Contacts of the helix formed by residues 220 - 227 (chain C) in PDB entry 2VM8
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 220 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219C GLY* 1.3 83.0 - - - +
221C GLU* 1.3 60.5 + - - +
223C HIS* 2.8 29.1 + - - +
224C VAL 3.9 1.0 + - - -
290C TYR* 4.1 9.1 - - + +
295C TRP* 3.6 33.9 - - + +
298C ALA* 3.6 46.4 - - + +
299C ALA 4.1 3.8 - - - +
302C VAL* 4.1 9.4 - - + -
348C PHE* 4.3 8.9 - - + -
351C ILE* 4.2 9.6 - - + -
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Residues in contact with GLU 221 (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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217C ILE* 3.6 24.6 - - + +
219C GLY* 3.4 16.7 + - - -
220C PRO* 1.3 75.7 - - - +
222C GLY* 1.3 56.8 + - - +
223C HIS 3.1 0.2 - - - -
224C VAL* 3.0 27.9 - - - +
225C LEU* 3.1 25.8 + - + +
290C TYR* 3.8 15.1 + - - +
291C TRP* 3.4 42.2 - - + +
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Residues in contact with GLY 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C ILE* 3.8 24.4 - - - +
217C ILE* 3.9 4.4 - - - +
219C GLY 3.0 12.1 + - - -
221C GLU* 1.3 78.5 - - - +
223C HIS* 1.3 65.8 + - - +
225C LEU* 3.9 2.9 - - - -
226C SER* 2.9 27.0 + - - -
348C PHE* 3.4 14.0 - - - -
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Residues in contact with HIS 223 (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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209C GLN* 5.6 4.2 + - - -
220C PRO 2.8 14.1 + - - +
222C GLY* 1.3 77.8 - - - +
224C VAL* 1.3 56.4 + - + +
226C SER* 2.9 6.6 + - - -
227C ARG* 2.7 51.2 - - - +
290C TYR* 4.5 4.7 - + + -
302C VAL* 3.7 33.8 - - + +
303C THR 2.9 31.9 + - - -
304C SER* 3.3 18.1 + - - -
306C PRO* 4.3 9.0 - - + -
348C PHE* 3.5 27.7 + - + -
349C THR* 6.0 0.6 - - - -
353C GLU* 3.5 14.8 - - + -
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Residues in contact with VAL 224 (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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220C PRO 3.9 0.2 + - - -
221C GLU* 3.0 21.7 - - - +
223C HIS* 1.3 79.9 - - - +
225C LEU* 1.3 60.8 - - + +
227C ARG 3.3 20.0 - - - +
228C PRO* 3.6 4.6 - - + +
290C TYR* 3.7 29.4 - - + -
291C TRP* 3.5 29.8 - - + -
306C PRO* 4.2 20.6 - - + -
309C PRO* 3.5 34.8 - - + -
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Residues in contact with LEU 225 (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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245A GLN* 5.0 0.5 + - - -
490A GLU* 3.7 53.5 - - + +
208C GLU* 4.9 5.4 - - - +
211C ARG* 5.6 0.2 + - - -
212C ILE* 4.4 13.0 - - + +
217C ILE* 4.9 8.1 - - + -
221C GLU* 3.1 40.4 + - + +
222C GLY* 4.1 8.1 - - - +
223C HIS 3.2 0.2 - - - -
224C VAL* 1.3 79.9 - - + +
226C SER* 1.3 56.6 + - - +
227C ARG 3.3 1.1 - - - -
228C PRO* 3.6 11.1 - - - +
291C TRP* 3.9 26.5 - - + +
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Residues in contact with SER 226 (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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204C ILE* 5.7 0.3 - - - +
205C ILE* 3.9 16.5 - - - +
208C GLU* 3.8 21.0 - - - +
209C GLN* 3.8 37.1 + - - +
212C ILE* 4.2 5.8 - - - -
222C GLY 2.9 15.9 + - - -
223C HIS* 2.9 17.3 + - - -
225C LEU* 1.3 74.9 - - - +
227C ARG* 1.3 64.9 + - - +
228C PRO* 3.4 8.6 - - - +
231C VAL* 4.9 1.0 - - - +
348C PHE* 3.7 9.7 - - - -
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Residues in contact with ARG 227 (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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169C ALA* 4.5 7.7 - - - +
170C PHE* 4.9 7.5 - - - +
198C HIS* 4.8 0.2 + - - -
200C GLU* 2.6 44.8 + - - +
205C ILE* 3.2 31.5 - - + +
209C GLN* 5.1 4.6 - - - +
223C HIS* 2.7 46.5 + - - +
224C VAL* 3.3 9.5 - - - +
225C LEU 3.3 0.2 - - - -
226C SER* 1.3 86.3 + - - +
228C PRO* 1.3 67.5 - - - +
229C GLU* 3.6 1.4 + - - -
231C VAL* 3.9 10.0 - - + +
304C SER* 2.5 43.5 + - - +
305C PRO* 3.7 1.8 - - - +
306C PRO* 3.7 21.5 - - + +
353C GLU* 4.8 3.5 + - - -
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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