Contacts of the helix formed by residues 282 - 288 (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 LEU 282 (chain X).
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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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Residues in contact with LEU 283 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82S GLU* 3.8 21.8 - - - +
257S ASP* 5.2 1.8 - - - +
279X GLN 4.1 1.3 + - - +
280X ARG* 3.0 23.8 + - - +
282X LEU* 1.3 75.5 - - - +
284X PRO* 1.3 63.8 - - + +
285X LEU 2.9 2.8 + - - -
286X VAL* 3.0 13.9 + - + +
287X GLU* 2.8 56.8 + - + +
320X ILE* 5.1 0.2 - - + -
322X GLU* 3.4 40.8 - - + +
323X LEU* 3.2 31.0 - - + +
326X ARG* 5.0 1.6 - - + -
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Residues in contact with PRO 284 (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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80S LYS* 5.8 4.7 - - - +
81S VAL* 6.4 0.7 - - - -
82S GLU* 5.0 14.8 - - + +
280X ARG 3.4 10.3 - - - +
281X ASP* 3.4 14.6 - - - +
283X LEU* 1.3 94.8 - - + +
285X LEU* 1.3 64.1 + - + +
287X GLU* 4.2 12.1 - - + +
288X GLY 2.9 24.0 + - - +
289X SER* 3.5 24.6 + - - +
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Residues in contact with LEU 285 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96X VAL* 3.8 27.6 - - + +
97X ASP* 3.8 21.1 - - - +
99X ILE* 4.3 17.0 - - + -
100X ILE* 4.1 28.3 - - + -
281X ASP 4.2 16.2 - - - +
282X LEU* 3.9 11.9 + - + +
283X LEU 2.9 1.2 + - - -
284X PRO* 1.3 83.0 - - + +
286X VAL* 1.3 63.7 + - + +
287X GLU 3.2 1.6 + - - -
288X GLY 4.1 1.0 + - - -
289X SER* 5.5 3.1 - - - -
291X VAL* 5.3 3.8 - - + -
300X THR* 3.8 23.6 + - + +
301X ASP* 5.7 0.2 - - - -
305X PHE* 3.0 29.8 - - + -
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Residues in contact with VAL 286 (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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49X THR* 5.1 2.8 - - - +
52X ASN* 4.3 6.0 + - - +
256X ILE* 5.6 7.0 - - + -
282X LEU* 3.6 17.2 + - + +
283X LEU* 3.1 30.5 - - + +
285X LEU* 1.3 76.6 - - + +
287X GLU* 1.3 62.0 + - - +
301X ASP* 5.5 1.3 - - - +
305X PHE* 3.3 41.1 - - + -
323X LEU* 4.4 13.7 - - + -
326X ARG* 3.3 39.5 + - + +
327X LEU* 5.3 6.1 - - + -
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Residues in contact with GLU 287 (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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80S LYS* 2.7 38.4 + - - +
82S GLU* 5.4 0.5 - - - +
257S ASP* 5.2 0.9 - - - +
394S ARG* 2.8 28.2 + - - +
456S ATP 4.6 2.3 + - - -
49X THR* 5.1 1.4 + - - +
283X LEU* 2.8 48.7 + - + +
284X PRO* 3.9 11.5 - - + +
285X LEU 4.4 0.2 - - - -
286X VAL* 1.3 79.0 - - - +
288X GLY* 1.3 60.1 + - - +
301X ASP* 4.1 15.7 - - - +
322X GLU* 5.5 0.2 - - - +
326X ARG* 3.4 28.6 + - + +
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Residues in contact with GLY 288 (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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68S ARG* 4.5 14.6 + - - -
80S LYS* 6.1 0.9 - - - -
284X PRO* 2.9 11.3 + - - +
285X LEU 4.1 0.6 + - - -
286X VAL 3.8 0.2 - - - -
287X GLU* 1.3 79.4 - - - +
289X SER* 1.3 61.7 + - - -
300X THR* 3.5 7.9 - - - -
301X ASP* 3.2 28.2 - - - +
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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