Contacts of the strand formed by residues 292 - 298 (chain C) in PDB entry 4RO0
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 ILE 292 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286C HIS* 4.2 26.2 - - + +
290C GLY 3.6 3.8 + - - +
291C VAL* 1.3 69.7 - - - +
293C ILE* 1.3 67.6 + - - +
294C ILE* 3.4 3.1 + - + +
320C GLY* 3.0 5.5 - - - -
321C ILE* 3.0 55.6 + - + +
292c ILE* 4.0 25.4 - - + -
293c ILE 4.1 15.7 - - - +
294c ILE* 4.3 16.4 - - + +
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Residues in contact with ILE 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C VAL* 5.1 16.2 - - + +
285C ILE* 3.8 42.0 - - + +
286C HIS* 4.0 14.7 - - + +
291C VAL* 4.0 11.2 - - + +
292C ILE* 1.3 77.7 - - - +
294C ILE* 1.3 62.2 + - - +
295C GLY 4.5 10.5 - - - +
296C VAL* 5.2 7.0 - - + -
306C PRO* 5.5 8.4 - - + +
312C PHE* 5.5 2.2 - - + -
318C ILE* 3.8 26.5 - - + -
319C LEU 3.9 3.6 - - - +
320C GLY* 4.5 1.6 - - - -
292c ILE* 4.0 12.1 - - - +
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Residues in contact with ILE 294 (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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264C MET* 3.9 16.4 - - + -
292C ILE* 3.4 5.6 + - + +
293C ILE* 1.3 74.9 - - - +
295C GLY* 1.3 52.4 + - - +
304C ILE* 3.6 11.4 - - + +
305C ASP* 2.6 35.7 + - - -
306C PRO* 4.5 1.8 - - - -
319C LEU* 2.7 26.6 + - + +
320C GLY 4.9 0.4 - - - -
321C ILE* 3.6 40.6 - - + +
251c PHE* 3.6 46.9 - - + -
292c ILE* 4.1 12.1 - - + +
294c ILE* 5.7 2.2 - - + -
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Residues in contact with GLY 295 (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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293C ILE* 3.8 5.1 - - - +
294C ILE* 1.3 83.8 - - - +
296C VAL* 1.3 67.4 + - - +
302C LEU* 4.1 9.4 - - - -
303C ILE 3.1 15.3 - - - -
304C ILE* 3.9 3.8 - - - -
306C PRO* 3.9 5.8 - - - -
317C ILE 3.9 0.2 - - - +
318C ILE* 3.9 0.9 - - - -
319C LEU* 2.9 29.3 + - - +
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Residues in contact with VAL 296 (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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280C VAL* 5.3 0.2 - - + -
293C ILE* 5.2 5.6 - - + -
295C GLY* 1.3 79.2 - - - +
297C GLY* 1.3 65.8 + - - +
302C LEU* 3.5 2.9 - - - +
303C ILE* 2.9 38.7 + - + +
306C PRO* 3.8 19.3 - - + -
310C TYR* 3.6 38.1 - - + +
312C PHE* 3.7 26.2 - - + -
316C ASP* 3.8 21.8 - - + +
317C ILE 3.3 10.3 - - - +
318C ILE* 5.3 1.8 - - + -
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Residues in contact with GLY 297 (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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296C VAL* 1.3 74.4 - - - +
298C ARG* 1.3 59.5 + - - -
301C GLU 3.5 7.6 - - - -
302C LEU* 4.0 2.9 - - - +
315C GLY 4.4 0.2 - - - +
316C ASP* 3.4 7.1 - - - +
317C ILE* 2.7 44.7 + - - +
247c TYR* 3.5 29.6 - - - -
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Residues in contact with ARG 298 (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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296C VAL 4.1 0.6 + - - -
297C GLY* 1.3 71.9 - - - -
299C GLY* 1.3 61.4 + - - +
300C ASP 3.1 0.2 + - - -
301C GLU* 3.0 32.8 + - + +
303C ILE* 5.3 7.7 - - + +
310C TYR* 2.9 33.0 + - - +
311C SER 3.4 9.7 + - - -
313C ARG* 2.0 77.0 - - - +
315C GLY 5.2 4.3 - - - +
316C ASP* 3.0 30.4 + - - +
247c TYR* 3.2 1.8 + - - -
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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