Contacts of the helix formed by residues 293 - 302 (chain A) in PDB entry 6NRB
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 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A LEU* 4.9 0.8 - - - +
242A GLN* 3.2 34.9 + - - +
243A LYS* 3.7 15.3 + - + +
291A GLY* 4.1 2.9 - - - -
292A ILE* 1.3 77.3 - - - +
294A ASP* 1.3 60.4 + - - +
295A MET* 2.9 10.5 + - + +
296A CYS* 3.0 5.1 + - - +
297A LEU 2.8 22.0 + - - -
310A ARG* 5.9 0.5 + - - -
334C ARG* 4.2 22.0 - - - +
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Residues in contact with ASP 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A GLN* 3.9 20.7 - - - +
292A ILE 3.6 0.8 + - - -
293A ASP* 1.3 72.2 - - - +
295A MET* 1.3 56.6 + - - +
297A LEU* 3.4 22.4 - - - +
298A LYS* 2.7 34.9 + - + +
309A ARG* 2.8 31.5 + - - +
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Residues in contact with MET 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A LYS* 3.5 37.9 - - + -
246A MET* 4.8 0.9 - - + -
267A GLU 4.2 5.4 - - - +
268A SER* 3.3 23.6 - - - +
293A ASP* 2.9 6.1 - - + +
294A ASP* 1.3 77.6 - - - +
296A CYS* 1.3 62.2 + - - +
298A LYS* 4.1 1.9 - - - +
299A TYR* 3.0 55.4 + - + +
334C ARG* 2.8 39.0 - - - +
336C GLU* 4.0 19.3 - - - +
337C GLU* 4.5 4.7 - - - +
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Residues in contact with CYS 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A LEU* 3.3 39.0 - - + -
243A LYS* 3.1 25.7 - - + +
275A ILE* 4.0 9.9 - - + -
293A ASP 3.0 9.3 + - - +
295A MET* 1.3 75.8 - - - +
297A LEU* 1.3 65.7 + - - +
299A TYR* 2.9 24.5 + - - +
300A PHE* 3.0 19.0 - - + -
336A GLY 3.1 27.8 - - - -
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A GLY* 3.3 24.2 - - - +
223A GLN* 3.6 22.7 - - + +
292A ILE* 3.5 12.5 - - + +
293A ASP 2.8 14.9 + - - +
294A ASP* 3.4 25.8 - - - +
296A CYS* 1.3 70.6 - - - +
298A LYS* 1.3 62.0 + - - +
300A PHE* 3.0 23.2 + - - +
301A VAL* 3.1 19.5 + - + +
307A ALA* 3.5 27.4 - - + +
309A ARG* 3.5 32.8 - - + +
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Residues in contact with LYS 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A GLN* 3.2 25.3 - - - +
272A LYS* 4.3 17.6 - - - +
294A ASP* 2.7 24.0 + - + +
295A MET* 4.1 1.8 - - - +
297A LEU* 1.3 73.5 - - - +
299A TYR* 1.3 67.5 + - - +
301A VAL* 2.8 10.4 + - + +
302A GLU* 2.8 56.9 + - + +
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Residues in contact with TYR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A LYS* 3.6 7.6 - - - -
268A SER* 3.1 30.6 + - - -
271A THR* 3.5 26.5 - - + -
272A LYS* 3.4 32.1 - - + -
275A ILE* 3.5 40.0 - - + +
276A GLN* 4.6 2.6 - - - +
295A MET* 3.0 47.4 - - + +
296A CYS* 2.9 8.3 + - - +
298A LYS* 1.3 84.7 - - - +
300A PHE* 1.3 55.4 + - - +
302A GLU* 3.1 24.1 - - - +
303A ALA* 2.9 26.9 + - - +
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Residues in contact with PHE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A LEU* 3.4 34.3 - - + -
275A ILE* 3.5 31.6 - - + -
278A ILE* 3.5 28.5 - - + -
286A ILE* 3.4 25.6 - - + -
296A CYS 3.0 28.0 - - - -
297A LEU* 3.0 8.1 + - - +
299A TYR* 1.3 77.8 - - - +
301A VAL* 1.3 52.2 + - - +
303A ALA* 3.0 4.6 + - - -
304A GLY 2.7 13.3 + - - -
305A ALA* 2.6 53.3 + - + +
307A ALA* 3.5 23.1 - - + -
340A PHE* 4.4 2.9 - + - -
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A GLN* 3.3 34.5 - - + +
224A GLY* 3.9 10.3 - - - +
225A MET* 3.4 44.4 - - + +
297A LEU* 3.1 19.1 - - + +
298A LYS* 2.8 23.0 + - + +
300A PHE* 1.3 77.1 - - - +
302A GLU* 1.3 58.3 + - + +
304A GLY* 3.2 14.7 + - - +
305A ALA 4.0 4.7 - - - +
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Residues in contact with GLU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LYS* 3.6 18.2 + - - +
276A GLN* 3.2 18.8 + - + +
298A LYS* 2.8 34.9 + - + +
299A TYR* 3.1 41.2 - - - +
301A VAL* 1.3 78.7 - - + +
303A ALA* 1.3 59.6 + - - +
304A GLY 3.3 0.7 - - - -
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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