Contacts of the helix formed by residues 282 - 288 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81U VAL* 6.1 0.2 - - + -
83U ALA* 6.2 1.8 - - + -
96U VAL* 3.3 26.9 - - + -
99U ILE* 3.6 24.2 - - + -
256U ILE* 3.4 37.9 - - + -
259U ILE* 6.0 1.3 - - + -
262U ILE* 5.4 7.4 - - + -
278U VAL* 2.9 31.3 + - + +
279U GLN* 4.4 7.2 - - - +
281U ASP* 1.3 78.6 - - - +
283U LEU* 1.3 60.5 + - - +
284U PRO 3.6 0.4 - - - -
285U LEU* 3.9 11.8 + - + +
286U VAL* 3.6 23.1 + - + +
323U LEU* 5.0 9.0 - - + +
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Residues in contact with LEU 283 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279U GLN 4.1 1.1 + - - +
280U ARG* 3.0 27.0 + - - +
282U LEU* 1.3 76.0 - - - +
284U PRO* 1.3 70.1 - - + +
285U LEU 2.9 2.7 + - - -
286U VAL* 3.0 13.5 + - + +
287U GLU* 2.8 51.1 + - + +
322U GLU* 3.3 42.4 - - + +
323U LEU* 3.2 31.0 - - + +
326U ARG* 5.1 1.3 - - + -
82V GLU* 4.2 18.6 - - - +
257V ASP* 5.3 2.0 - - - +
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Residues in contact with PRO 284 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280U ARG 3.4 9.0 - - - +
281U ASP* 3.4 14.6 - - - +
283U LEU* 1.3 94.1 - - + +
285U LEU* 1.3 64.6 + - + +
287U GLU* 4.2 12.3 - - + +
288U GLY 2.9 23.8 + - - +
289U SER* 3.5 25.4 + - - -
80V LYS* 6.0 2.2 - - - +
82V GLU* 5.2 13.0 - - + +
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Residues in contact with LEU 285 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96U VAL* 3.8 27.4 - - + +
97U ASP* 3.8 21.5 - - - +
99U ILE* 4.3 17.3 - - + -
100U ILE* 4.1 27.8 - - + -
281U ASP 4.2 16.2 - - - +
282U LEU* 4.0 11.9 - - + +
283U LEU 2.9 1.0 + - - -
284U PRO* 1.3 85.3 - - + +
286U VAL* 1.3 64.3 + - + +
287U GLU 3.2 0.4 - - - -
288U GLY 4.1 1.0 + - - -
289U SER* 5.5 3.1 - - - -
291U VAL* 5.2 3.8 - - + -
300U THR* 3.8 23.5 + - + +
301U ASP* 5.7 0.2 - - - -
305U PHE* 3.0 29.0 - - + -
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Residues in contact with VAL 286 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49U THR* 5.1 2.9 - - - +
52U ASN* 4.4 5.7 + - - +
256U ILE* 5.6 7.0 - - + -
282U LEU* 3.6 16.6 + - + +
283U LEU* 3.1 30.7 - - + +
285U LEU* 1.3 75.4 - - - +
287U GLU* 1.3 62.1 + - - +
301U ASP* 5.5 1.4 - - - +
305U PHE* 3.3 41.6 - - + -
323U LEU* 4.4 13.7 - - + -
326U ARG* 3.3 39.4 + - + +
327U LEU* 5.2 8.1 - - + -
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Residues in contact with GLU 287 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49U THR* 5.1 1.6 + - - -
283U LEU* 2.8 47.6 + - + +
284U PRO* 3.9 11.3 - - + +
285U LEU 4.5 0.4 - - - -
286U VAL* 1.3 80.4 - - - +
288U GLY* 1.3 60.6 + - - +
301U ASP* 4.0 14.6 - - - +
322U GLU* 5.4 0.3 - - - +
326U ARG* 3.4 27.6 + - + +
80V LYS* 2.9 36.9 + - - +
257V ASP* 5.4 2.3 - - - +
394V ARG* 2.8 29.5 + - - +
459V ATP 5.5 0.9 + - - -
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Residues in contact with GLY 288 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284U PRO* 2.9 8.9 + - - +
285U LEU 4.1 0.8 + - - -
286U VAL 3.8 0.2 - - - -
287U GLU* 1.3 81.2 - - - +
289U SER* 1.3 61.0 + - - -
300U THR* 3.5 8.1 - - - -
301U ASP* 3.2 28.5 - - - +
68V ARG* 4.6 13.2 + - - -
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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