Contacts of the helix formed by residues 284 - 294 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281B CYS* 4.1 8.1 - - - +
283B THR* 1.3 85.4 + - - +
285B GLN* 1.3 66.1 + - - +
286B SER* 3.2 22.5 + - - +
287B ARG* 3.2 45.2 + - - +
288B CYS* 3.1 21.5 + - - +
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Residues in contact with GLN 285 (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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279B GLY 4.5 7.5 + - - +
281B CYS* 4.3 17.6 - - - +
284B GLU* 1.3 72.4 - - - +
286B SER* 1.3 57.9 + - - +
288B CYS* 3.2 5.2 + - - +
289B LEU* 3.0 32.0 + - + +
343B GLU* 3.6 31.7 + - - +
344B ALA* 3.9 22.9 - - + +
347B ALA* 3.6 20.2 - - - +
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Residues in contact with SER 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B GLU* 5.0 1.7 - - - +
213B GLN* 4.9 4.3 + - - +
284B GLU* 3.2 21.3 + - - +
285B GLN* 1.3 77.8 - - - +
287B ARG* 1.3 63.9 + - - +
289B LEU* 3.5 10.9 + - - +
290B ARG* 3.1 23.4 + - - +
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Residues in contact with ARG 287 (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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271B HIS* 3.7 24.0 + - + +
283B THR* 3.5 40.8 - - - +
284B GLU* 3.2 46.8 + - + +
285B GLN 3.2 0.4 - - - -
286B SER* 1.3 82.2 + - - +
288B CYS* 1.3 64.3 + - - +
290B ARG* 3.5 15.4 + - - +
291B ALA* 3.0 24.8 + - - +
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Residues in contact with CYS 288 (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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271B HIS* 3.6 17.3 - - - +
272B CYS* 2.1 58.4 - - - -
281B CYS* 4.1 8.1 - - - -
284B GLU 3.1 9.6 + - - +
285B GLN 3.2 9.2 + - - +
287B ARG* 1.3 73.4 - - - +
289B LEU* 1.3 60.2 + - - +
291B ALA 3.1 1.2 + - - -
292B TYR* 2.8 27.4 + - - +
340B CYS* 3.8 9.9 - - - -
341B LEU* 3.9 21.8 - - - -
344B ALA* 4.6 5.2 - - + -
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Residues in contact with LEU 289 (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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213B GLN* 3.9 13.5 - - - +
217B LEU* 3.8 19.5 - - + -
285B GLN* 3.0 17.9 + - + +
286B SER* 3.9 11.9 - - - +
287B ARG 3.4 0.4 - - - -
288B CYS* 1.3 75.3 - - - +
290B ARG* 1.3 63.3 + - - +
292B TYR* 3.3 6.3 + - + +
293B LEU* 2.9 30.9 + - - +
341B LEU* 5.0 5.4 - - + -
344B ALA* 3.9 21.1 - - + +
345B ILE* 3.8 29.2 - - + -
348B LYS* 3.8 40.2 - - + -
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Residues in contact with ARG 290 (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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209B GLU* 2.6 45.7 + - + +
213B GLN* 4.4 3.7 - - - +
286B SER 3.1 15.1 + - - +
287B ARG* 3.6 15.4 - - - +
288B CYS 3.3 0.2 - - - -
289B LEU* 1.3 79.8 - - - +
291B ALA* 1.3 57.2 + - - +
293B LEU* 3.6 5.4 + - - +
294B GLY* 3.0 24.6 + - - -
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Residues in contact with ALA 291 (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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264B ARG* 4.6 2.8 - - - +
267B ASP* 3.7 17.9 - - + +
268B PHE* 3.5 32.6 - - + +
271B HIS* 4.3 7.9 - - + +
272B CYS* 4.7 0.2 - - - -
287B ARG 3.0 18.9 + - - +
288B CYS* 3.1 3.6 + - - +
290B ARG* 1.3 73.1 - - - +
292B TYR* 1.3 66.5 + - - +
294B GLY* 3.3 10.5 + - - -
295B LEU* 3.4 16.1 + - - +
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Residues in contact with TYR 292 (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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216B LEU* 5.4 2.7 - - + -
217B LEU* 4.8 8.5 - - + -
268B PHE* 3.9 21.0 - + + -
288B CYS 2.8 17.0 + - - +
289B LEU* 3.6 8.1 - - + +
291B ALA* 1.3 76.7 - - - +
293B LEU* 1.3 82.1 + - + +
295B LEU* 3.1 21.6 + - + +
296B ILE* 4.1 4.6 + - + +
302B PRO* 3.4 42.4 + - + +
303B ASN* 4.0 1.6 + - - -
304B PHE* 5.7 4.5 - + - -
312B VAL* 2.3 48.8 - - + +
335B PHE* 4.3 4.0 - + - -
341B LEU* 3.7 28.7 - - + -
345B ILE* 4.3 17.0 - - + +
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Residues in contact with LEU 293 (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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204B PHE* 4.0 34.0 - - + +
212B ALA* 4.9 2.2 - - + -
213B GLN* 3.6 40.4 - - + +
216B LEU* 3.7 33.4 - - + -
217B LEU* 4.5 12.6 - - + -
289B LEU 2.9 24.2 + - - +
290B ARG* 4.1 4.3 - - - +
292B TYR* 1.3 86.7 - - + +
294B GLY* 1.3 56.7 + - - +
295B LEU 3.1 0.2 - - - -
296B ILE* 3.1 35.0 + - + +
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Residues in contact with GLY 294 (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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201B LEU* 4.5 0.9 - - - +
204B PHE* 5.5 3.6 - - - -
264B ARG* 2.8 50.3 + - - +
290B ARG 3.0 16.7 + - - -
291B ALA* 3.5 8.7 - - - -
292B TYR 3.2 0.8 - - - -
293B LEU* 1.3 75.6 - - - +
295B LEU* 1.3 56.9 - - - +
296B ILE 3.4 1.3 + - - -
298B THR* 3.8 3.5 - - - +
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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