Contacts of the helix formed by residues 282 - 288 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81T VAL* 6.1 0.2 - - + -
83T ALA* 6.2 1.8 - - + -
96T VAL* 3.3 27.4 - - + -
99T ILE* 3.5 24.5 - - + -
256T ILE* 3.5 37.7 - - + -
259T ILE* 6.1 0.9 - - + -
262T ILE* 5.4 7.2 - - + -
278T VAL* 3.0 31.0 + - + +
279T GLN* 4.4 7.2 - - - +
280T ARG 2.9 0.8 - - - -
281T ASP* 1.3 79.0 - - - +
283T LEU* 1.3 60.0 + - - +
284T PRO 3.6 0.9 - - - -
285T LEU* 3.9 11.1 + - + +
286T VAL* 3.6 24.2 + - + +
323T LEU* 4.9 9.3 - - + +
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Residues in contact with LEU 283 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279T GLN 4.1 1.1 + - - +
280T ARG* 3.0 26.1 + - - +
282T LEU* 1.3 76.9 - - - +
284T PRO* 1.3 63.2 - - + +
285T LEU 2.9 2.7 + - - -
286T VAL* 3.0 12.3 + - + +
287T GLU* 2.8 56.6 + - + +
320T ILE* 5.2 0.2 - - + -
322T GLU* 3.3 41.5 - - + +
323T LEU* 3.2 30.1 - - + +
326T ARG* 5.1 1.8 - - + -
82U GLU* 4.1 19.3 - - - +
257U ASP* 5.4 2.2 - - - +
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Residues in contact with PRO 284 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280T ARG 3.3 9.6 - - - +
281T ASP* 3.4 14.4 - - - +
283T LEU* 1.3 96.3 - - + +
285T LEU* 1.3 63.8 + - + +
287T GLU* 3.8 11.9 - - + +
288T GLY 2.9 33.4 + - - +
289T SER* 3.5 15.8 + - - +
80U LYS 6.1 1.1 - - - +
82U GLU* 5.4 11.9 - - + +
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Residues in contact with LEU 285 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96T VAL* 3.7 27.6 - - + +
97T ASP* 3.8 22.2 - - - +
99T ILE* 4.3 17.0 - - + -
100T ILE* 4.1 27.6 - - + -
281T ASP 4.2 16.2 - - - +
282T LEU* 4.1 11.2 - - + +
283T LEU 3.0 0.8 - - - -
284T PRO* 1.3 85.4 - - + +
286T VAL* 1.3 63.1 + - + +
287T GLU 3.2 0.7 + - - -
288T GLY 4.1 1.2 + - - -
289T SER* 5.5 3.1 - - - -
291T VAL* 5.2 5.4 - - + -
300T THR* 3.8 21.4 + - + +
301T ASP* 5.7 0.2 - - - -
305T PHE* 3.1 29.5 - - + -
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Residues in contact with VAL 286 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49T THR* 5.1 2.8 - - - +
52T ASN* 4.4 5.4 + - - +
256T ILE* 5.6 7.2 - - + -
282T LEU* 3.6 16.1 + - + +
283T LEU* 3.1 31.2 - - + +
285T LEU* 1.3 76.6 - - + +
287T GLU* 1.3 61.1 + - - +
301T ASP* 5.6 0.7 - - - +
305T PHE* 3.3 41.7 - - + -
323T LEU* 4.4 13.7 - - + -
326T ARG* 3.3 41.4 + - + +
327T LEU* 5.2 6.1 - - + -
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Residues in contact with GLU 287 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49T THR* 5.1 1.2 + - - -
283T LEU* 2.8 48.6 + - + +
284T PRO* 3.9 9.1 - - + +
285T LEU 4.4 0.2 - - - -
286T VAL* 1.3 79.8 - - - +
288T GLY* 1.3 61.4 + - - +
301T ASP* 4.0 14.9 - - - +
322T GLU* 5.5 0.3 - - - +
326T ARG* 3.4 28.9 + - + +
80U LYS* 2.9 36.7 + - - +
257U ASP* 5.4 2.1 - - - +
394U ARG* 2.9 29.5 + - - +
458U ATP 4.2 1.0 + - - -
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Residues in contact with GLY 288 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284T PRO* 2.9 11.5 + - - +
285T LEU 4.1 1.0 + - - -
286T VAL 3.8 0.2 - - - -
287T GLU* 1.3 78.5 - - - +
289T SER* 1.3 62.5 + - - -
300T THR* 3.5 7.9 - - - -
301T ASP* 3.1 28.5 - - - +
68U ARG* 4.8 11.6 + - - -
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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