Contacts of the helix formed by residues 282 - 288 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81W VAL* 6.2 0.2 - - + -
83W ALA* 6.2 1.8 - - + -
96W VAL* 3.3 26.5 - - + -
99W ILE* 3.6 24.2 - - + -
256W ILE* 3.5 37.7 - - + -
259W ILE* 6.1 1.1 - - + -
262W ILE* 5.4 7.6 - - + -
278W VAL* 3.0 31.0 + - + +
279W GLN* 4.4 7.6 - - - +
280W ARG 3.0 1.0 - - - -
281W ASP* 1.3 77.7 - - - +
283W LEU* 1.3 63.0 + - - +
284W PRO 3.6 0.2 - - - -
285W LEU* 3.9 12.1 + - + +
286W VAL* 3.7 22.8 + - + +
323W LEU* 4.9 9.1 - - + +
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Residues in contact with LEU 283 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279W GLN 4.1 1.1 + - - +
280W ARG* 3.0 26.5 + - - +
282W LEU* 1.3 75.3 - - - +
284W PRO* 1.3 69.1 - - + +
285W LEU 2.9 2.7 + - - -
286W VAL* 2.9 13.7 + - + +
287W GLU* 2.8 52.2 + - + +
322W GLU* 3.3 41.7 - - + +
323W LEU* 3.2 31.2 - - + +
326W ARG* 5.0 1.6 - - + -
82X GLU* 4.3 17.7 - - - +
257X ASP* 5.4 2.5 - - - +
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Residues in contact with PRO 284 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280W ARG 3.3 9.2 - - - +
281W ASP* 3.4 14.6 - - - +
283W LEU* 1.3 95.5 - - + +
285W LEU* 1.3 63.1 + - + +
287W GLU* 4.2 12.3 - - + +
288W GLY 2.9 32.6 + - - -
289W SER* 3.5 15.6 + - - +
82X GLU* 5.3 12.1 - - + -
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Residues in contact with LEU 285 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96W VAL* 3.7 27.1 - - + +
97W ASP* 3.8 21.8 - - - +
99W ILE* 4.3 17.5 - - + -
100W ILE* 4.1 27.8 - - + -
281W ASP 4.2 15.9 - - - +
282W LEU* 3.9 12.1 + - + +
283W LEU 2.9 0.8 + - - -
284W PRO* 1.3 84.1 - - + +
286W VAL* 1.3 64.7 + - + +
287W GLU 3.2 0.7 + - - -
288W GLY 4.1 0.9 + - - -
289W SER* 5.5 3.4 - - - -
291W VAL* 5.2 3.4 - - + -
300W THR* 3.7 23.7 + - + +
305W PHE* 3.1 29.8 - - + -
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Residues in contact with VAL 286 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49W THR* 5.1 2.3 - - - +
52W ASN* 4.4 5.9 + - - +
256W ILE* 5.6 6.7 - - + -
282W LEU* 3.7 16.4 + - + +
283W LEU* 3.1 31.0 - - + +
285W LEU* 1.3 78.3 - - + +
287W GLU* 1.3 60.5 + - - +
301W ASP* 5.6 0.9 - - - +
305W PHE* 3.4 41.2 - - + -
323W LEU* 4.4 14.1 - - + -
326W ARG* 3.3 41.4 + - + +
327W LEU* 5.2 6.1 - - + -
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Residues in contact with GLU 287 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49W THR* 5.1 1.4 + - - -
283W LEU* 2.8 46.1 + - + +
284W PRO* 3.8 10.5 - - + +
285W LEU 4.4 0.2 - - - -
286W VAL* 1.3 80.9 - - + +
288W GLY* 1.3 61.2 + - - +
301W ASP* 4.0 15.6 - - - +
322W GLU* 5.4 0.2 - - - +
326W ARG* 3.4 26.7 + - + +
80X LYS* 3.2 35.0 + - - +
257X ASP* 5.5 1.8 - - - +
394X ARG* 2.7 31.7 + - - +
461X ATP 5.3 1.6 + - - -
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Residues in contact with GLY 288 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284W PRO* 2.9 12.1 + - - +
285W LEU 4.1 0.8 + - - -
286W VAL 3.8 0.2 - - - -
287W GLU* 1.3 77.4 - - - +
289W SER* 1.3 62.0 + - - -
300W THR* 3.5 7.9 - - - -
301W ASP* 3.2 28.3 - - - +
68X ARG* 4.9 11.1 + - - -
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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