Contacts of the strand formed by residues 279 - 285 (chain A) in PDB entry 3V9G
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 LEU 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A PHE* 3.6 35.1 - - + +
205A ALA* 4.3 1.8 - - + -
273A VAL* 3.5 29.2 - - + +
274A THR* 4.0 7.2 - - - -
276A SER 3.3 8.9 + - - +
277A GLU 3.4 1.1 - - - +
278A HIS* 1.3 76.7 - - - +
280A CYS* 1.3 58.4 + - - +
281A GLY 3.4 26.5 - - - +
282A ILE* 4.1 15.7 - - + -
298A VAL* 3.8 28.9 - - + -
305A PHE* 3.9 14.4 - - + +
307A THR* 4.4 6.8 + - - +
309A PRO* 3.7 21.0 - - + +
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Residues in contact with CYS 280 (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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200A LEU* 3.5 39.7 - - + +
201A GLU 3.3 20.6 - - - +
202A GLY* 3.5 22.2 - - - -
203A PHE 3.0 23.6 + - - -
204A VAL* 4.0 8.1 - - - -
228A ASN* 4.6 0.2 - - - -
278A HIS 3.2 0.6 + - - -
279A LEU* 1.3 73.9 - - - +
281A GLY* 1.3 58.1 + - - +
307A THR* 4.2 11.4 - - + -
308A PHE 4.2 1.9 - - - +
309A PRO* 3.4 11.5 - - - +
310A ARG* 2.9 17.3 + - - +
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Residues in contact with GLY 281 (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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203A PHE 3.7 1.0 + - - -
204A VAL* 3.4 7.7 - - - -
205A ALA 2.9 24.0 + - - -
279A LEU* 3.4 13.1 - - - +
280A CYS* 1.3 85.3 - - - +
282A ILE* 1.3 63.8 + - - -
309A PRO* 4.6 2.0 - - - -
310A ARG* 3.1 13.7 - - - -
541A TRP* 4.4 10.5 - - - -
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Residues in contact with ILE 282 (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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205A ALA* 3.4 13.7 - - + +
207A ILE* 4.1 22.0 - - + -
273A VAL* 5.0 3.8 - - + -
274A THR* 4.0 26.9 - - + -
279A LEU* 4.1 14.4 - - + -
281A GLY* 1.3 78.8 - - - +
283A ASN* 1.3 61.6 + - - +
284A PHE* 4.2 14.4 - - + -
291A PHE* 5.6 1.3 - - + -
294A LEU* 4.3 22.2 - - + -
298A VAL* 4.0 14.4 - - + -
310A ARG 2.8 9.4 + - - +
311A LEU* 3.5 16.9 - - + -
312A ALA 2.9 28.9 + - - +
541A TRP* 4.0 3.7 - - - -
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Residues in contact with ASN 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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204A VAL* 4.5 5.8 - - + +
205A ALA 2.8 12.6 + - - +
206A ALA* 3.5 2.9 - - - -
207A ILE 2.9 26.7 + - - +
219A LEU* 2.8 49.6 + - - +
223A PRO* 3.7 6.5 - - - +
281A GLY 4.3 0.2 - - - -
282A ILE* 1.3 70.9 - - - +
284A PHE* 1.3 60.4 + - - +
312A ALA* 3.6 11.0 - - - +
537A TYR* 3.0 25.9 + - - -
541A TRP* 3.3 28.7 - - + -
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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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207A ILE* 3.7 31.0 - - + -
219A LEU* 4.3 2.3 - - - +
282A ILE* 4.2 11.4 - - + -
283A ASN* 1.3 75.2 + - - +
285A THR* 1.3 68.6 + - - +
286A GLY* 3.4 21.1 - - - -
287A SER 3.5 36.3 - - - -
290A THR* 3.8 28.0 - - + -
291A PHE* 3.6 31.6 - + + -
294A LEU* 3.9 12.1 - - + -
312A ALA 2.9 14.7 + - - +
313A GLY* 3.3 4.8 - - - -
314A GLU* 3.0 24.2 + - - +
315A CYS* 4.4 2.0 - - - -
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Residues in contact with THR 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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207A ILE* 3.2 17.0 + - - +
208A SER 4.2 1.0 - - - -
209A PRO* 3.7 34.4 - - + +
215A ILE* 3.8 18.0 - - + +
219A LEU* 3.5 26.9 - - - +
284A PHE* 1.3 86.5 + - - +
286A GLY* 1.3 61.6 + - - +
314A GLU* 3.2 26.4 - - + +
348A CYS* 5.0 13.2 - - - -
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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