Contacts of the helix formed by residues 311 - 317 (chain B) in PDB entry 2G1O
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 GLY 311 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221B ASP 3.0 16.8 - - - -
224B ALA* 3.3 5.6 - - - -
226B TYR 3.1 23.4 + - - -
227B ILE* 4.3 1.0 - - - +
309B ALA 3.7 0.4 - - - -
310B LEU* 1.3 74.3 - - - +
312B ALA* 1.3 68.0 + - - -
313B THR 3.1 2.7 - - - -
314B PHE* 2.9 12.9 + - - +
315B ILE* 3.0 17.8 + - - +
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASP 4.3 0.9 - - - +
15B TYR* 3.9 9.0 - - + -
157B TYR* 3.7 28.9 - - + -
221B ASP 4.2 0.2 + - - -
224B ALA 2.7 13.4 + - - +
225B SER* 3.0 23.1 + - - +
311B GLY* 1.3 69.8 - - - -
313B THR* 1.3 52.3 + - - +
315B ILE* 4.1 2.0 - - - +
316B ARG* 2.7 57.6 + - - +
886B 2IG 5.2 0.7 - - - -
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Residues in contact with THR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B SER 3.5 2.6 + - - -
226B TYR* 3.4 12.6 - - - -
227B ILE* 3.5 26.5 - - + -
274B LEU* 4.1 6.6 - - + +
278B ASP 3.6 24.4 - - - +
279B TYR* 4.3 4.9 - - + -
294B ALA* 3.0 39.2 + - + +
311B GLY 3.0 1.2 + - - -
312B ALA* 1.3 80.1 - - - +
314B PHE* 1.3 63.5 + - - +
316B ARG* 3.6 22.9 + - - +
317B LYS* 3.6 7.8 + - - +
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Residues in contact with PHE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B VAL* 6.0 0.4 - - + -
227B ILE* 3.8 12.3 - - + +
265B PHE* 3.8 29.8 - + - -
267B LEU* 4.2 4.5 - - + -
272B TYR* 3.4 37.2 - + + -
274B LEU* 4.5 7.0 - - + -
310B LEU* 3.8 44.9 - - + -
311B GLY 2.9 7.8 + - - +
313B THR* 1.3 78.1 - - - +
315B ILE* 1.3 61.9 + - + +
317B LYS* 3.0 8.7 + - - +
318B PHE* 2.9 42.9 + + + -
331B PHE* 3.8 35.7 - + - -
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Residues in contact with ILE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B PHE* 4.4 18.6 - - + +
157B TYR* 4.1 34.4 + - + +
220B VAL* 5.0 7.6 - - + -
221B ASP 4.0 2.9 - - - +
222B THR* 3.6 42.2 - - + +
310B LEU 4.3 6.1 - - - +
311B GLY* 3.0 22.6 + - - +
312B ALA 3.8 4.0 - - - +
314B PHE* 1.3 75.9 - - + +
316B ARG* 1.3 65.6 + - - +
318B PHE 2.9 29.7 - - - +
319B TYR* 4.0 2.3 + - - -
320B THR* 4.2 14.6 - - - +
334B ALA* 4.7 1.7 - - - +
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Residues in contact with ARG 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ASP* 2.8 49.6 + - - +
15B TYR* 3.1 27.3 + - - -
157B TYR* 3.7 17.4 - - + +
158B ASN 3.3 14.4 - - - +
159B ARG* 3.6 37.5 + - + +
225B SER 4.8 1.4 + - - -
226B TYR* 5.9 0.2 - - - -
278B ASP 5.3 4.0 + - - -
281B PHE* 4.3 16.0 - - - -
294B ALA* 4.5 1.2 - - - +
312B ALA* 2.7 33.9 + - - +
313B THR* 3.6 32.6 + - - +
315B ILE* 1.3 74.4 - - - +
317B LYS* 1.3 60.4 + - - +
334B ALA* 3.9 9.9 - - - +
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Residues in contact with LYS 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ARG* 4.1 11.8 + - - +
273B THR 3.2 18.6 + - - -
274B LEU* 3.3 16.6 - - + -
275B THR* 4.7 11.3 + - - +
278B ASP* 2.6 36.6 + - - +
313B THR 3.6 3.7 + - - +
314B PHE 3.0 9.9 + - - +
316B ARG* 1.3 81.6 - - - +
318B PHE* 1.3 85.8 + - + +
333B LEU* 4.0 21.2 - - + +
334B ALA* 3.1 21.8 + - - +
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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