2 + - - -
137C VAL 4.6 1.3 + - - -
138C GLU* 2.8 30.8 + - - +
143C ARG* 3.5 57.0 - - + +
145C VAL* 3.7 31.6 - - + -
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Residues in contact with LEU 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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62A MET* 3.6 33.4 - - - -
196A ASP* 2.8 27.7 + - + +
197A ILE* 3.8 2.0 - - - +
199A TYR* 1.3 86.7 - - + +
201A ARG* 1.3 58.2 + - - +
203A GLN* 2.9 16.0 + - - +
205A LEU* 2.8 49.5 + - + +
206A ALA* 3.7 25.8 - - + -
1296A GVR 4.0 25.1 - - + -
143C ARG* 5.8 3.4 - - - +
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Residues in contact with ARG 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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197A ILE* 2.8 30.6 + - + +
198A GLU* 3.7 5.8 - - - +
200A LEU* 1.3 76.5 - - - +
202A SER* 1.3 55.9 + - - +
204A ASN* 2.9 26.0 + - - +
205A LEU 3.3 6.1 - - - +
206A ALA* 3.3 19.6 + - + +
207A LEU* 3.2 40.5 + - - +
208A GLY* 4.0 2.0 - - - -
209A GLY 2.9 28.6 + - - +
210A SER* 4.5 6.5 - - - -
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Residues in contact with SER 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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198A GLU 3.0 14.2 + - - -
199A TYR* 2.6 26.1 + - - -
201A ARG* 1.3 74.8 - - - +
203A GLN* 1.3 71.2 + - - +
204A ASN* 3.3 5.5 + - - +
134C GLU* 3.4 23.4 - - - +
145C VAL* 4.3 5.8 - - - +
147C VAL* 4.5 14.1 - - - +
258C ARG* 3.9 20.6 - - - -
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Residues in contact with GLN 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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199A TYR* 3.3 36.6 + - + +
200A LEU* 2.9 9.0 + - - +
202A SER* 1.3 94.4 + - - +
204A ASN* 1.3 68.3 + - - +
205A LEU* 3.1 25.5 + - + +
134C GLU* 2.7 26.0 + - - +
136C SER* 2.9 17.1 + - - -
145C VAL* 4.3 1.2 - - - +
1303C ZN 2.2 29.9 - - - -
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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