Contacts of the helix formed by residues 186 - 195 (chain C) in PDB entry 2VT4
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 ASP 186 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184C ASP* 3.8 18.5 + - - +
185C GLU* 1.3 79.6 - - - +
187C PRO* 1.3 83.8 - - - +
188C GLN* 3.3 29.0 - - - +
189C ALA* 3.0 11.1 + - + +
190C LEU* 2.9 20.1 + - - +
317C ARG* 5.7 3.7 + - - +
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Residues in contact with PRO 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C GLU 3.6 4.2 - - - +
186C ASP* 1.3 94.1 - - - +
188C GLN* 1.3 60.7 + - + +
190C LEU* 3.2 10.5 + - + +
191C LYS* 2.9 29.6 + - - +
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Residues in contact with GLN 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C ASP* 3.2 17.9 + - - +
187C PRO* 1.3 82.3 - - + +
189C ALA* 1.3 61.4 + - - +
191C LYS* 3.3 14.0 - - + +
192C CYS* 3.2 20.3 + - - +
202C VAL* 5.5 0.7 - - - -
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Residues in contact with ALA 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C ASP* 3.6 32.1 - - + +
186C ASP* 3.0 16.1 + - + +
188C GLN* 1.3 78.5 - - - +
190C LEU* 1.3 62.1 + - - +
192C CYS* 2.9 15.9 + - - +
193C TYR* 3.1 33.5 + - + +
202C VAL* 3.7 19.2 - - + +
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Residues in contact with LEU 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C ASP 4.2 10.8 - - - +
185C GLU* 3.6 30.1 - - - +
186C ASP 2.9 15.4 + - - +
187C PRO* 3.7 9.4 - - + +
189C ALA* 1.3 75.5 - - - +
191C LYS* 1.3 62.8 + - - +
193C TYR* 3.3 29.7 + - + +
194C GLN* 3.4 17.8 + - - +
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Residues in contact with LYS 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C PRO 2.9 13.1 + - - +
188C GLN* 3.3 18.8 - - + +
190C LEU* 1.3 75.8 - - - +
192C CYS* 1.3 61.4 + - - +
194C GLN* 3.4 5.9 + - - +
195C ASP* 3.4 20.5 + - + +
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Residues in contact with CYS 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C GLN 3.2 8.1 + - - +
189C ALA* 2.9 12.7 + - - +
191C LYS* 1.3 75.0 - - - +
193C TYR* 1.3 63.6 - - + +
194C GLN 3.0 6.3 + - - -
195C ASP* 3.1 9.2 + - - +
198C CYS* 2.1 53.1 - - - +
200C ASP* 3.8 26.2 - - - -
202C VAL* 4.7 7.0 - - + -
401C NA 2.6 26.6 - - - -
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Residues in contact with TYR 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C SER* 4.7 9.2 + - - -
182C TRP* 3.6 28.5 - + - -
183C ARG* 3.3 44.6 + - + +
184C ASP 3.0 34.8 + - - -
189C ALA* 3.1 31.1 + - + +
190C LEU* 3.3 21.3 + - + +
192C CYS* 1.3 82.5 - - + +
194C GLN* 1.3 61.5 + - + +
195C ASP 3.5 0.2 - - - -
200C ASP 5.1 2.0 - - - -
202C VAL* 2.6 30.5 + - + -
401C NA 3.9 8.4 - - - -
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Residues in contact with GLN 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C SER* 5.6 0.4 - - - -
190C LEU 3.4 14.6 + - - +
191C LYS* 3.4 5.1 + - - +
192C CYS 3.0 1.0 - - - -
193C TYR* 1.3 83.7 - - + +
195C ASP* 1.3 58.9 + - - +
196C PRO* 3.1 13.2 - - - +
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Residues in contact with ASP 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C SER* 4.9 0.4 - - - -
191C LYS* 3.4 14.3 + - + +
192C CYS* 3.1 5.0 + - - +
194C GLN* 1.3 78.2 - - - +
196C PRO* 1.4 57.9 - - - +
197C GLY* 3.0 21.2 + - - -
198C CYS* 2.9 35.5 + - + +
401C NA 2.4 26.9 - - - -
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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