Contacts of the helix formed by residues 298 - 308 (chain C) in PDB entry 2RHB
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 298 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194C PHE 5.2 0.2 + - - -
196C GLN* 3.3 46.0 - - - +
206C ARG* 5.0 10.1 - - + +
207C SER* 4.3 12.6 - - - +
210C GLU* 3.5 14.4 - - - +
297C LEU* 1.3 73.3 - - - +
299C LEU* 1.3 65.2 + - - +
300C ASP* 3.5 29.2 - - + +
301C ASP* 2.9 41.9 + - - +
302C PHE* 3.0 10.0 + - - +
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Residues in contact with LEU 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C MET* 3.9 12.8 - - + +
210C GLU* 3.2 23.0 + - + +
213C PHE* 3.5 40.6 - - + -
221C PHE* 3.6 17.9 - - + -
232C PHE* 3.7 29.6 - - + -
236C VAL* 5.0 3.1 - - + -
250C LEU* 4.1 16.4 - - + -
252C ILE* 4.2 18.1 - - + +
297C LEU 3.2 5.6 + - - -
298C LEU* 1.3 72.0 - - - +
300C ASP* 1.3 56.3 + - - +
302C PHE* 3.3 3.7 + - + -
303C VAL* 2.9 37.7 + - + +
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Residues in contact with ASP 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C SER* 2.6 34.9 + - - -
209C MET* 3.6 34.6 + - + +
210C GLU* 4.2 0.5 - - - +
298C LEU* 3.5 19.9 - - + +
299C LEU* 1.3 77.0 + - - +
301C ASP* 1.3 57.8 + - - +
303C VAL* 3.4 2.6 + - - +
304C GLU* 3.0 29.8 + - - +
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Residues in contact with ASP 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C TYR* 3.5 33.8 - - + +
194C PHE 4.5 11.3 + - - +
196C GLN* 5.0 0.3 + - - -
297C LEU* 4.5 8.8 - - + +
298C LEU* 2.9 41.4 + - + +
300C ASP* 1.3 80.2 - - - +
302C PHE* 1.3 56.9 + - - +
304C GLU* 3.4 8.0 + - - +
305C ILE* 3.0 33.6 + - - +
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Residues in contact with PHE 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C PHE* 3.8 28.7 - + - -
235C ILE* 3.7 25.1 - - + -
236C VAL* 3.6 20.9 - - + -
249C HIS* 6.1 2.0 - - + -
250C LEU* 3.7 39.7 - - + -
297C LEU* 4.4 14.5 - - + +
298C LEU 3.0 8.1 + - - +
299C LEU* 3.7 6.1 - - + +
301C ASP* 1.3 75.5 - - - +
303C VAL* 1.3 59.4 + - - +
305C ILE* 3.2 11.8 + - + +
306C ILE* 2.9 42.7 + - + +
329C PHE* 6.0 1.8 - + - -
341C PHE* 4.0 30.5 - + - -
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Residues in contact with VAL 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C MET* 3.8 28.5 - - + -
225C TYR* 5.9 1.1 - - + +
227C LEU* 4.4 13.5 - - + -
232C PHE* 3.6 26.2 - - + -
299C LEU* 2.9 23.0 + - + +
300C ASP 3.7 5.6 - - - +
302C PHE* 1.3 74.7 - - - +
304C GLU* 1.3 64.8 + - - +
306C ILE* 3.4 8.2 - - - +
307C LYS* 3.0 53.6 + - + +
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Residues in contact with GLU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C TYR* 2.7 29.2 + - - +
300C ASP 3.0 14.2 + - - +
301C ASP* 3.5 11.8 - - - +
303C VAL* 1.3 78.8 - - - +
305C ILE* 1.3 60.6 + - - +
307C LYS* 4.0 4.0 - - - +
308C SER* 3.1 30.6 + - - +
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Residues in contact with ILE 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C TYR* 3.4 43.5 - - + +
297C LEU* 4.1 21.3 - - + -
301C ASP 3.0 24.6 + - - +
302C PHE* 3.2 9.8 + - + +
304C GLU* 1.3 76.0 - - - +
306C ILE* 1.3 64.5 + - - +
308C SER* 3.4 17.5 + - - -
309C GLN* 3.6 19.9 + - - +
320C VAL* 3.9 33.0 - - + -
322C ILE* 5.5 0.4 - - + -
341C PHE* 4.7 14.8 - - + -
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Residues in contact with ILE 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C LEU* 5.3 0.7 - - + -
230C TYR* 3.9 33.9 - - + +
232C PHE* 4.1 20.6 - - + -
235C ILE* 4.6 1.8 - - + -
302C PHE* 2.9 28.6 + - + +
303C VAL* 3.4 17.3 - - - +
305C ILE* 1.3 78.0 - - - +
307C LYS* 1.3 66.6 + - + +
309C GLN* 3.4 20.0 + - + +
311C LEU* 5.0 1.9 - - - +
331C LEU* 4.9 3.8 - - + -
338C VAL* 4.4 15.9 - - + +
341C PHE* 3.8 46.7 - - + -
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Residues in contact with LYS 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C TYR 3.9 8.7 + - - -
226C LYS* 3.8 27.5 + - - +
227C LEU* 3.8 23.3 - - + -
230C TYR* 3.6 35.2 + - + +
303C VAL* 3.0 33.0 + - + +
304C GLU* 4.0 4.3 - - - +
306C ILE* 1.3 76.7 - - + +
308C SER* 1.3 57.1 + - - +
309C GLN 3.0 15.3 + - - +
311C LEU* 5.8 0.2 - - - +
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Residues in contact with SER 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C TYR* 5.7 0.5 + - - -
304C GLU* 3.1 21.9 + - - +
305C ILE* 3.4 11.0 + - - -
306C ILE 3.4 0.4 - - - -
307C LYS* 1.3 74.2 - - - +
309C GLN* 1.3 61.3 + - - +
310C ASP 4.2 0.7 + - - -
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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