Contacts of the helix formed by residues 214 - 220 (chain A) in PDB entry 2VR2
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 PRO 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A GLY* 1.3 80.2 - - - +
215A GLU* 1.3 67.7 + - - +
216A GLY 3.2 0.2 - - - -
217A HIS* 3.2 19.8 + - + +
218A GLU 3.8 1.4 + - - -
284A TYR* 3.7 14.0 - - + +
289A TRP* 3.6 28.0 - - + +
292A ALA* 3.6 33.9 - - + +
293A ALA* 3.6 24.5 - - + +
296A VAL* 3.8 12.6 - - + -
342A PHE* 4.4 8.3 - - + -
345A ILE* 4.2 4.5 - - + -
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Residues in contact with GLU 215 (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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211A ILE* 3.8 22.6 - - + +
213A GLY* 3.5 17.9 + - - -
214A PRO* 1.3 78.5 - - - +
216A GLY* 1.3 59.0 + - - +
218A GLU* 3.4 5.4 + - - +
219A LEU* 3.0 37.3 + - + +
284A TYR* 3.7 25.8 + - - +
285A TRP* 3.9 31.5 - - + +
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Residues in contact with GLY 216 (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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206A MET* 3.9 4.7 - - - +
211A ILE* 3.6 19.7 - - - +
213A GLY 3.2 9.8 + - - -
215A GLU* 1.3 79.5 - - - +
217A HIS* 1.3 58.4 + - - +
218A GLU 3.4 0.2 - - - -
219A LEU* 3.8 7.6 - - - -
220A CYS* 3.0 33.6 + - - +
342A PHE* 3.6 16.0 - - - -
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Residues in contact with HIS 217 (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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214A PRO* 3.2 17.7 + - + +
216A GLY* 1.3 75.9 - - - +
218A GLU* 1.3 59.2 + - - +
220A CYS* 3.3 5.9 - - - -
221A ARG* 3.1 52.4 + - - -
284A TYR* 4.2 9.4 - + - -
296A VAL* 3.6 24.1 - - + +
297A MET 2.6 27.2 + - - -
300A PRO* 3.8 16.8 - - + +
342A PHE* 3.6 31.8 + - + -
343A THR* 6.1 0.2 - - - -
347A ASN* 3.1 26.3 + - - -
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Residues in contact with GLU 218 (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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214A PRO 3.8 1.2 + - - -
215A GLU 3.4 5.4 + - - +
216A GLY 3.4 0.2 - - - -
217A HIS* 1.3 76.9 - - - +
219A LEU* 1.3 70.9 + - + +
220A CYS 3.2 0.2 - - - -
221A ARG 3.0 19.1 + - - -
222A PRO* 3.5 8.8 - - - +
223A GLU 5.0 0.2 + - - -
284A TYR* 3.8 25.6 - - + -
285A TRP* 3.5 28.3 - - + -
300A PRO* 3.8 10.1 - - + +
301A LEU 3.3 15.6 - - - +
302A ARG* 2.9 26.2 + - - -
303A PRO* 3.5 23.4 - - + +
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Residues in contact with LEU 219 (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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206A MET* 3.4 33.1 - - + +
211A ILE* 4.9 7.0 - - + -
215A GLU* 3.0 35.8 + - + +
216A GLY* 4.1 3.6 - - - +
217A HIS 3.5 0.4 - - - -
218A GLU* 1.3 79.6 - - + +
220A CYS* 1.3 59.2 + - - +
221A ARG 3.2 0.2 - - - -
222A PRO* 3.4 13.1 - - - +
285A TRP* 4.1 25.8 - - + +
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Residues in contact with CYS 220 (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 LEU 4.1 15.8 - - - +
199A ILE* 4.2 15.5 - - - +
202A GLY* 3.6 31.6 - - - +
203A ALA* 3.7 1.1 - - - +
206A MET* 3.8 10.7 - - + +
216A GLY 3.0 17.3 + - - +
217A HIS* 3.3 20.6 - - - -
218A GLU 3.2 0.4 - - - -
219A LEU* 1.3 76.1 - - - +
221A ARG* 1.3 71.5 + - - +
222A PRO* 3.5 6.1 - - - +
225A VAL* 4.9 2.9 - - - +
342A PHE* 3.9 17.5 - - - -
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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