Contacts of the helix formed by residues 186 - 195 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404C SOG 4.6 13.5 + - - -
184D ASP* 3.7 18.1 - - - +
185D GLU* 1.3 77.4 - - - +
187D PRO* 1.3 64.7 - - + +
188D GLN* 4.1 7.1 - - + +
189D ALA* 2.9 20.0 + - + +
190D LEU* 2.7 31.5 + - - +
317D ARG* 3.8 14.3 + - - +
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Residues in contact with PRO 187 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185D GLU 3.6 1.3 - - - +
186D ASP* 1.3 88.7 - - + +
188D GLN* 1.3 63.9 + - + +
190D LEU* 3.5 12.5 - - + +
191D LYS* 2.7 53.8 + - - +
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Residues in contact with GLN 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D ASP* 4.6 7.4 - - + +
187D PRO* 1.3 87.4 - - + +
189D ALA* 1.3 62.9 + - - +
191D LYS* 3.3 9.8 + - - +
192D CYS* 3.2 18.4 + - - +
202D VAL* 5.6 2.0 - - + -
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Residues in contact with ALA 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D ASP* 4.0 18.2 - - + +
186D ASP* 2.9 14.9 + - + +
188D GLN* 1.3 77.2 - - - +
190D LEU* 1.3 58.0 + - - +
192D CYS* 3.1 8.6 + - - +
193D TYR* 3.0 50.7 + - + +
202D VAL* 3.9 31.0 - - + +
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Residues in contact with LEU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B TRP* 3.7 29.6 - - + +
113B LEU* 5.4 11.9 - - + -
184D ASP 4.0 12.3 - - - +
185D GLU* 3.3 28.7 - - - +
186D ASP 2.7 11.7 + - - +
187D PRO* 3.1 11.0 + - + +
189D ALA* 1.3 73.8 - - - +
191D LYS* 1.3 62.8 + - + +
193D TYR* 3.1 30.1 + - + +
194D GLN* 3.1 20.3 + - - +
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Residues in contact with LYS 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D PRO* 2.7 35.6 + - + +
188D GLN* 3.3 9.6 + - - +
190D LEU* 1.3 72.3 - - + +
192D CYS* 1.3 57.4 + - - +
194D GLN* 3.2 24.9 + - + +
195D ASP* 2.9 31.2 + - - +
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Residues in contact with CYS 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D GLN 3.2 10.7 + - - +
189D ALA* 3.1 14.0 + - - +
191D LYS* 1.3 76.5 - - - +
193D TYR* 1.3 55.8 + - + +
195D ASP 3.1 6.2 - - - +
198D CYS* 2.1 52.0 - - - -
200D ASP* 3.7 31.0 - - - -
202D VAL* 4.3 7.9 - - + -
401D NA 2.5 30.9 - - - -
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Residues in contact with TYR 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LEU* 3.8 19.0 - - + +
109B TRP* 3.7 16.6 - + + -
111D SER* 5.3 5.9 - - - -
182D TRP* 3.5 24.0 - + - -
183D ARG* 3.3 44.1 - - + +
184D ASP* 2.9 38.2 + - - -
189D ALA* 3.0 23.8 + - + +
190D LEU* 3.1 22.1 + - + +
192D CYS* 1.3 83.5 - - + +
194D GLN* 1.3 62.7 + - - +
195D ASP 4.7 0.2 - - - -
200D ASP 5.2 2.7 - - - -
202D VAL* 2.7 27.8 + - + -
401D NA 4.0 6.5 - - - -
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Residues in contact with GLN 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B THR* 6.2 2.2 - - + -
109B TRP* 3.9 15.8 - - + -
111D SER* 6.1 0.3 - - - -
190D LEU* 3.1 16.7 + - - +
191D LYS* 3.3 36.6 - - + +
193D TYR* 1.3 76.7 - - - +
195D ASP* 1.3 63.3 + - - +
196D PRO* 3.2 12.6 - - - +
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Residues in contact with ASP 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D LYS 2.9 20.0 + - - +
192D CYS 3.1 1.2 - - - +
193D TYR 4.7 0.2 - - - -
194D GLN* 1.3 71.0 - - - +
196D PRO* 1.3 66.2 - - - +
197D GLY* 2.9 25.8 + - - -
198D CYS* 3.2 23.0 + - + +
401D NA 2.4 30.7 - - - -
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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