Contacts of the strand formed by residues 298 - 311 (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 GLN 298 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B LYS* 4.7 3.8 - - - +
288B GLY* 2.7 39.9 + - - +
291B LEU* 3.8 11.0 - - + +
295B TYR* 3.8 25.8 - - + +
296B ASP 4.1 1.2 + - - +
297B ASN* 1.3 80.2 + - - +
299B ASP* 1.3 63.9 + - - +
300B LEU* 4.0 0.9 - - - +
330B ASN* 3.1 27.1 + - - +
332B PHE* 3.6 48.3 - - + +
333B THR* 5.9 0.2 - - - +
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Residues in contact with ASP 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLN* 3.8 4.1 - - - +
286B SER 3.6 5.6 - - - +
287B LYS* 3.3 34.0 - - - +
298B GLN* 1.3 79.7 + - - +
300B LEU* 1.3 60.2 + - - +
301B VAL 4.7 1.8 - - - +
302B LYS* 3.8 30.8 + - + +
326B LEU 5.4 0.5 - - - +
327B LEU* 4.6 23.6 - - + +
328B LYS 5.7 1.2 + - - -
332B PHE* 3.7 18.9 - - - -
333B THR* 5.3 2.3 - - - +
338B ILE* 4.9 0.7 - - - +
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Residues in contact with LEU 300 (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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250B SER* 5.8 1.6 - - - -
251B ARG 5.5 1.3 - - - +
252B TYR* 3.8 36.6 - - + -
259B ALA* 4.8 2.7 - - + -
262B THR* 3.8 23.1 - - + -
286B SER* 2.7 29.1 + - - +
288B GLY* 3.8 15.0 - - - +
291B LEU* 4.0 13.7 - - + -
298B GLN 4.1 0.2 - - - +
299B ASP* 1.3 77.2 - - - +
301B VAL* 1.3 64.7 + - + +
327B LEU* 4.1 4.8 - - - +
332B PHE* 3.8 26.0 - - + -
338B ILE* 3.9 27.3 - - + +
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASP* 3.5 28.7 - - + +
118B THR* 3.8 7.9 - - + -
284B ASN* 4.0 4.9 - - + +
285B GLN* 3.1 3.3 - - - +
286B SER* 2.8 55.1 + - - +
299B ASP* 4.8 0.5 - - - +
300B LEU* 1.3 80.4 + - + +
302B LYS* 1.3 67.9 + - - +
303B TYR* 3.4 36.1 - - + -
327B LEU* 3.7 6.5 - - - -
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Residues in contact with LYS 302 (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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283B TYR* 3.5 25.8 - - - +
284B ASN 3.2 5.2 - - - -
285B GLN* 3.0 29.3 + - + +
287B LYS* 5.3 2.2 - - - +
299B ASP* 3.8 25.0 + - + +
301B VAL* 1.3 77.7 - - - +
303B TYR* 1.3 63.9 + - - +
325B ASN* 3.3 0.3 - - - +
326B LEU* 2.8 48.6 + - + +
327B LEU* 2.9 23.3 - - + +
413B LDA 3.9 23.0 - - - -
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Residues in contact with TYR 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PHE* 4.2 13.9 - + - -
114B TRP* 3.9 18.2 - - + -
115B GLY* 2.8 21.3 + - - -
117B ASP* 2.4 29.4 + - + -
283B TYR* 3.4 7.0 - - - -
284B ASN* 2.9 46.3 + - + -
301B VAL* 3.4 35.7 - - + -
302B LYS* 1.3 76.1 - - - +
304B ILE* 1.3 74.9 + - - +
305B SER* 4.3 3.1 - - - -
323B LYS* 3.8 32.1 - - + -
324B ILE 3.3 15.0 - - - +
325B ASN* 4.1 6.1 - - - +
326B LEU* 4.1 3.3 - - - +
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Residues in contact with ILE 304 (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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281B ILE* 4.6 13.0 - - + -
282B GLY 3.3 10.1 - - - +
283B TYR* 3.7 17.3 - - + -
303B TYR* 1.3 79.7 - - - +
305B SER* 1.3 70.6 + - - +
306B VAL* 4.2 3.4 - - + -
322B TYR 3.6 0.5 - - - +
323B LYS* 3.6 3.5 - - - -
324B ILE* 2.8 55.9 + - + +
326B LEU* 3.8 27.8 - - + -
413B LDA 4.2 23.3 - - + -
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Residues in contact with SER 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PHE* 3.5 37.2 - - - +
112B PRO* 4.8 1.6 - - - +
114B TRP* 4.3 5.4 - - - -
280B SER* 4.6 3.3 + - - -
281B ILE* 3.2 8.8 - - - +
282B GLY 2.7 37.2 + - - -
303B TYR* 4.3 9.0 - - - -
304B ILE* 1.3 74.6 - - - +
306B VAL* 1.3 62.5 + - - +
321B ASP* 2.8 22.0 + - - -
322B TYR 3.5 5.2 - - - -
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B SER 3.7 2.7 - - - -
281B ILE* 3.6 30.5 - - + -
304B ILE* 4.2 3.6 - - + -
305B SER* 1.3 74.7 + - - +
307B GLY* 1.3 58.4 + - - +
320B VAL* 5.4 0.2 - - - +
321B ASP* 3.8 2.0 - - - -
322B TYR* 2.8 65.9 + - + +
324B ILE* 4.1 15.3 - - + -
409B LDA 4.0 20.6 - - + +
410B LDA 5.5 5.2 - - + -
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Residues in contact with GLY 307 (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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112B PRO* 4.2 3.6 - - - -
279B PRO* 3.3 4.0 - - - +
280B SER 2.7 38.9 + - - -
306B VAL* 1.3 74.9 - - - +
308B SER* 1.3 59.4 + - - -
320B VAL* 3.0 15.0 - - - -
321B ASP* 4.0 5.5 + - - -
409B LDA 3.9 15.8 - - - +
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Residues in contact with SER 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PRO* 3.9 3.6 - - - +
277B LEU* 3.4 18.4 - - - +
278B LYS 3.3 17.6 - - - -
279B PRO* 3.3 7.2 - - - +
280B SER 4.3 0.7 - - - +
307B GLY* 1.3 76.5 - - - -
309B TYR* 1.3 82.6 + - - +
319B VAL* 3.2 7.1 - - - +
320B VAL* 2.9 39.5 + - - +
409B LDA 4.1 15.3 - - - -
417B LDA 5.6 4.2 - - - +
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Residues in contact with TYR 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 2.6 30.2 + - - -
111B PHE 2.9 14.4 + - - -
112B PRO* 3.6 24.0 - - + -
270B GLN* 4.3 8.5 - - - -
277B LEU* 3.6 3.7 - - - +
278B LYS* 3.0 46.2 + - + +
280B SER* 4.6 1.8 - - - -
308B SER* 1.3 89.6 + - - +
310B TYR* 1.3 62.4 + - - +
311B TYR* 3.2 44.2 - + + -
317B SER* 5.5 3.4 - - - -
318B ALA 3.4 4.7 - - - +
319B VAL* 3.5 21.5 - - + -
417B LDA 5.3 1.1 - - - -
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Residues in contact with TYR 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B PHE* 3.7 27.8 + + - -
276B GLY 3.5 1.8 - - - -
277B LEU* 4.0 17.0 - - + -
309B TYR* 1.3 74.1 - - - +
311B TYR* 1.3 61.7 - - - +
312B PHE* 3.5 48.3 + + - -
317B SER* 3.2 5.3 - - - -
318B ALA* 2.7 40.0 + - + +
406B LDA 3.3 44.9 + - + +
417B LDA 3.5 54.2 - - + +
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Residues in contact with TYR 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 4.2 12.3 - - + -
275B PHE 4.7 0.5 - - - +
276B GLY* 2.9 37.1 + - - +
278B LYS* 3.2 38.5 + - + -
309B TYR* 3.2 44.3 - + + -
310B TYR* 1.3 75.0 - - - +
312B PHE* 1.3 65.8 + - - +
313B ASN* 3.3 11.4 - - - +
314B LYS* 4.5 20.4 - - - +
316B MET 4.0 2.7 - - - -
317B SER* 4.0 17.0 - - - -
406B LDA 5.8 0.2 + - - -
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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