Contacts of the strand formed by residues 261 - 271 (chain B) in PDB entry 5NXR
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 LYS 261 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246B THR* 3.1 7.2 - - - +
247B GLN* 4.0 22.9 - - + +
259B ALA* 4.0 3.0 - - - +
260B ASN* 1.3 82.9 - - - +
262B THR* 1.3 70.8 + - - +
263B GLU* 6.1 2.0 - - + +
288B GLY* 3.5 0.7 - - - -
289B LYS* 2.8 46.7 + - + +
290B ASN* 4.0 22.0 - - - +
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Residues in contact with THR 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B THR 5.0 0.8 + - - +
245B GLN* 3.3 9.0 - - - +
246B THR* 2.5 52.7 + - - +
250B SER* 4.1 12.6 + - - -
259B ALA* 3.6 21.1 - - + -
261B LYS* 1.3 81.5 - - - +
263B GLU* 1.3 64.0 + - - +
264B ASN* 3.1 25.1 + - - -
286B SER* 4.1 2.7 - - - +
287B LYS 3.1 7.2 - - - +
289B LYS* 5.6 0.2 - - - -
300B LEU* 3.8 20.0 - - + -
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Residues in contact with GLU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B TYR* 3.6 23.3 - - + +
244B GLY 3.6 4.3 - - - -
245B GLN* 3.8 12.2 - - + +
261B LYS* 6.1 3.1 - - + +
262B THR* 1.3 75.4 - - - +
264B ASN* 1.3 64.2 + - - +
285B GLN* 3.9 1.4 - - - +
286B SER* 3.4 1.2 - - - -
287B LYS* 2.8 45.8 + - + +
289B LYS* 3.5 38.4 + - + +
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Residues in contact with ASN 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B THR* 3.4 24.2 + - - +
119B MET* 3.2 29.2 - - + +
242B MET* 3.9 2.6 - - + +
243B TYR* 3.1 12.9 - - - -
244B GLY 2.8 48.8 + - - +
246B THR* 4.1 4.4 - - - +
262B THR* 3.1 22.8 + - - -
263B GLU* 1.3 76.7 - - - +
265B VAL* 1.3 60.7 + - - +
285B GLN 3.3 3.4 - - - -
286B SER* 2.8 32.6 + - - -
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Residues in contact with VAL 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B MET 3.4 9.4 - - - +
243B TYR* 4.5 12.1 - - + -
264B ASN* 1.3 75.0 - - - +
266B GLU* 1.3 70.3 + - - +
267B LEU* 4.0 28.0 - - + -
283B TYR* 3.9 12.9 - - + +
284B ASN* 3.6 1.2 - - - -
285B GLN* 2.9 60.6 + - + +
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Residues in contact with GLU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASN* 2.9 17.6 + - - +
108B THR* 2.5 41.8 + - + +
116B ALA* 3.5 14.7 + - - -
118B THR* 2.6 33.9 + - - +
241B ALA* 3.3 3.6 - - - -
242B MET* 2.8 46.9 + - + +
265B VAL* 1.3 80.0 - - - +
267B LEU* 1.3 64.6 + - - +
283B TYR 3.4 4.7 - - - +
284B ASN* 3.0 31.7 + - - +
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B THR* 5.2 0.9 - - - -
111B PHE* 3.7 4.3 - - - -
240B ALA 3.4 4.3 - - - +
241B ALA* 3.6 22.7 - - + -
242B MET 4.8 0.7 - - - +
265B VAL* 4.0 19.5 - - + -
266B GLU* 1.3 85.0 - - - +
268B VAL* 1.3 65.3 + - - +
282B GLY* 3.3 1.3 - - - -
283B TYR* 2.8 49.7 + - + +
413B LDA 3.7 48.5 - - + -
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Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B THR* 4.2 10.1 - - - -
110B VAL* 3.7 28.5 - - + -
111B PHE* 3.8 21.5 - - + -
238B TYR* 4.1 4.9 - - + -
239B LEU* 3.2 4.9 - - - +
240B ALA* 2.9 57.7 + - + +
267B LEU* 1.3 77.6 - - - +
269B ALA* 1.3 65.4 + - - +
270B GLN* 4.1 3.4 - - - +
280B SER* 3.7 20.0 - - - +
281B ILE 3.4 13.7 - - - +
282B GLY* 4.5 0.2 - - - -
413B LDA 4.0 6.2 - - - +
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Residues in contact with ALA 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B TYR 3.3 5.4 - - - -
239B LEU* 4.3 11.4 - - + -
268B VAL* 1.3 74.4 - - - +
270B GLN* 1.3 60.6 + - - +
280B SER* 3.4 1.2 + - - -
281B ILE* 2.8 51.4 + - + +
405B LDA 5.3 7.4 - - + -
413B LDA 4.2 20.1 - - + +
414B LDA 3.9 10.7 - - + +
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Residues in contact with GLN 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B VAL* 3.4 36.4 + - - +
236B ASN 3.9 0.2 - - - +
237B VAL* 3.6 5.2 - - - +
238B TYR* 2.8 65.3 + - + +
268B VAL* 4.1 1.7 - - + +
269B ALA* 1.3 76.6 - - - +
271B TYR* 1.3 60.0 + - - +
278B LYS* 3.4 36.2 - - + +
279B PRO 3.1 18.6 - - - +
280B SER* 2.8 27.2 + - - -
309B TYR* 4.3 1.6 - - - -
414B LDA 4.2 4.9 - - - +
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Residues in contact with TYR 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ASN 4.1 6.9 + - - -
236B ASN* 3.3 27.7 + - + +
237B VAL* 3.6 23.1 - - + -
270B GLN* 1.3 74.8 - - - +
272B LEU* 1.3 72.1 + - - +
273B PHE* 3.5 35.1 - + - -
278B LYS* 3.2 23.9 - - - -
279B PRO* 3.2 17.6 + - + +
405B LDA 3.9 29.2 - - + +
414B LDA 3.6 70.4 - - + +
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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