Contacts of the strand formed by residues 282 - 288 (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 GLN 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A TRP* 5.0 7.3 - - - -
276A MET* 4.3 2.9 - - - +
277A GLY* 2.8 30.2 + - - -
278A GLU 6.1 0.2 - - - +
279A VAL* 3.0 41.2 + - + +
280A THR 3.0 7.3 + - - +
281A ASN* 1.3 81.6 + - - +
283A SER* 1.3 56.5 + - - +
361A PRO* 3.8 30.7 - - + +
362A PHE 3.3 4.3 - - - +
363A VAL* 4.1 18.8 - - + +
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Residues in contact with SER 283 (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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177A TRP* 4.9 2.6 - - - -
192A VAL* 3.8 23.9 - - - +
274A TYR* 4.0 9.0 - - - -
275A LEU 3.1 17.5 - - - -
276A MET* 4.6 0.7 - - - -
277A GLY* 3.8 2.9 - - - +
281A ASN 5.4 0.2 + - - -
282A GLN* 1.3 76.7 - - - +
284A PHE* 1.3 65.8 + - - +
361A PRO* 3.5 8.0 - - - +
362A PHE* 2.8 47.9 + - - +
364A THR* 5.2 5.0 + - - -
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Residues in contact with PHE 284 (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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177A TRP* 3.5 55.0 - + + -
178A TYR 3.4 27.6 - - - -
179A THR* 3.8 14.4 - - - -
274A TYR* 3.2 5.7 - - - -
275A LEU* 2.8 60.2 + - + -
276A MET 3.9 5.6 - - - -
277A GLY* 4.6 3.1 - - - -
283A SER* 1.3 77.4 - - - +
285A ARG* 1.3 66.4 + - - +
286A ILE* 4.2 7.4 - - + -
342A PHE* 4.0 16.6 - + + -
358A VAL* 3.9 9.6 - - + -
359A GLU 3.3 14.6 - - - +
360A GLY* 4.3 0.4 - - - -
362A PHE* 4.3 2.5 - - - -
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Residues in contact with ARG 285 (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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195A GLU* 4.2 6.5 + - - -
272A SER* 4.3 9.2 - - - -
273A LEU 3.2 9.2 - - - +
274A TYR* 3.0 50.3 + - + -
284A PHE* 1.3 75.8 - - - +
286A ILE* 1.3 63.7 + - - +
287A THR* 4.0 15.4 + - - +
357A ALA 3.7 0.3 - - - +
358A VAL* 3.3 5.9 - - - +
359A GLU* 2.6 65.8 + - - +
362A PHE* 3.6 28.8 - - + -
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Residues in contact with ILE 286 (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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271A ILE 3.7 1.0 - - - +
272A SER* 3.3 1.6 - - - -
273A LEU* 2.9 47.3 + - + +
275A LEU* 4.5 6.5 - - + -
284A PHE* 4.2 20.4 - - + -
285A ARG* 1.3 78.8 - - - +
287A THR* 1.3 62.3 + - - +
288A ILE* 4.1 6.9 + - + +
321A MET* 3.8 28.7 - - + -
325A ILE* 3.9 17.7 - - + -
329A PHE* 4.1 11.2 - - + -
342A PHE* 4.2 25.6 - - + -
357A ALA 3.3 5.6 - - - +
358A VAL* 4.3 9.6 - - + -
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Residues in contact with THR 287 (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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270A VAL* 3.7 31.9 - - + -
271A ILE 3.4 3.1 - - - +
272A SER* 3.1 21.1 + - - +
285A ARG* 4.0 16.1 + - - +
286A ILE* 1.3 75.2 - - - +
288A ILE* 1.3 63.3 + - - +
289A LEU* 4.3 7.6 - - + -
329A PHE* 3.6 8.8 - - - -
355A THR 4.6 4.0 - - - +
356A ALA* 3.4 22.2 - - - +
357A ALA* 2.9 22.5 + - - -
359A GLU* 4.4 4.0 + - - -
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Residues in contact with ILE 288 (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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270A VAL* 3.4 6.1 - - - -
271A ILE* 2.7 53.6 + - + +
273A LEU* 5.2 3.1 - - + -
286A ILE* 4.4 11.0 - - + +
287A THR* 1.3 76.0 - - - +
289A LEU* 1.3 67.7 + - - +
292A GLN* 3.5 31.6 - - + +
293A TYR* 4.3 14.7 - - + +
324A VAL* 4.3 4.0 - - + +
325A ILE* 3.9 34.5 - - + +
329A PHE* 3.5 31.6 - - + -
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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