Contacts of the helix formed by residues 274 - 282 (chain V) in PDB entry 1G3I
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 SER 274 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272V ASP* 4.0 16.6 - - - +
273V VAL* 1.3 75.1 - - - +
275V ARG* 1.3 61.8 + - - +
276V GLU 3.1 2.5 - - - -
277V GLY* 3.1 16.7 + - - +
278V VAL* 3.2 19.6 + - - +
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Residues in contact with ARG 275 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273U VAL* 5.7 9.9 - - - +
261V LYS* 3.7 23.6 + - - +
262V ILE* 2.7 45.5 - - + +
263V CYS 4.4 9.3 + - - +
264V LYS* 6.0 0.4 - - - -
265V LYS 4.2 16.4 + - - -
269V SER* 4.1 13.4 + - - +
272V ASP* 3.8 34.2 + - + +
273V VAL 3.1 0.8 - - - -
274V SER* 1.3 80.8 - - - +
276V GLU* 1.3 56.7 + - - +
277V GLY 3.3 0.2 - - - -
278V VAL* 4.2 3.4 + - - +
279V GLN* 3.8 7.1 + - - +
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Residues in contact with GLU 276 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262V ILE 4.4 1.8 - - - -
264V LYS* 4.5 29.1 + - + +
273V VAL* 3.1 27.3 + - + +
275V ARG* 1.3 78.3 - - - +
277V GLY* 1.3 63.8 + - - +
279V GLN* 4.0 11.0 - - - +
280V ARG* 3.2 34.5 + - - +
320V ILE* 3.8 27.0 - - + +
261W LYS* 5.4 4.9 + - - -
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Residues in contact with GLY 277 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273V VAL 3.4 3.9 + - - -
274V SER* 3.1 13.4 + - - -
276V GLU* 1.3 78.4 - - - +
278V VAL* 1.3 52.6 + - - +
280V ARG* 2.8 9.3 + - - +
281V ASP* 2.7 43.9 + - - +
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Residues in contact with VAL 278 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83V ALA* 4.8 12.3 - - + +
96V VAL* 6.0 3.8 - - + -
262V ILE* 4.4 20.9 - - + -
274V SER 3.2 14.2 + - - +
275V ARG* 4.4 6.3 - - - +
277V GLY* 1.3 69.0 - - - +
279V GLN* 1.3 57.5 + - - +
280V ARG 2.8 13.8 + - - -
281V ASP* 3.1 9.2 + - - +
282V LEU* 2.9 42.8 + - + +
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Residues in contact with GLN 279 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262V ILE* 3.0 42.4 - - + +
263V CYS* 4.1 3.1 - - - -
264V LYS 5.2 0.2 + - - -
275V ARG 3.8 9.2 + - - +
276V GLU* 4.0 10.2 - - - +
277V GLY 3.3 0.2 - - - -
278V VAL* 1.3 78.8 - - - +
280V ARG* 1.3 57.9 + - - +
282V LEU* 4.2 5.9 - - - +
283V LEU 4.1 2.9 + - - -
318V ASP 4.5 0.7 - - - +
319V LEU* 3.1 30.2 - - + +
320V ILE* 2.4 71.8 - - + +
323V LEU* 3.5 25.4 - - + +
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Residues in contact with ARG 280 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276V GLU* 3.2 26.5 + - - +
277V GLY* 2.8 14.5 + - - +
278V VAL 2.8 1.8 + - - -
279V GLN* 1.3 77.3 - - - +
281V ASP* 1.3 57.7 + - - +
282V LEU 3.0 4.5 - - - -
283V LEU* 3.0 29.9 + - - +
284V PRO* 3.4 4.5 - - - +
320V ILE* 3.5 33.2 - - - +
322V GLU* 3.7 12.6 + - - -
82W GLU* 3.8 38.4 + - + +
258W GLU* 3.1 30.1 + - - +
261W LYS* 3.6 32.0 - - - +
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Residues in contact with ASP 281 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96V VAL* 3.0 42.6 - - + +
277V GLY* 2.7 27.6 + - - +
278V VAL* 3.1 6.6 + - - +
280V ARG* 1.3 73.6 - - - +
282V LEU* 1.3 55.8 + - - +
283V LEU 3.2 1.6 - - - -
284V PRO* 3.4 15.6 - - - +
285V LEU* 4.2 4.3 - - - +
82W GLU* 5.0 9.9 - - - +
83W ALA 5.6 1.2 - - - +
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Residues in contact with LEU 282 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83V ALA* 6.2 2.0 - - + -
96V VAL* 3.3 26.5 - - + -
99V ILE* 3.6 25.4 - - + -
256V ILE* 3.5 37.2 - - + -
259V ILE* 6.1 1.6 - - + -
262V ILE* 5.5 7.2 - - + -
278V VAL* 2.9 30.7 + - + +
279V GLN* 4.4 7.2 - - - +
280V ARG 3.0 0.2 - - - -
281V ASP* 1.3 77.0 - - - +
283V LEU* 1.3 61.9 + - - +
284V PRO 3.6 0.4 - - - -
285V LEU* 3.9 11.1 + - + +
286V VAL* 3.7 23.3 + - + +
323V LEU* 4.9 9.0 - - + +
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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