Contacts of the helix formed by residues 295 - 305 (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 GLU 295 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D TRP* 3.6 41.9 - - + -
260D ARG* 4.4 1.3 - - - +
293D ASP* 3.1 15.0 + - - +
294D CYS* 1.3 82.0 - - - +
296D ALA* 1.3 95.0 + - - +
297D GLU* 3.3 8.4 + - - +
298D VAL* 3.9 9.9 - - + +
299D ARG* 3.1 23.5 + - - +
98E PRO* 4.8 5.5 - - - +
99E PRO* 3.8 28.9 - - - +
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Residues in contact with ALA 296 (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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294D CYS 3.9 1.6 + - - -
295D GLU* 1.3 84.7 + - - +
297D GLU* 1.3 73.3 + - - +
299D ARG* 3.0 20.7 + - - +
300D ALA* 3.0 17.7 + - - +
338D ASN* 3.5 29.6 - - + +
341D VAL* 3.7 4.0 - - - +
99E PRO* 6.1 0.2 - - + -
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Residues in contact with GLU 297 (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* 4.5 17.9 - - + -
261D TYR* 3.7 27.8 - - + -
295D GLU* 3.5 11.2 + - + +
296D ALA* 1.3 79.8 - - - +
298D VAL* 1.3 58.0 + - - +
299D ARG 2.8 1.0 + - - -
300D ALA* 3.0 4.5 + - - +
301D ALA* 2.5 37.9 + - - +
338D ASN* 6.2 0.4 - - - -
340D HIS* 5.9 4.0 - - - +
99E PRO* 3.9 16.5 - - + +
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Residues in contact with VAL 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D TRP* 3.6 11.9 - - + +
260D ARG* 3.9 3.1 - - + -
261D TYR* 3.3 37.2 - - + +
264D ALA* 4.1 1.8 - - + +
290D LEU* 3.6 26.9 - - + +
293D ASP* 3.3 43.1 - - + +
295D GLU* 3.5 7.9 + - + +
297D GLU* 1.3 78.7 - - - +
299D ARG* 1.3 56.3 - - - +
301D ALA* 3.4 8.3 - - - +
302D ALA* 2.8 27.4 + - - +
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Residues in contact with ARG 299 (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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290D LEU 3.6 6.7 - - - -
291D MSE 3.1 27.9 - - - +
292D LYS* 4.3 2.9 - - - +
293D ASP 3.3 32.2 + - - +
294D CYS 4.3 5.1 + - - -
295D GLU 3.1 21.3 + - - +
296D ALA* 3.0 18.0 + - - +
297D GLU 2.8 4.8 + - - -
298D VAL* 1.3 69.8 - - - +
300D ALA* 1.3 70.2 + - - +
302D ALA* 2.7 16.1 + - - +
303D SER* 2.8 13.5 + - - -
333D LEU* 4.5 3.8 - - + +
336D ASP* 2.7 42.7 + - - -
337D ALA* 5.7 1.2 - - - +
338D ASN* 4.0 9.5 - - - +
341D VAL* 3.9 14.1 - - + +
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Residues in contact with ALA 300 (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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296D ALA 3.0 5.3 + - - +
297D GLU* 3.6 7.6 - - - +
299D ARG* 1.3 77.6 - - - +
301D ALA* 1.3 55.6 + - - +
303D SER* 2.7 34.7 + - - -
304D HIS* 3.1 13.6 + - + +
338D ASN* 5.0 0.4 - - - +
340D HIS* 3.9 11.4 - - + +
341D VAL* 3.5 38.0 - - + +
344D ALA* 4.3 3.9 - - + +
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Residues in contact with ALA 301 (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* 4.2 20.4 - - + +
264D ALA* 3.8 18.1 - - + +
265D ASP* 5.0 5.9 - - - +
297D GLU 2.5 22.8 + - - +
298D VAL* 3.4 9.4 - - - +
300D ALA* 1.3 74.6 - - - +
302D ALA* 1.3 62.6 + - - +
303D SER 3.2 0.2 + - - -
304D HIS* 3.3 21.4 + - - +
305D LYS* 3.8 11.8 - - - +
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Residues in contact with ALA 302 (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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264D ALA* 4.1 9.6 - - + +
267D PHE* 6.5 0.2 - - + -
287D PHE* 3.3 37.0 - - + -
290D LEU* 3.9 23.3 - - + -
291D MSE 4.0 12.1 - - + -
298D VAL 2.8 12.8 + - - +
299D ARG 2.7 14.6 + - - +
301D ALA* 1.3 73.0 - - - +
303D SER* 1.3 62.2 + - - +
305D LYS* 3.2 11.5 + - - +
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Residues in contact with SER 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D MSE 5.2 0.4 - - - +
299D ARG 2.8 12.0 + - - -
300D ALA* 2.7 20.2 + - - -
302D ALA* 1.3 77.1 - - - +
304D HIS* 1.3 51.4 + - - -
305D LYS 2.7 0.7 + - - -
306D VAL* 2.6 42.2 + - - +
333D LEU* 3.6 22.6 - - - +
341D VAL* 3.9 7.2 - - - +
344D ALA* 4.4 0.4 - - - -
345D LEU* 3.8 33.1 - - - +
348D VAL* 4.2 4.9 - - - +
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Residues in contact with HIS 304 (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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300D ALA* 3.1 13.1 + - + -
301D ALA* 3.7 12.5 + - - +
303D SER* 1.3 78.8 - - - +
305D LYS* 1.3 68.5 + - + +
306D VAL 3.4 0.7 + - - -
307D LYS* 4.7 1.9 + - - +
308D GLU* 5.3 1.9 + - - +
344D ALA* 3.6 31.0 - - + +
347D SER* 4.7 12.4 + - - -
348D VAL* 4.3 19.4 - - + +
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Residues in contact with LYS 305 (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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264D ALA 3.7 16.4 - - - +
265D ASP* 3.2 44.1 + - - +
267D PHE* 4.4 5.6 - - + -
268D THR* 3.9 33.5 + - + +
269D GLU* 4.4 4.9 + - - -
287D PHE* 4.4 10.3 - - + -
301D ALA 3.8 12.3 - - - +
302D ALA* 3.6 9.0 - - - +
303D SER 2.7 5.5 + - - -
304D HIS* 1.3 82.7 - - - +
306D VAL* 1.3 62.3 + - - +
307D LYS 3.2 2.1 + - - -
308D GLU* 3.4 10.8 + - - +
309D PHE* 2.9 26.2 + - + +
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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