Contacts of the helix formed by residues 274 - 282 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272X ASP* 2.9 15.3 - - - +
273X VAL* 1.3 76.1 - - - +
275X ARG* 1.3 62.4 + - - +
276X GLU 3.1 0.4 - - - -
277X GLY* 3.1 16.8 + - - +
278X VAL* 3.2 19.4 + - - +
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Residues in contact with ARG 275 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273W VAL* 5.5 11.9 - - - +
261X LYS* 3.7 23.8 + - - +
262X ILE* 2.6 45.6 - - + +
263X CYS 4.4 9.9 + - - +
264X LYS* 6.0 0.4 - - - -
265X LYS 4.2 16.2 + - - -
269X SER* 4.0 13.8 + - - +
272X ASP* 3.7 34.6 + - + +
273X VAL 3.0 1.2 - - - -
274X SER* 1.3 81.9 - - - +
276X GLU* 1.3 55.1 + - - +
277X GLY 3.3 0.2 - - - -
278X VAL* 4.2 3.5 + - - +
279X GLN* 3.8 7.1 + - - +
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Residues in contact with GLU 276 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261S LYS* 5.4 5.0 + - - -
262X ILE 4.3 2.9 - - - +
264X LYS* 4.5 29.2 + - + +
273X VAL* 3.1 27.0 + - + +
275X ARG* 1.3 78.7 - - - +
277X GLY* 1.3 59.3 + - - +
278X VAL 3.5 0.4 - - - -
279X GLN* 4.0 10.1 - - - +
280X ARG* 3.2 38.3 + - - +
320X ILE* 3.8 27.3 - - + +
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Residues in contact with GLY 277 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273X VAL 3.4 4.0 + - - -
274X SER* 3.1 13.8 + - - -
276X GLU* 1.3 79.3 - - - +
278X VAL* 1.3 53.8 + - - +
280X ARG* 2.8 9.2 + - - +
281X ASP* 2.7 45.6 + - - +
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Residues in contact with VAL 278 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83X ALA* 4.8 12.8 - - + +
96X VAL* 6.0 3.6 - - + -
262X ILE* 4.4 22.0 - - + -
274X SER 3.2 14.2 + - - +
275X ARG* 4.5 5.6 - - - +
277X GLY* 1.3 69.6 - - - +
279X GLN* 1.3 59.0 + - - +
280X ARG 2.8 14.0 + - - -
281X ASP* 3.1 8.7 + - - +
282X LEU* 2.9 42.2 + - + +
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Residues in contact with GLN 279 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262X ILE* 3.0 41.1 - - + +
263X CYS* 4.1 2.8 - - - -
264X LYS 5.2 0.3 + - - -
275X ARG 3.8 10.1 + - - +
276X GLU* 4.0 10.6 - - - +
277X GLY 3.3 0.2 - - - -
278X VAL* 1.3 79.8 - - - +
280X ARG* 1.3 57.2 + - - +
282X LEU* 4.2 6.3 - - - +
283X LEU 4.1 2.9 + - - -
318X ASP 4.5 0.5 - - - +
319X LEU* 3.1 32.1 - - + +
320X ILE* 2.4 71.3 - - + +
323X LEU* 3.5 26.1 - - + +
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Residues in contact with ARG 280 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82S GLU* 3.9 39.1 + - + +
258S GLU* 3.1 29.5 + - - +
261S LYS* 3.4 33.9 - - - +
276X GLU* 3.2 27.4 + - - +
277X GLY* 2.8 14.3 + - - +
278X VAL 2.8 2.2 + - - -
279X GLN* 1.3 77.9 - - - +
281X ASP* 1.3 56.8 + - - +
282X LEU 3.0 4.7 - - - -
283X LEU* 3.0 28.9 + - - +
284X PRO* 3.4 4.0 - - - +
320X ILE* 3.5 33.5 - - - +
322X GLU* 3.7 12.1 + - - -
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Residues in contact with ASP 281 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82S GLU* 4.9 10.3 - - - +
83S ALA 5.4 2.1 - - - +
96X VAL* 3.1 40.5 - - + +
277X GLY* 2.7 26.9 + - - +
278X VAL* 3.1 5.5 + - - +
280X ARG* 1.3 73.4 - - - +
282X LEU* 1.3 55.3 + - - +
283X LEU 3.2 1.6 - - - -
284X PRO* 3.4 15.6 - - - +
285X LEU* 4.2 4.7 - - - +
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Residues in contact with LEU 282 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83X ALA* 6.2 1.6 - - + -
96X VAL* 3.3 27.1 - - + -
99X ILE* 3.6 24.9 - - + -
256X ILE* 3.4 38.1 - - + -
259X ILE* 6.1 1.8 - - + -
262X ILE* 5.5 7.2 - - + -
278X VAL* 2.9 31.6 + - + +
279X GLN* 4.4 7.0 - - - +
280X ARG 3.0 0.2 - - - -
281X ASP* 1.3 76.6 - - - +
283X LEU* 1.3 62.2 + - - +
285X LEU* 3.9 12.3 + - + +
286X VAL* 3.6 23.8 + - + +
323X LEU* 4.9 8.6 - - + +
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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