Contacts of the helix formed by residues 265 - 274 (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 ASP 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A TYR* 3.5 33.0 + - + +
97A ALA 5.1 0.4 + - - -
264A ALA* 1.3 74.1 - - - +
266A GLY* 1.3 69.1 + - - +
267A PRO* 3.2 25.3 - - - +
268A LEU* 3.4 23.3 + - + +
269A PHE* 3.0 22.2 + - - +
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Residues in contact with GLY 266 (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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233A LYS* 4.3 21.4 - - - +
264A ALA 3.4 3.2 + - - -
265A ASP* 1.3 73.0 + - - +
267A PRO* 1.3 65.9 - - - +
269A PHE* 3.3 3.5 + - - +
270A GLY* 2.9 25.8 + - - -
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Residues in contact with PRO 267 (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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265A ASP* 3.2 19.3 - - - +
266A GLY* 1.3 85.4 - - - +
268A LEU* 1.3 55.1 + - - +
270A GLY* 3.3 2.3 + - - -
271A ASP* 2.7 47.6 + - - +
293A HIS* 6.3 3.4 - - + -
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Residues in contact with LEU 268 (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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97A ALA 4.0 15.7 - - - +
98A ASP* 4.5 1.1 - - - -
99A LYS* 4.0 21.5 - - + +
102A LEU* 3.6 24.9 - - + -
264A ALA* 5.2 1.6 - - + -
265A ASP* 3.4 24.5 + - + +
267A PRO* 1.3 76.9 - - - +
269A PHE* 1.3 62.7 + - - +
271A ASP* 3.3 10.6 + - + +
272A THR* 2.9 38.6 + - - +
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Residues in contact with PHE 269 (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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102A LEU* 3.9 29.4 - - + -
205A ALA* 4.0 14.4 - - + -
207A ILE* 3.7 33.9 - - + -
231A LEU* 3.6 25.8 - - + -
233A LYS* 3.8 32.1 - - + -
262A VAL* 4.0 19.5 - - + -
264A ALA* 4.0 11.4 - - + -
265A ASP 3.0 17.2 + - - +
266A GLY 3.6 3.6 - - - +
268A LEU* 1.3 75.9 - - - +
270A GLY* 1.3 66.0 + - - +
272A THR* 3.2 1.7 + - - -
273A VAL* 3.0 44.4 + - + +
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Residues in contact with GLY 270 (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* 5.6 0.7 - - - -
266A GLY 2.9 15.0 + - - -
267A PRO* 3.7 3.8 - - - -
269A PHE* 1.3 79.0 - - - +
271A ASP* 1.3 56.1 + - - +
273A VAL* 4.2 4.5 - - - -
274A THR* 2.8 39.1 + - - +
294A LEU* 3.8 22.2 - - - -
297A GLN* 4.0 5.6 - - - -
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Residues in contact with ASP 271 (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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267A PRO* 2.7 35.6 + - - +
268A LEU* 3.6 11.7 - - + +
270A GLY* 1.3 73.3 - - - +
272A THR* 1.3 60.3 + - - +
274A THR* 3.5 5.7 + - - -
275A SER* 2.8 30.4 + - - +
293A HIS* 4.6 5.4 - - - -
297A GLN* 2.9 25.6 + - - +
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Residues in contact with THR 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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99A LYS* 4.4 10.6 - - + +
102A LEU* 3.8 31.7 - - + +
103A ASN* 3.8 29.4 + - - +
106A ILE* 4.8 3.8 - - + -
268A LEU* 2.9 29.3 + - - +
269A PHE 3.8 2.7 - - - -
271A ASP* 1.3 77.6 - - - +
273A VAL* 1.3 64.8 + - + +
275A SER* 3.2 14.1 + - - -
276A SER* 3.3 13.0 + - - -
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Residues in contact with VAL 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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102A LEU* 5.8 0.7 - - + -
106A ILE* 4.9 2.0 - - + -
203A PHE* 3.9 32.0 - - + -
205A ALA* 4.0 16.4 - - + -
207A ILE* 5.7 1.1 - - + -
231A LEU* 4.4 8.5 - - + -
269A PHE* 3.0 49.6 + - + +
270A GLY* 3.7 9.9 - - - +
272A THR* 1.3 75.3 - - + +
274A THR* 1.3 70.4 + - + +
275A SER 3.1 6.0 + - - -
276A SER* 3.4 11.0 + - - +
279A LEU* 3.5 24.4 - - + +
282A ILE* 5.0 5.2 - - + -
294A LEU* 5.5 1.1 - - + -
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Residues in contact with THR 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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270A GLY 2.8 23.1 + - - +
271A ASP* 3.5 5.7 + - - -
273A VAL* 1.3 76.4 - - + +
275A SER* 1.3 57.4 + - - +
276A SER 3.6 0.4 - - - -
279A LEU* 4.0 7.0 - - - -
282A ILE* 4.0 17.3 - - + -
294A LEU* 4.2 10.8 - - + +
297A GLN* 3.6 33.8 + - + +
298A VAL* 3.7 25.8 - - + -
301A ASN* 2.9 22.5 + - - +
305A PHE* 3.4 16.3 - - - -
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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