Contacts of the helix formed by residues 311 - 316 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A ASP 3.2 17.5 - - - -
224A ALA* 3.3 9.9 - - - -
226A TYR 3.3 21.0 + - - -
227A ILE* 4.1 2.4 - - - +
309A ALA 3.4 1.0 + - - -
310A LEU* 1.3 75.7 - - - +
312A ALA* 1.3 66.7 + - - -
313A THR 3.2 2.9 - - - -
314A PHE* 3.0 11.1 + - - +
315A ILE* 3.1 15.2 + - - +
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ASP 4.6 1.3 - - - +
13A THR* 5.7 0.4 - - - -
15A TYR* 3.9 29.6 - - + -
157A TYR* 3.9 19.4 - - + -
221A ASP 4.3 0.6 + - - -
224A ALA 2.8 15.0 + - - +
225A SER* 3.0 19.4 + - - +
311A GLY* 1.3 71.6 - - - -
313A THR* 1.3 62.7 + - - +
315A ILE* 4.4 0.4 - - - +
316A ARG* 3.0 35.5 + - - +
885A 2IG 5.1 1.6 - - - -
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Residues in contact with THR 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A SER 3.1 6.2 + - - -
226A TYR* 3.3 10.4 - - - -
227A ILE* 3.8 18.8 - - + -
274A LEU* 4.2 8.1 - - + +
278A ASP* 3.5 26.2 - - - +
279A TYR* 4.1 10.5 - - + -
294A ALA* 2.8 45.6 + - + +
295A ILE* 5.2 0.4 - - + -
311A GLY 3.2 1.0 + - - -
312A ALA* 1.3 74.7 - - - +
314A PHE* 1.3 60.1 + - - +
316A ARG* 3.3 22.1 + - - +
317A LYS* 4.4 4.9 + - - +
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Residues in contact with PHE 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A VAL* 5.9 0.2 - - + -
227A ILE* 3.8 26.6 - - + +
265A PHE* 3.7 27.8 - + + -
267A LEU* 4.1 5.6 - - + -
272A TYR* 3.6 32.3 - + + -
274A LEU* 4.4 7.9 - - + -
310A LEU* 3.9 36.6 - - + -
311A GLY 3.0 9.4 + - - +
313A THR* 1.3 79.8 - - - +
315A ILE* 1.3 64.5 + - + +
316A ARG 3.3 0.9 - - - -
317A LYS* 3.4 2.9 + - - +
318A PHE* 3.1 44.5 + + + -
331A PHE* 4.0 30.3 - + - -
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Residues in contact with ILE 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A PHE* 4.5 16.4 - - + +
156A TYR* 5.8 0.2 - - - -
157A TYR* 3.7 42.0 + - + +
220A VAL* 4.8 8.3 - - + -
222A THR* 3.8 39.9 - - + +
310A LEU 4.3 8.7 - - - +
311A GLY 3.1 18.5 + - - +
312A ALA 3.2 0.4 + - - +
314A PHE* 1.3 78.4 - - + +
316A ARG* 1.3 65.9 + - - +
317A LYS 3.1 2.9 + - - -
318A PHE 3.2 22.5 + - - +
319A TYR* 4.2 1.6 + - - -
320A THR* 4.0 18.4 - - - +
334A ALA* 4.6 1.9 - - - +
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Residues in contact with ARG 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ASP* 2.8 52.5 + - - +
15A TYR* 3.4 27.4 + - - +
156A TYR* 5.5 0.5 - - - -
157A TYR* 3.2 27.7 - - + +
158A ASN 3.6 7.0 - - - +
159A ARG* 3.9 35.9 + - + +
225A SER 4.9 0.8 + - - -
278A ASP 4.5 6.9 + - - -
281A PHE* 4.9 4.6 - - - -
294A ALA* 4.5 7.7 - - - +
312A ALA* 3.0 26.4 + - - +
313A THR* 3.3 38.9 + - - +
314A PHE 3.3 0.4 - - - -
315A ILE* 1.3 77.2 - - - +
317A LYS* 1.3 58.4 + - + +
334A ALA* 3.6 13.0 - - - +
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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