Contacts of the strand formed by residues 298 - 311 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A LYS* 4.7 1.3 - - - -
288A GLY* 2.7 39.8 + - - +
291A LEU* 3.8 10.3 - - + -
295A TYR* 3.8 25.4 - - + +
296A ASP 4.1 1.4 + - - +
297A ASN* 1.3 80.9 + - - +
299A ASP* 1.3 63.9 + - - +
300A LEU* 4.0 0.9 - - - +
330A ASN* 3.1 28.1 + - - +
332A PHE* 3.6 49.0 - - + +
333A THR* 5.9 0.2 - - - +
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Residues in contact with ASP 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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285A GLN* 3.4 24.4 + - - -
286A SER 3.7 4.7 - - - +
287A LYS* 3.4 16.0 - - - +
298A GLN* 1.3 81.2 + - - +
300A LEU* 1.3 60.3 + - - +
301A VAL 4.7 1.8 - - - +
302A LYS* 3.8 26.9 + - + +
326A LEU 5.6 0.2 - - - +
327A LEU* 4.6 23.0 - - + +
328A LYS 5.9 0.3 + - - -
332A PHE* 3.7 18.5 - - - -
333A THR* 5.3 2.1 - - - +
338A ILE* 4.9 1.0 - - - +
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Residues in contact with LEU 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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250A SER* 5.8 2.0 - - - -
251A ARG 5.5 1.6 - - - +
252A TYR* 3.8 35.2 - - + -
259A ALA* 4.8 3.4 - - + -
262A THR* 3.8 23.6 - - + -
286A SER* 2.7 27.5 + - - +
288A GLY* 3.8 14.4 - - - +
291A LEU* 4.0 13.2 - - + -
298A GLN 4.1 0.4 - - - +
299A ASP* 1.3 76.6 - - - +
301A VAL* 1.3 69.8 + - + +
327A LEU* 4.2 4.7 - - - +
332A PHE* 3.8 26.0 - - + -
338A ILE* 3.9 26.9 - - + +
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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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117A ASP* 3.4 34.5 - - + +
118A THR* 4.8 1.6 - - + +
284A ASN* 4.0 4.7 - - + +
285A GLN* 3.1 5.1 - - - +
286A SER* 2.8 46.0 + - - +
299A ASP* 3.7 0.5 - - - +
300A LEU* 1.3 87.0 - - + +
302A LYS* 1.3 66.4 + - - +
303A TYR* 3.7 30.5 - - + -
327A LEU* 3.7 5.6 - - - -
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Residues in contact with LYS 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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283A TYR* 3.6 26.0 - - - +
284A ASN 3.2 5.6 - - - -
285A GLN* 3.7 24.2 + - + +
299A ASP* 3.8 23.3 + - + +
301A VAL* 1.3 77.7 - - - +
303A TYR* 1.3 62.4 + - - +
325A ASN* 3.3 0.9 - - - +
326A LEU* 2.8 54.1 + - + +
327A LEU* 2.9 22.7 - - + +
401A LDA 4.7 12.1 - - - +
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Residues in contact with TYR 303 (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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111A PHE* 4.2 13.7 - + - -
114A TRP* 4.0 13.7 - + + -
115A GLY* 2.8 21.5 + - - -
117A ASP* 2.4 30.4 + - - -
283A TYR* 3.4 6.8 - - - -
284A ASN* 2.9 49.9 + - + -
301A VAL* 3.7 27.6 - - + -
302A LYS* 1.3 76.5 - - - +
304A ILE* 1.3 74.9 + - - +
305A SER* 4.3 3.4 - - - -
323A LYS* 3.8 37.0 - - + -
324A ILE 3.3 14.6 - - - +
325A ASN* 4.1 5.4 - - - +
326A LEU* 4.2 3.6 - - - +
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Residues in contact with ILE 304 (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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281A ILE* 4.6 10.8 - - + -
282A GLY 3.3 10.3 - - - +
283A TYR* 3.7 17.3 - - + -
303A TYR* 1.3 79.1 - - - +
305A SER* 1.3 70.5 + - - +
306A VAL* 4.3 6.1 - - + -
322A TYR 3.6 0.3 - - - +
323A LYS* 3.6 3.3 - - - -
324A ILE* 2.8 56.1 + - + +
326A LEU* 3.8 27.8 - - + -
401A LDA 4.4 31.9 - - + -
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Residues in contact with SER 305 (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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111A PHE* 3.5 37.0 - - - +
112A PRO* 4.8 1.7 - - - +
114A TRP* 4.3 5.4 - - - -
280A SER* 4.6 3.5 + - - -
281A ILE* 3.2 9.4 - - - +
282A GLY 2.7 37.4 + - - -
303A TYR* 4.3 8.3 - - - -
304A ILE* 1.3 74.6 - - - +
306A VAL* 1.3 61.7 + - - +
321A ASP* 2.8 22.1 + - - -
322A TYR 3.4 4.5 - - - -
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Residues in contact with VAL 306 (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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280A SER 3.7 3.1 - - - +
281A ILE* 3.9 23.8 - - + +
304A ILE* 4.6 3.1 - - + -
305A SER* 1.3 78.7 + - - +
307A GLY* 1.3 62.9 + - - +
320A VAL* 5.5 0.9 - - - +
321A ASP* 3.8 2.5 - - - -
322A TYR* 2.8 46.0 + - + +
324A ILE* 4.1 21.1 - - + -
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Residues in contact with GLY 307 (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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112A PRO* 4.2 3.6 - - - -
279A PRO* 3.3 4.3 - - - +
280A SER 2.7 40.0 + - - +
306A VAL* 1.3 80.7 - - - +
308A SER* 1.3 60.7 + - - -
320A VAL* 3.0 17.5 - - - -
321A ASP* 4.0 4.7 + - - -
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Residues in contact with SER 308 (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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112A PRO* 3.9 4.0 - - - +
277A LEU* 3.4 17.8 - - - +
278A LYS 3.3 18.0 - - - -
279A PRO* 3.3 7.9 - - - +
280A SER 4.3 0.7 - - - +
307A GLY* 1.3 77.9 - - - -
309A TYR* 1.3 82.1 + - - +
319A VAL* 3.2 7.3 - - - +
320A VAL* 2.9 39.2 + - - +
411A LDA 5.5 3.3 - - - +
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Residues in contact with TYR 309 (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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110A VAL* 2.6 30.7 + - - -
111A PHE 2.9 13.7 + - - -
112A PRO* 3.6 24.6 - - + -
270A GLN* 4.3 9.4 - - - -
277A LEU* 3.6 3.3 - - - +
278A LYS* 3.0 46.2 + - + +
280A SER* 4.6 1.6 - - - -
308A SER* 1.3 88.3 + - - +
310A TYR* 1.3 62.3 + - - +
311A TYR* 3.2 44.2 - + + -
317A SER* 5.6 2.7 - - - -
318A ALA 3.4 6.5 - - - +
319A VAL* 3.5 21.5 - - + -
411A LDA 5.3 0.9 - - - -
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Residues in contact with TYR 310 (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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275A PHE 3.6 24.7 + - - -
276A GLY 3.5 9.2 - - - -
277A LEU* 4.0 14.1 - - + -
309A TYR* 1.3 74.5 - - - +
311A TYR* 1.3 63.8 + - - +
312A PHE* 3.5 48.8 + + - -
317A SER* 3.2 5.2 - - - -
318A ALA* 2.7 40.8 + - + +
410A LDA 3.4 32.4 + - + +
411A LDA 3.7 62.2 - - + +
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Residues in contact with TYR 311 (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 LEU* 4.3 12.6 - - + -
275A PHE 4.9 0.5 - - - +
276A GLY* 2.9 37.0 + - - +
278A LYS* 3.2 37.9 + - + -
309A TYR* 3.2 44.0 - + + -
310A TYR* 1.3 75.5 - - - +
312A PHE* 1.3 65.7 + - - +
313A ASN* 3.3 13.8 - - - +
314A LYS* 6.2 1.6 - - - -
316A MET 4.0 2.7 - - - -
317A SER* 4.0 18.6 - - - -
351A GLN* 6.3 0.9 - - - -
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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