Contacts of the strand formed by residues 271 - 276 (chain A) in PDB entry 3VG1
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 ILE 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A VAL* 4.6 3.4 - - + -
195A GLU 3.5 3.8 - - - +
196A ILE* 3.5 27.8 - - + -
222A LEU* 5.1 10.5 - - + -
232A ALA* 6.3 0.2 - - + -
236A ILE* 4.1 11.2 - - + -
269A PRO 4.7 0.7 - - - +
270A VAL* 1.3 76.8 - - - +
272A SER* 1.3 63.6 + - - +
273A LEU* 4.2 22.0 - - + -
287A THR* 3.4 1.5 - - - -
288A ILE* 2.7 51.1 + - + +
293A TYR* 3.6 26.5 - - + -
312A ILE* 3.5 31.9 - - + -
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Residues in contact with SER 272 (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 ARG 3.9 0.2 - - - +
194A VAL* 3.4 8.1 - - - +
195A GLU* 2.9 48.3 + - - +
198A GLY* 5.6 1.9 + - - -
270A VAL* 4.2 5.2 - - - +
271A ILE* 1.3 74.8 - - - +
273A LEU* 1.3 63.1 + - - +
274A TYR* 4.1 19.3 - - - -
285A ARG* 4.3 11.8 + - - -
286A ILE 3.3 5.4 - - - -
287A THR* 3.1 25.3 + - - +
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Residues in contact with LEU 273 (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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191A ILE* 4.7 15.0 - - + -
193A ARG 3.8 1.8 - - - -
194A VAL* 4.0 26.2 - - + -
222A LEU* 4.5 13.0 - - + -
224A LEU* 5.7 5.6 - - + -
271A ILE* 4.2 12.6 - - + -
272A SER* 1.3 79.2 - - - +
274A TYR* 1.3 65.0 + - - +
275A LEU* 3.8 7.2 + - + +
285A ARG* 3.2 0.9 - - - -
286A ILE* 2.9 58.9 + - + +
288A ILE* 5.2 3.1 - - + -
321A MET* 4.4 21.8 - - + -
325A ILE* 4.3 20.9 - - + -
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Residues in contact with TYR 274 (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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191A ILE* 3.4 7.4 - - - +
192A VAL* 2.9 42.1 + - + -
193A ARG* 2.8 42.3 + - + +
195A GLU* 2.9 46.4 + - + -
272A SER* 4.1 9.6 - - - -
273A LEU* 1.3 75.0 - - - +
275A LEU* 1.3 61.3 + - - +
283A SER* 4.0 15.0 - - - +
284A PHE 3.2 5.8 - - - +
285A ARG* 3.0 40.7 + - + -
362A PHE* 3.7 33.1 - + + -
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Residues in contact with LEU 275 (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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179A THR* 3.9 11.0 - - + +
189A VAL* 4.5 7.4 - - + -
190A ILE 3.6 7.9 - - - +
191A ILE* 3.7 29.8 - - + -
192A VAL* 4.4 0.7 - - - -
273A LEU* 4.5 9.0 - - + +
274A TYR* 1.3 76.9 - - - +
276A MET* 1.3 66.9 + - - +
283A SER* 3.1 17.8 - - - -
284A PHE* 2.8 44.4 + - + +
286A ILE* 4.5 7.6 - - + -
321A MET* 4.1 20.9 - - + -
342A PHE* 3.6 36.6 - - + -
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Residues in contact with MET 276 (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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179A THR* 2.6 37.1 + - - +
180A PRO* 3.4 14.2 - - + +
190A ILE* 2.9 53.0 + - + +
192A VAL* 3.9 18.8 - - + +
275A LEU* 1.3 72.4 - - - +
277A GLY* 1.3 73.8 + - - +
282A GLN 4.3 4.3 - - - +
283A SER* 4.6 0.4 - - - -
284A PHE* 3.9 1.2 - - - -
369A ASP* 3.5 23.8 - - - +
370A CYS* 4.8 2.9 - - - +
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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