Contacts of the helix formed by residues 284 - 294 (chain A) in PDB entry 2GH0
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 GLU 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A CYS* 4.1 8.9 - - - +
283A THR* 1.3 83.2 + - - +
285A GLN* 1.3 67.2 + - - +
286A SER* 4.0 17.4 + - - +
287A ARG* 3.2 28.6 + - + +
288A CYS* 3.2 11.4 + - - +
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Residues in contact with GLN 285 (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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279A GLY 5.6 1.6 + - - -
281A CYS* 4.2 20.9 - - + +
284A GLU* 1.3 73.2 - - - +
286A SER* 1.3 62.8 + - - +
288A CYS* 3.2 3.3 + - - +
289A LEU* 3.0 27.0 + - + +
340A CYS 5.2 0.4 + - - -
343A GLU* 3.8 23.4 + - - +
344A ALA* 3.8 28.3 - - + +
347A ALA* 3.7 20.1 - - - +
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Residues in contact with SER 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLU* 4.9 1.4 - - - +
213A GLN* 4.8 4.8 + - - +
284A GLU* 3.3 16.7 + - - +
285A GLN* 1.3 78.1 - - - +
287A ARG* 1.3 67.6 + - - +
289A LEU* 3.5 10.1 + - - +
290A ARG* 3.2 33.9 + - - +
348A LYS* 6.3 1.8 - - - +
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Residues in contact with ARG 287 (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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271A HIS* 3.5 39.2 + - + +
283A THR* 3.5 20.0 - - - +
284A GLU* 3.2 20.7 + - + +
286A SER* 1.3 81.2 + - - +
288A CYS* 1.3 59.0 + - - +
290A ARG* 3.5 26.0 + - - +
291A ALA* 3.1 29.1 + - - +
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Residues in contact with CYS 288 (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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271A HIS* 3.6 19.4 - - - +
272A CYS* 2.2 56.9 - - - -
281A CYS* 4.2 2.7 - - - -
284A GLU 3.2 8.4 + - - +
285A GLN* 3.2 10.1 + - - +
287A ARG* 1.3 73.6 - - - +
289A LEU* 1.3 59.3 + - - +
291A ALA* 3.2 1.2 + - - +
292A TYR* 2.9 25.6 + - - +
340A CYS* 3.8 16.2 - - - -
341A LEU* 3.9 21.3 - - - -
344A ALA* 4.5 5.4 - - - -
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Residues in contact with LEU 289 (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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213A GLN* 3.8 29.2 - - - +
217A LEU* 3.9 13.0 - - + -
285A GLN* 3.0 21.5 + - + +
286A SER* 3.9 7.2 - - - +
287A ARG 3.4 0.4 - - - -
288A CYS* 1.3 74.0 - - - +
290A ARG* 1.3 58.1 + - - +
292A TYR* 3.4 5.9 + - + +
293A LEU* 2.9 34.8 + - - +
341A LEU* 4.6 7.4 - - + -
344A ALA* 3.6 35.9 - - + +
345A ILE* 3.7 27.6 - - + +
348A LYS* 3.9 25.8 - - + -
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Residues in contact with ARG 290 (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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209A GLU* 2.4 51.4 + - + +
213A GLN* 4.2 8.0 - - - +
286A SER* 3.2 23.1 + - - +
287A ARG* 3.7 42.7 - - - +
288A CYS 3.2 0.2 - - - -
289A LEU* 1.3 78.6 - - - +
291A ALA* 1.3 57.8 + - - +
293A LEU* 3.6 3.3 + - - +
294A GLY* 3.0 24.9 + - - -
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Residues in contact with ALA 291 (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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267A ASP* 3.6 40.7 - - + +
268A PHE* 3.7 14.8 - - - +
271A HIS* 4.3 7.9 - - + +
287A ARG 3.1 18.1 + - - +
288A CYS* 3.2 4.2 + - - +
290A ARG* 1.3 76.7 - - - +
292A TYR* 1.3 65.0 + - - +
294A GLY* 3.4 9.0 + - - -
295A LEU* 3.6 15.4 + - - +
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Residues in contact with TYR 292 (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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216A LEU* 5.2 2.7 - - + -
217A LEU* 4.9 8.1 - - + -
268A PHE* 3.8 19.8 - + + -
288A CYS 2.9 16.6 + - - +
289A LEU* 3.6 7.6 - - + +
291A ALA* 1.3 75.0 - - - +
293A LEU* 1.3 82.8 + - + +
295A LEU* 3.0 20.6 + - - +
296A ILE* 4.2 4.5 + - + +
302A PRO* 3.4 43.3 + - + +
303A ASN* 3.9 6.6 + - - -
304A PHE* 5.6 2.5 - + - -
312A VAL* 3.3 35.2 - - + +
335A PHE* 4.4 4.7 - + - -
341A LEU* 3.8 42.4 - - + -
345A ILE* 4.4 13.9 - - + -
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Residues in contact with LEU 293 (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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204A PHE* 3.9 37.7 - - + +
212A ALA* 4.5 2.2 - - + +
213A GLN* 3.4 43.1 - - + +
216A LEU* 3.5 32.3 - - + -
217A LEU* 4.6 11.9 - - + -
289A LEU 2.9 23.3 + - - +
290A ARG* 4.2 3.8 - - - +
292A TYR* 1.3 87.5 - - + +
294A GLY* 1.3 57.3 + - - +
296A ILE* 3.1 30.0 + - + +
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Residues in contact with GLY 294 (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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201A LEU* 4.4 0.9 - - - +
204A PHE* 5.3 4.7 - - - -
264A ARG* 3.0 48.0 + - - +
267A ASP* 5.7 0.2 - - - -
290A ARG 3.0 18.3 + - - -
291A ALA* 3.7 7.6 - - - -
292A TYR 3.2 1.0 - - - -
293A LEU* 1.3 75.4 - - - +
295A LEU* 1.3 57.7 + - - +
296A ILE 3.4 1.3 - - - -
298A THR* 4.1 3.1 - - - +
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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