Contacts of the helix formed by residues 234 - 244 (chain A) in PDB entry 3C9G
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 LEU 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A VAL* 4.4 23.1 - - + -
191A ILE* 3.8 7.6 - - + -
214A PHE* 5.1 1.3 - - + -
232A TYR 3.5 12.5 + - - +
233A SER* 1.3 74.7 + - - +
235A ASP* 1.3 64.8 + - - +
236A ARG 3.4 2.5 - - - -
237A PHE* 3.3 13.2 + - + +
238A ARG* 3.0 28.3 + - + +
293A PHE* 3.7 31.6 - - + -
303A PHE* 4.1 12.3 - - + -
306A TYR* 4.2 22.4 - - + +
307A ILE* 3.8 25.8 - - + -
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Residues in contact with ASP 235 (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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215A PRO* 6.5 0.2 - - + -
233A SER* 3.1 17.9 + - - +
234A LEU* 1.3 79.3 + - - +
236A ARG* 1.3 64.3 + - - +
238A ARG* 3.5 7.4 + - - +
239A GLU* 3.1 40.8 + - - +
306A TYR* 4.7 10.0 + - - -
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Residues in contact with ARG 236 (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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212A ASN* 3.1 28.9 + - - +
213A ILE 3.3 13.0 - - - +
215A PRO* 3.6 25.2 - - + +
233A SER* 4.7 2.2 + - - +
234A LEU 3.4 0.4 - - - -
235A ASP* 1.3 79.7 - - - +
237A PHE* 1.3 62.4 + - - +
239A GLU* 3.4 22.5 + - - +
240A LEU* 3.1 52.1 + - + +
243A LYS* 5.5 5.1 - - - +
275A SER* 4.8 9.5 + - - -
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Residues in contact with PHE 237 (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 ILE* 3.7 23.9 + - + +
214A PHE* 4.0 21.5 - + + -
234A LEU* 3.3 12.0 + - + +
235A ASP 3.3 0.4 - - - -
236A ARG* 1.3 79.6 - - - +
238A ARG* 1.3 60.5 + - - +
240A LEU* 4.1 2.8 - - - +
241A LEU* 2.9 54.5 + - + +
254A ILE* 5.0 4.3 - - + -
265A ILE* 3.9 21.5 - - + -
267A LEU* 4.3 20.6 - - + -
277A ILE* 4.4 6.7 - - + -
279A PHE* 4.3 6.5 - + - -
293A PHE* 4.0 25.8 - + - -
307A ILE* 3.7 35.7 - - + -
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Residues in contact with ARG 238 (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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234A LEU 3.0 22.8 + - - +
235A ASP* 4.0 7.1 + - - +
237A PHE* 1.3 73.2 - - - +
239A GLU* 1.3 67.2 + - + +
241A LEU* 3.2 5.6 + - - +
242A ARG* 2.8 59.6 + - - +
305A ASP 5.3 0.2 + - - -
306A TYR* 2.7 72.7 + - - +
307A ILE* 3.5 18.4 - - + -
315A ARG* 3.1 39.7 - - - +
316A PRO* 3.5 18.4 + - - +
317A VAL* 4.8 5.7 - - - +
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Residues in contact with GLU 239 (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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235A ASP* 3.1 36.8 + - - +
236A ARG* 3.6 24.0 + - - +
238A ARG* 1.3 79.0 - - + +
240A LEU* 1.3 53.5 + - + +
242A ARG* 3.2 8.8 + - - +
243A LYS* 2.7 67.3 + - + +
315A ARG* 6.0 3.8 - - - +
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Residues in contact with LEU 240 (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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212A ASN 3.8 22.2 - - - +
213A ILE* 4.5 6.7 - - + -
236A ARG* 3.1 40.4 + - + +
237A PHE* 4.1 2.9 - - - +
239A GLU* 1.3 76.7 - - + +
241A LEU* 1.3 65.2 + - - +
242A ARG 3.0 1.6 - - - -
243A LYS* 4.4 13.2 - - + +
244A GLN* 3.0 47.0 + - + +
275A SER* 3.7 19.1 - - - +
277A ILE* 3.3 31.6 - - + -
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Residues in contact with LEU 241 (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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237A PHE* 2.9 42.0 + - + +
238A ARG* 3.2 6.3 + - - +
240A LEU* 1.3 77.2 - - - +
242A ARG* 1.3 58.2 + - - +
244A GLN* 5.0 1.3 - - - -
245A ARG* 3.9 0.2 - - - -
246A ILE* 2.9 45.5 + - + +
247A LEU* 3.6 15.8 - - + +
250A ALA* 4.1 14.4 - - + -
277A ILE* 3.6 33.2 - - + -
279A PHE* 4.2 9.0 - - + -
307A ILE* 3.5 37.9 - - + +
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Residues in contact with ARG 242 (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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238A ARG* 2.8 63.7 + - - +
239A GLU* 3.5 8.5 - - - +
240A LEU 3.0 0.2 - - - -
241A LEU* 1.3 78.7 - - - +
243A LYS* 1.3 59.0 + - + +
244A GLN 3.0 4.7 - - - -
245A ARG* 3.0 26.5 + - - +
247A LEU* 4.0 22.7 - - + +
306A TYR 3.2 12.7 + - - -
307A ILE 3.1 22.3 + - - -
309A PRO* 3.7 14.8 - - - +
315A ARG* 2.7 38.5 - - - +
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Residues in contact with LYS 243 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A ARG* 5.5 4.9 - - - +
239A GLU* 2.7 50.3 + - + +
240A LEU* 3.6 12.1 + - + +
242A ARG* 1.3 73.4 - - + +
244A GLN* 1.3 61.4 + - + +
245A ARG* 3.4 3.4 + - - +
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Residues in contact with GLN 244 (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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240A LEU* 3.0 39.0 + - - +
241A LEU* 5.4 0.2 - - - -
242A ARG 3.0 0.6 - - - -
243A LYS* 1.3 80.5 - - + +
245A ARG* 1.3 70.9 + - - +
246A ILE* 3.1 24.3 - - + +
275A SER 2.9 27.1 + - - -
276A ARG* 3.7 11.2 - - + +
277A ILE* 3.0 33.1 + - - +
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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