Contacts of the helix formed by residues 264 - 274 (chain C) in PDB entry 3RCY
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 THR 264 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74C PHE* 3.9 26.5 - - + -
78C TYR* 4.0 15.2 - - + -
86C PRO* 3.2 20.3 - - + +
91C ILE* 4.1 8.3 - - + -
263C THR* 1.3 90.4 + - - +
265C LYS* 1.3 59.0 + - - +
266C ALA* 3.2 13.6 + - - +
267C GLU 2.9 18.2 + - - -
268C PHE* 3.2 17.5 + - - -
287C ALA* 2.8 24.9 + - - +
292C GLU* 3.3 11.7 - - - -
293C MET* 4.5 1.1 - - - -
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Residues in contact with LYS 265 (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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74C PHE* 3.5 19.6 - - - -
75C ARG* 4.6 11.4 - - - +
78C TYR* 6.0 1.6 - - - -
264C THR* 1.3 71.4 - - - +
266C ALA* 1.3 60.8 + - + +
267C GLU 3.1 0.2 - - - -
268C PHE* 3.8 1.8 - - - +
269C ALA* 2.9 33.7 + - - +
292C GLU* 2.8 43.4 + - - +
295C LYS* 3.9 30.3 - - + +
296C VAL* 3.7 22.0 - - + +
299C MET* 3.7 29.8 - - + -
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Residues in contact with ALA 266 (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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240A ASP* 3.8 24.9 - - + +
78C TYR* 3.5 22.4 - - + +
86C PRO* 4.0 8.1 - - + -
264C THR* 3.1 13.4 + - - +
265C LYS* 1.3 82.8 - - + +
267C GLU* 1.3 60.2 + - - +
269C ALA* 5.2 0.7 - - - -
270C PRO* 3.2 21.0 - - - +
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Residues in contact with GLU 267 (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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85A ARG* 2.7 47.1 + - - -
267A GLU* 5.6 0.5 - - - +
85C ARG* 5.2 2.3 + - - -
86C PRO* 3.6 21.1 - - + +
242C VAL* 5.2 1.7 - - - +
262C LEU* 3.4 17.8 - - + +
263C THR* 2.8 34.2 + - - +
264C THR 2.9 3.4 + - - +
266C ALA* 1.3 81.5 - - - +
268C PHE* 1.3 63.3 + - - +
269C ALA 3.4 0.4 - - - -
270C PRO* 3.3 11.1 - - - +
271C VAL* 3.4 19.2 + - - +
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Residues in contact with PHE 268 (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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258C THR 4.4 0.9 - - - -
259C GLY* 3.4 39.0 - - - -
262C LEU* 3.9 30.5 - - + -
264C THR 3.2 25.9 + - - +
265C LYS 4.3 0.2 - - - +
267C GLU* 1.3 76.7 - - - +
269C ALA* 1.3 65.9 + - - +
271C VAL* 3.2 7.1 + - + +
272C LEU* 3.2 26.4 + - - +
280C LEU* 3.9 37.2 - - + -
282C PRO* 3.6 21.8 - - + -
287C ALA* 4.1 15.5 - - + -
293C MET* 4.2 1.8 - - + -
296C VAL* 3.7 33.2 - - + -
299C MET* 5.7 1.1 - - - -
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Residues in contact with ALA 269 (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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265C LYS 2.9 20.2 + - - +
266C ALA* 5.0 1.1 - - - +
268C PHE* 1.3 76.4 - - - +
270C PRO* 1.4 61.9 - - + +
272C LEU* 3.3 9.5 + - - +
273C ARG* 2.9 47.8 + - - +
299C MET* 4.4 19.9 - - + -
303C TYR* 5.1 0.9 + - - -
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Residues in contact with PRO 270 (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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242C VAL* 4.1 16.4 - - + -
266C ALA 3.2 25.6 - - - +
267C GLU* 3.3 10.1 - - - +
269C ALA* 1.4 93.4 - - + +
271C VAL* 1.3 56.0 + - - +
273C ARG* 4.0 19.3 - - + +
274C GLU* 2.9 40.7 + - + +
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Residues in contact with VAL 271 (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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242C VAL* 4.1 23.3 - - + +
245C MET* 6.1 0.4 - - - -
258C THR* 4.1 9.2 - - + -
262C LEU* 3.6 24.5 - - + -
267C GLU 3.4 15.9 + - - +
268C PHE* 3.2 10.7 + - - +
270C PRO* 1.3 76.2 - - - +
272C LEU* 1.3 60.3 + - - +
275C GLY 3.3 1.6 + - - -
276C ALA* 2.8 35.1 + - + -
277C ALA* 3.7 32.6 + - + +
280C LEU* 3.9 15.7 - - + -
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Residues in contact with LEU 272 (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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268C PHE 3.2 15.1 + - - +
269C ALA* 3.6 7.4 - - - +
271C VAL* 1.3 77.6 - - - +
273C ARG* 1.3 63.7 + - - +
275C GLY* 3.0 14.9 + - - -
277C ALA 4.3 10.3 - - - +
280C LEU* 3.9 32.5 - - + -
296C VAL* 4.6 1.1 - - + +
299C MET* 3.6 21.3 - - + +
300C ALA* 3.6 26.0 - - - +
303C TYR* 3.5 35.6 - - + -
305C ALA* 4.0 26.2 - - + -
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Residues in contact with ARG 273 (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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241A ASN* 5.3 13.5 + - - +
243A GLY* 6.2 1.4 - - - -
269C ALA* 2.9 33.1 + - - +
270C PRO* 3.2 28.8 + - + +
272C LEU* 1.3 77.4 - - - +
274C GLU* 1.3 74.7 + - - +
275C GLY 3.2 0.6 + - - -
303C TYR* 3.5 25.1 + - - +
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Residues in contact with GLU 274 (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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274A GLU* 6.6 0.9 - - - -
242C VAL* 3.8 23.1 - - + -
243C GLY* 5.6 2.2 - - - +
246C ALA* 3.4 19.2 - - + +
250C ARG* 4.2 8.1 + - - -
270C PRO* 2.9 24.6 + - + +
273C ARG* 1.3 93.7 + - + +
275C GLY* 1.3 62.2 + - - +
276C ALA 4.5 0.2 - - - +
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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