Contacts of the strand formed by residues 266 - 271 (chain A) in PDB entry 1NHX
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 LEU 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A MET* 1.3 76.0 - - - +
267A VAL* 1.3 68.7 + - - +
268A LEU* 3.9 27.8 - - + +
280A LEU 4.4 2.0 - - - +
281A ALA* 3.2 6.2 - - - +
282A ALA* 2.9 57.1 + - + +
284A PHE* 4.1 10.3 - - + -
290A LYS* 3.4 40.0 - - + +
293A LEU* 4.1 4.7 - - + -
294A ALA* 4.0 15.5 - - + +
309A GLY 3.4 13.9 - - - +
310A ASP* 4.0 13.7 - - - +
432A ILE* 6.3 0.4 - - + -
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Residues in contact with VAL 267 (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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265A MET 4.3 1.1 - - - +
266A LEU* 1.3 80.9 - - - +
268A LEU* 1.3 66.7 + - - +
279A TYR* 4.5 1.1 - - + -
280A LEU 3.4 9.0 - - - +
281A ALA* 4.6 6.1 - - + -
294A ALA 4.8 0.3 - - - +
307A CYS* 4.0 1.2 - - - -
308A VAL* 2.9 48.2 + - + -
309A GLY* 3.0 17.8 + - - +
312A ILE 5.0 2.0 - - - +
313A ALA* 3.7 28.0 - - + -
325A ALA* 4.3 10.1 - - + -
326A ILE 5.5 2.2 - - - +
327A ASN* 5.9 0.7 - - + -
426A VAL* 3.9 14.4 - - + -
428A ILE* 3.8 18.4 - - + -
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Residues in contact with LEU 268 (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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266A LEU* 3.9 18.2 - - + -
267A VAL* 1.3 74.6 - - - +
269A GLY* 1.3 72.8 + - - +
270A ILE* 4.1 14.1 - - + +
279A TYR* 3.3 9.5 - - - -
280A LEU* 2.9 54.9 + - + +
293A LEU* 3.4 35.7 - - + +
294A ALA 4.0 10.1 - - - +
305A VAL* 4.4 9.0 - - + -
306A GLU 3.2 13.7 - - - +
308A VAL 4.3 1.3 - - - +
432A ILE* 6.1 2.0 - - + -
537A LEU* 4.2 16.8 - - + -
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Residues in contact with GLY 269 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A LEU* 1.3 74.5 - - - +
270A ILE* 1.3 60.0 + - - +
271A THR 4.3 0.2 - - - -
277A LYS* 4.1 13.2 - - - -
278A LYS 3.4 7.6 - - - -
279A TYR* 3.7 21.4 - - - -
304A LYS 3.8 0.3 - - - +
305A VAL* 3.4 3.3 - - - -
306A GLU* 2.7 43.1 + - - +
308A VAL* 4.9 0.4 - - - +
417A ASP* 4.4 1.8 - - - -
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Residues in contact with ILE 270 (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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268A LEU* 4.1 7.0 - - + -
269A GLY* 1.3 73.7 - - - +
271A THR* 1.3 64.1 + - - +
277A LYS* 3.2 2.6 - - - +
278A LYS* 2.8 48.8 + - + +
280A LEU* 3.8 26.7 - - + -
296A MET* 5.5 0.9 - - + -
303A TRP* 3.5 35.2 - - + -
304A LYS 3.3 8.7 - - - +
305A VAL* 4.2 11.2 - - + -
534A SER* 5.1 4.3 - - - +
537A LEU* 3.7 36.3 - - + +
541A PHE* 3.5 17.5 - - + -
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Residues in contact with THR 271 (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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270A ILE* 1.3 72.9 - - - +
272A ASN* 1.3 73.2 + - - +
275A GLY* 3.7 28.3 - - - +
276A GLU 3.2 4.3 - - - +
277A LYS* 3.5 26.7 - - + +
302A GLY 4.1 0.4 - - - +
303A TRP* 3.3 11.1 - - - -
304A LYS* 2.9 49.4 + - + +
306A GLU* 4.3 4.5 + - - -
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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