Contacts of the helix formed by residues 255 - 266 (chain D) in PDB entry 3C6M
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 ASP 255 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221D ILE* 3.7 32.4 - - + +
254D GLU* 1.3 75.0 - - - +
256D CYS* 1.3 78.5 + - - +
257D ILE* 3.1 16.5 + - - +
258D PRO* 3.7 28.7 - - + +
259D VAL* 3.3 17.5 - - - +
282D ILE 4.8 3.2 - - - +
283D SER* 5.5 0.7 - - - -
284D THR* 4.5 14.0 + - - +
401D MTA 3.0 19.0 + - - -
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Residues in contact with CYS 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D LEU* 4.3 17.0 - - + -
219D VAL* 3.7 26.5 - - + +
254D GLU 3.5 0.2 + - - -
255D ASP* 1.3 76.4 + - - +
257D ILE* 1.3 68.3 + - - +
259D VAL* 3.3 3.6 + - + +
260D LEU* 2.9 44.8 + - + +
277D LEU* 4.1 21.8 - - - -
298D ILE* 5.5 1.1 - - - -
401D MTA 3.2 33.3 + - + +
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Residues in contact with ILE 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D ASP* 3.1 15.4 + - - +
256D CYS* 1.3 83.0 - - - +
258D PRO* 1.4 69.7 - - + +
260D LEU* 3.2 6.8 + - + +
261D LYS* 3.0 53.6 + - + +
282D ILE 5.5 0.2 - - - +
294D PHE* 3.8 24.7 - - + -
297D LEU* 4.9 9.2 - - + -
298D ILE* 3.7 31.0 - - + -
301D LEU* 4.2 16.2 - - + +
401D MTA 4.6 4.0 - - - +
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Residues in contact with PRO 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D GLU* 5.4 6.1 - - + +
255D ASP* 3.7 28.9 - - + +
257D ILE* 1.4 97.7 - - + +
259D VAL* 1.3 57.3 + - + +
261D LYS* 3.7 14.2 - - + +
262D ARG* 3.1 32.2 + - - +
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Residues in contact with VAL 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D LEU* 5.6 0.4 - - + -
219D VAL* 3.8 20.9 - - + -
252D LEU* 4.4 5.8 - - + -
254D GLU* 3.5 36.8 - - + +
255D ASP 3.3 18.2 - - - +
256D CYS* 3.3 10.4 + - - +
257D ILE 3.2 1.4 - - - -
258D PRO* 1.3 74.4 - - - +
260D LEU* 1.3 61.1 + - + +
262D ARG* 3.4 12.4 + - - +
263D TYR* 3.1 60.4 + - + +
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Residues in contact with LEU 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D LEU* 3.7 29.8 - - + -
197D LEU* 4.1 26.5 - - + -
256D CYS* 2.9 27.6 + - - +
257D ILE* 3.6 6.5 - - + +
259D VAL* 1.3 72.2 - - + +
261D LYS* 1.3 67.0 + - - +
262D ARG 3.2 0.2 + - - -
263D TYR* 3.2 7.7 + - + +
264D ALA* 3.0 24.4 + - - +
273D VAL* 5.6 0.2 - - + -
298D ILE* 4.6 4.7 - - + +
301D LEU* 3.8 41.2 - - + +
302D SER* 4.3 9.2 - - - +
305D VAL* 3.7 22.5 - - + +
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Residues in contact with LYS 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D ILE* 3.0 40.1 + - + +
258D PRO* 3.7 12.3 - - + +
260D LEU* 1.3 76.6 - - - +
262D ARG* 1.3 55.0 + - - +
264D ALA* 3.5 7.0 + - - +
265D LYS* 3.0 28.2 + - - +
297D LEU* 5.1 10.4 - - - +
301D LEU* 4.0 25.3 - - + +
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Residues in contact with ARG 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252D LEU* 5.2 4.6 - - - +
254D GLU* 3.0 37.2 + - - -
258D PRO* 3.1 19.4 + - - +
259D VAL* 3.7 23.3 - - - +
260D LEU 3.1 0.2 - - - -
261D LYS* 1.3 75.2 - - - +
263D TYR* 1.3 65.3 + - + +
265D LYS* 3.1 11.7 + - + +
266D GLU* 2.8 58.1 + - - +
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Residues in contact with TYR 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D LEU* 4.1 19.3 - - + -
217D THR* 3.4 23.9 - - - +
250D GLN* 5.0 0.3 + - - -
252D LEU* 3.8 14.0 - - - +
259D VAL* 3.1 37.1 + - + +
260D LEU* 3.2 4.7 + - - +
262D ARG* 1.3 84.8 - - + +
264D ALA* 1.3 57.6 + - - +
266D GLU* 3.7 17.3 - - - -
267D GLY 3.0 5.9 + - - -
268D ARG* 2.9 71.0 + - + +
270D PHE* 3.5 30.1 - + - -
305D VAL* 3.4 17.9 - - + -
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Residues in contact with ALA 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D LEU 3.0 16.9 + - - +
261D LYS* 3.7 7.6 - - - +
263D TYR* 1.3 73.4 - - - +
265D LYS* 1.3 66.6 + - - +
267D GLY* 3.1 13.8 + - - -
301D LEU* 6.0 3.1 - - + -
304D LYS* 4.0 32.1 - - + -
305D VAL* 3.6 6.5 - - + +
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Residues in contact with LYS 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D LYS 3.0 18.6 + - - +
262D ARG* 3.1 12.1 + - + +
264D ALA* 1.3 78.0 - - - +
266D GLU* 1.3 55.6 + - - +
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Residues in contact with GLU 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D ARG* 2.8 50.9 + - - +
263D TYR* 3.7 27.1 - - - +
264D ALA 3.1 0.2 - - - -
265D LYS* 1.3 77.0 - - - +
267D GLY* 1.3 61.8 + - - +
268D ARG* 3.5 11.9 + - + +
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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