Contacts of the helix formed by residues 256 - 266 (chain D) in PDB entry 2NYM
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 SER 256 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218D ASP* 2.6 41.1 + - - +
221D ARG* 3.8 4.5 - - - -
254D ASP* 2.9 12.5 + - - +
255D LYS* 1.3 75.6 - - - +
257D TRP* 1.3 66.6 + - - +
258D ARG* 2.7 11.3 + - - +
259D VAL* 2.8 15.7 + - - +
260D ARG* 3.4 7.8 + - - -
96E THR* 3.1 24.6 + - - +
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Residues in contact with TRP 257 (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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255D LYS 3.2 6.1 + - - -
256D SER* 1.3 70.3 - - - +
258D ARG* 1.3 95.5 + - + +
260D ARG* 3.3 31.7 - - - +
261D TYR* 2.7 54.7 + + + +
295D GLU* 3.6 28.0 - - + -
297D GLU* 4.5 9.6 - - + -
298D VAL* 3.6 4.3 - - + +
96E THR* 4.4 14.5 + - - -
97E LEU 3.0 23.7 + - - -
98E PRO* 3.8 1.5 - - + +
99E PRO* 3.2 48.8 - - + +
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Residues in contact with ARG 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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218D ASP* 3.6 22.5 + - - +
222D LEU* 4.4 20.3 - - + +
256D SER* 2.7 15.0 + - - +
257D TRP* 1.3 111.7 - - + +
259D VAL* 1.3 69.9 + - + +
261D TYR* 3.0 17.5 + - - +
262D MSE 3.3 8.3 + - - +
96E THR* 4.4 10.7 - - - +
97E LEU* 4.3 22.4 + - - +
98E PRO 4.6 6.7 + - - -
99E PRO* 5.1 2.4 - - - +
100E SER 5.7 0.6 - - - +
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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
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218D ASP* 3.9 9.0 - - + +
221D ARG* 3.7 19.1 - - + +
222D LEU* 3.7 29.8 - - - +
225D VAL* 3.8 22.7 - - + -
251D ALA* 3.7 20.0 - - + +
254D ASP* 3.7 25.8 - - + +
256D SER* 2.8 16.7 + - - +
258D ARG* 1.3 71.5 - - - +
260D ARG* 1.3 67.1 + - - +
262D MSE 2.8 19.4 + - - +
263D VAL* 3.4 4.2 + - - +
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Residues in contact with ARG 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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251D ALA 4.0 10.5 - - - +
252D ALA 3.2 26.7 - - - +
253D GLU* 3.9 5.1 + - - +
254D ASP 2.7 41.8 + - - +
255D LYS* 3.1 17.2 + - - +
256D SER 3.4 0.4 + - - -
257D TRP* 3.2 31.2 + - - +
258D ARG 3.2 0.4 - - - -
259D VAL* 1.3 76.5 - - - +
261D TYR* 1.3 64.9 + - - +
262D MSE 2.9 1.7 + - - -
263D VAL* 3.0 17.0 + - - +
264D ALA* 3.1 9.2 + - - +
290D LEU* 4.0 5.7 - - + +
293D ASP* 2.6 42.7 + - - +
294D CYS* 4.5 13.8 - - - +
295D GLU* 4.4 3.0 - - - +
298D VAL* 3.9 9.4 - - + -
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Residues in contact with TYR 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 TRP* 2.7 25.6 + + + +
258D ARG* 3.1 17.5 - - - +
260D ARG* 1.3 73.0 - - - +
262D MSE 1.3 73.7 + - - +
264D ALA* 3.0 7.1 - - - +
265D ASP* 2.9 37.6 + - + -
297D GLU* 3.7 41.1 - - + -
298D VAL* 3.3 16.7 - - + +
301D ALA* 4.2 16.4 - - + +
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Residues in contact with MSE 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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222D LEU* 3.9 38.8 - - + +
223D LEU* 5.2 6.1 - - + -
225D VAL* 3.7 19.7 - - + -
226D GLU* 3.5 42.0 - - + +
258D ARG 4.2 3.4 - - - +
259D VAL 2.8 14.5 + - - +
261D TYR* 1.3 78.9 - - + +
263D VAL* 1.3 65.8 + - - +
264D ALA 2.5 6.0 + - - -
265D ASP* 2.6 17.1 + - - +
266D LYS* 2.7 26.1 + - + -
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Residues in contact with VAL 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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225D VAL* 3.9 24.7 - - + -
248D LEU* 4.2 11.0 - - + -
251D ALA* 3.7 31.6 - - + +
252D ALA* 4.1 17.5 - - + +
259D VAL 4.0 3.4 - - - +
260D ARG 3.0 8.7 + - - +
262D MSE 1.3 76.0 - - - +
264D ALA* 1.3 61.4 + - - +
266D LYS 3.8 1.1 - - - +
267D PHE* 3.0 46.8 + - + -
270D LEU* 4.0 19.1 - - + -
283D LEU* 5.8 0.7 - - + -
290D LEU* 4.5 7.2 - - + -
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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 ARG 3.1 7.3 + - - +
261D TYR* 3.0 16.5 + - - +
262D MSE 2.5 5.3 + - - -
263D VAL* 1.3 73.4 - - - +
265D ASP* 1.3 63.3 + - - +
267D PHE* 3.0 22.9 + - - +
290D LEU* 4.2 14.7 - - + +
298D VAL* 4.1 10.1 - - + +
301D ALA* 3.8 24.5 - - + -
302D ALA* 4.1 9.0 - - - +
305D LYS* 3.7 11.4 - - - +
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Residues in contact with ASP 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 TYR* 2.9 33.7 + - + +
262D MSE 2.6 15.9 + - - +
264D ALA* 1.3 72.8 - - - +
266D LYS* 1.3 79.9 + - - +
267D PHE 3.1 1.1 + - - -
269D GLU* 3.8 4.7 - - - +
301D ALA* 5.0 5.2 - - + +
305D LYS* 3.2 38.4 + - - +
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Residues in contact with LYS 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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225D VAL* 5.2 2.7 - - + -
226D GLU* 2.8 40.2 + - - +
229D VAL* 4.0 18.2 - - + -
262D MSE 2.7 38.7 + - + +
263D VAL* 3.8 3.4 - - - -
265D ASP* 1.3 95.5 + - + +
267D PHE* 1.3 58.5 + - - +
268D THR 3.5 1.3 - - - -
269D GLU* 3.8 24.5 + - + +
270D LEU* 2.8 34.2 + - + +
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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