Contacts of the strand formed by residues 277 - 289 (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 LEU 277 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LEU* 3.5 2.6 - - - +
273A PHE* 2.8 45.6 + - + +
275A PHE* 3.5 28.7 + - + -
276A GLY* 1.3 78.3 - - - +
278A LYS* 1.3 62.5 + - - +
279A PRO* 3.9 23.1 - - + -
308A SER* 3.4 20.2 - - - +
309A TYR 3.6 6.7 - - - +
310A TYR* 4.0 9.0 - - + -
411A LDA 3.9 30.7 - - + -
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Residues in contact with LYS 278 (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 GLN* 3.4 32.0 - - + +
271A TYR 3.2 20.0 - - - +
272A LEU* 3.8 26.5 - - + +
277A LEU* 1.3 76.2 - - - +
279A PRO* 1.4 73.7 - - - +
280A SER 3.6 0.2 + - - -
308A SER* 3.3 3.7 - - - -
309A TYR* 3.0 47.0 + - + -
311A TYR* 3.2 39.6 + - + -
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Residues in contact with PRO 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A GLN* 3.1 18.4 - - - +
271A TYR* 3.2 24.6 + - + +
273A PHE* 3.7 28.3 - - + -
277A LEU* 3.9 12.8 - - + -
278A LYS* 1.4 91.1 - - - +
280A SER* 1.3 57.9 + - - +
307A GLY 3.3 10.8 - - - +
308A SER* 3.3 6.3 - - - +
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Residues in contact with SER 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A PHE* 4.5 2.4 - - - -
112A PRO* 3.9 29.4 - - - +
268A VAL* 3.7 13.0 - - - +
269A ALA 3.4 5.2 - - - -
270A GLN* 2.8 27.5 + - - -
278A LYS 4.3 4.0 - - - -
279A PRO* 1.3 75.3 - - - +
281A ILE* 1.3 61.8 + - - +
305A SER* 3.7 5.1 + - - +
306A VAL* 3.7 1.1 - - - +
307A GLY 2.7 36.7 + - - +
309A TYR* 4.6 1.8 - - - -
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Residues in contact with ILE 281 (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 VAL* 3.4 5.0 - - - +
269A ALA* 2.8 54.7 + - + +
280A SER* 1.3 76.7 - - - +
282A GLY* 1.3 62.6 + - - +
304A ILE* 4.6 11.0 - - + -
305A SER* 3.2 9.6 - - - +
306A VAL* 3.9 23.3 - - + -
401A LDA 3.8 17.5 - - + +
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Residues in contact with GLY 282 (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* 3.8 18.6 - - - -
267A LEU 3.3 10.1 - - - -
268A VAL* 4.3 1.1 - - - -
281A ILE* 1.3 78.4 - - - +
283A TYR* 1.3 61.1 + - - +
304A ILE* 3.3 10.9 - - - +
305A SER* 2.7 42.4 + - - -
401A LDA 4.5 4.7 - - - -
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Residues in contact with TYR 283 (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* 3.7 2.5 - - - -
265A VAL* 3.7 19.5 - - + -
266A GLU* 3.4 1.9 - - - -
267A LEU* 2.8 49.0 + - + +
282A GLY* 1.3 74.1 - - - +
284A ASN* 1.3 72.6 + - - +
285A GLN* 2.7 45.3 + - + -
302A LYS* 3.6 15.1 - - + +
303A TYR 3.4 15.3 - - - -
304A ILE* 3.7 7.2 - - + -
326A LEU* 3.8 18.4 - - + -
401A LDA 3.5 60.3 - - + +
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Residues in contact with ASN 284 (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* 3.6 13.9 - - - -
115A GLY* 4.4 0.7 - - - -
116A ALA 3.5 7.4 + - - +
117A ASP* 2.9 35.4 - - - +
118A THR* 3.7 5.8 - - + +
265A VAL 3.6 2.5 - - - -
266A GLU* 3.4 24.4 + - - +
283A TYR* 1.3 92.9 - - - +
285A GLN* 1.3 62.2 + - - +
301A VAL* 4.3 2.7 - - + -
302A LYS* 3.2 4.7 + - - -
303A TYR* 2.9 65.7 + - + +
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Residues in contact with GLN 285 (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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118A THR* 3.3 7.4 - - - +
263A GLU 3.9 1.2 - - - +
264A ASN* 3.3 3.8 - - - -
265A VAL* 2.9 43.0 + - + +
283A TYR* 2.7 40.1 + - + +
284A ASN* 1.3 74.8 - - - +
286A SER* 1.3 68.4 + - - +
287A LYS* 3.4 26.7 - - + +
299A ASP* 3.4 22.6 + - - +
301A VAL 3.1 10.1 - - - +
302A LYS* 3.7 23.9 - - + +
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Residues in contact with SER 286 (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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118A THR* 3.7 14.9 + - - -
262A THR* 4.1 3.5 - - - +
263A GLU 3.4 4.3 - - - -
264A ASN* 2.8 20.5 + - - -
285A GLN* 1.3 73.6 - - - +
287A LYS* 1.3 59.0 + - - +
299A ASP* 3.6 2.8 - - - +
300A LEU* 2.7 50.1 + - - +
301A VAL* 2.8 35.0 + - - +
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Residues in contact with LYS 287 (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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262A THR* 3.1 6.7 - - - -
263A GLU* 2.8 62.0 + - + +
285A GLN* 3.4 33.0 - - + +
286A SER* 1.3 72.2 + - - +
288A GLY* 1.3 61.9 + - - +
289A LYS* 4.0 21.2 + - - +
297A ASN* 5.8 0.7 - - - +
298A GLN 3.8 4.3 - - - +
299A ASP* 3.4 11.9 - - - +
300A LEU* 4.5 1.8 - - - -
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Residues in contact with GLY 288 (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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261A LYS 3.5 6.3 - - - -
287A LYS* 1.3 74.9 - - - +
289A LYS* 1.3 62.0 + - - +
291A LEU* 3.9 18.8 - - - -
297A ASN* 3.2 6.6 - - - +
298A GLN 2.7 39.6 + - - -
300A LEU* 3.8 16.2 - - - +
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Residues in contact with LYS 289 (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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260A ASN* 3.6 0.9 - - - +
261A LYS* 2.8 53.4 + - + +
262A THR* 5.3 0.9 - - - -
263A GLU* 3.6 28.3 + - + +
287A LYS* 4.2 27.6 - - - +
288A GLY* 1.3 76.9 - - - -
290A ASN* 1.3 73.9 + - - +
291A LEU* 3.3 7.1 + - - +
296A ASP 3.7 0.4 - - - -
297A ASN* 3.1 29.6 + - - +
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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