Contacts of the helix formed by residues 259 - 263 (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 ILE 259 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U LEU* 5.3 2.5 - - + -
83U ALA* 5.0 2.2 - - - -
256U ILE* 4.4 23.8 - - + +
257U ASP 3.5 0.9 + - - -
258U GLU* 1.3 70.4 - - - +
260U ASP* 1.3 60.9 + - - +
261U LYS 2.8 2.7 - - - -
262U ILE* 2.6 64.7 + - + +
263U CYS* 4.1 0.6 - - - -
282U LEU* 6.0 1.1 - - + -
307U ALA* 4.1 22.0 - - + +
308U SER 3.0 22.8 + - - +
311U PHE* 3.5 23.6 - - + -
319U LEU* 4.6 15.3 - - + -
323U LEU* 4.5 20.2 - - + -
327U LEU* 5.2 3.8 - - + -
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Residues in contact with ASP 260 (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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258U GLU* 3.8 8.6 - - - +
259U ILE* 1.3 80.0 + - - +
261U LYS* 1.3 72.2 + - - +
262U ILE 2.6 13.2 + - - -
263U CYS* 2.9 26.5 + - - +
309U GLY* 3.0 27.2 - - - -
310U ALA* 3.3 12.5 + - - +
311U PHE* 3.1 39.1 + - + +
312U GLN* 5.1 3.6 + - - -
313U VAL* 4.6 19.3 - - + +
314U ALA* 5.0 3.9 - - + +
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Residues in contact with LYS 261 (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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276T GLU* 5.4 5.3 + - - -
280T ARG* 3.5 34.3 - - - +
82U GLU* 5.2 1.1 - - - +
83U ALA* 5.5 6.1 - - + -
258U GLU* 4.0 30.7 - - + +
259U ILE 2.7 4.2 + - - -
260U ASP* 1.3 86.7 - - - +
262U ILE* 1.3 62.7 + - + +
263U CYS 3.6 0.7 - - - -
275U ARG* 3.7 27.0 + - - +
312U GLN* 5.3 9.1 - - - +
313U VAL* 6.4 1.6 - - + -
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Residues in contact with ILE 262 (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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83U ALA* 3.4 34.3 - - + -
256U ILE* 6.1 0.2 - - + -
259U ILE* 2.6 46.7 + - + +
260U ASP 2.6 1.6 + - - -
261U LYS* 1.3 77.8 - - + +
263U CYS* 1.3 60.3 + - - +
264U LYS 4.2 0.2 + - - -
275U ARG* 2.6 42.4 - - + +
276U GLU* 4.1 0.7 + - - -
278U VAL* 4.4 13.5 - - + -
279U GLN* 3.0 48.4 - - + +
282U LEU* 5.4 6.5 - - + -
323U LEU* 5.7 0.4 - - + -
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Residues in contact with CYS 263 (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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259U ILE 4.1 0.9 - - - -
260U ASP* 2.9 33.4 + - - +
261U LYS 3.6 0.6 - - - -
262U ILE* 1.3 82.5 - - - +
264U LYS* 1.3 65.8 + - - +
265U LYS 3.3 11.0 + - - +
269U SER* 4.6 0.2 + - - -
275U ARG* 4.4 14.8 + - - -
279U GLN* 4.1 2.2 - - - -
311U PHE* 4.4 7.4 - - - -
314U ALA* 3.9 23.6 - - + -
318U ASP* 3.5 14.1 - - + +
319U LEU* 3.3 33.2 - - - -
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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