Contacts of the strand formed by residues 261 - 271 (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 LYS 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A THR* 3.1 8.3 - - - +
247A GLN* 4.0 22.9 - - + +
259A ALA* 4.0 2.3 - - - +
260A ASN* 1.3 84.9 - - + +
262A THR* 1.3 71.0 + - - +
288A GLY* 3.5 0.7 - - - -
289A LYS* 2.8 48.3 + - + +
290A ASN* 4.0 21.5 - - - +
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Residues in contact with THR 262 (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 5.0 0.8 + - - +
245A GLN* 3.3 8.7 - - - +
246A THR* 2.5 53.6 + - - +
250A SER* 4.1 12.2 + - - -
259A ALA* 3.6 20.6 - - + -
261A LYS* 1.3 83.7 - - - +
263A GLU* 1.3 60.2 + - - +
264A ASN* 3.2 24.8 + - - -
286A SER* 4.1 2.5 - - - +
287A LYS 3.1 8.3 - - - +
289A LYS* 5.3 1.3 - - - -
300A LEU* 3.8 20.2 - - + -
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Residues in contact with GLU 263 (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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243A TYR* 2.9 40.3 + - + +
244A GLY 3.6 2.2 - - - -
245A GLN* 3.9 10.7 + - - +
262A THR* 1.3 73.8 - - - +
264A ASN* 1.3 61.2 + - - +
265A VAL* 5.9 0.2 - - - -
285A GLN* 3.9 0.9 - - - +
286A SER* 3.4 1.0 - - - -
287A LYS* 2.8 58.6 + - + +
289A LYS* 3.6 27.0 + - - +
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Residues in contact with ASN 264 (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* 3.4 24.5 + - - +
119A MET* 3.2 29.4 - - + +
242A MET* 4.5 2.5 - - + -
243A TYR* 3.1 10.2 - - - -
244A GLY 2.8 49.4 + - - +
246A THR* 4.1 4.2 - - - +
262A THR* 3.2 22.8 + - - -
263A GLU* 1.3 78.5 - - - +
265A VAL* 1.3 63.6 + - - +
285A GLN 3.3 2.9 - - - -
286A SER* 2.8 32.2 + - - -
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Residues in contact with VAL 265 (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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242A MET* 3.4 6.3 - - - +
243A TYR* 3.6 21.1 - - + -
263A GLU 5.9 0.2 - - - -
264A ASN* 1.3 80.1 - - - +
266A GLU* 1.3 68.8 + - - +
267A LEU* 5.3 8.7 - - + -
283A TYR* 3.7 28.9 - - + -
284A ASN* 3.6 1.0 - - - -
285A GLN* 2.9 48.2 + - + +
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Residues in contact with GLU 266 (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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105A ASN* 2.9 17.9 + - - +
108A THR* 2.5 42.2 + - + +
111A PHE* 5.9 0.4 - - + -
116A ALA* 3.5 14.3 + - - -
118A THR* 2.6 40.1 + - + +
241A ALA* 3.3 3.8 - - - -
242A MET* 2.8 47.6 + - + +
265A VAL* 1.3 81.3 - - - +
267A LEU* 1.3 64.5 + - - +
283A TYR 3.4 4.0 - - - -
284A ASN* 3.4 25.8 + - - +
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Residues in contact with LEU 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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108A THR* 5.1 0.9 - - - -
111A PHE* 3.7 4.5 - - - -
240A ALA 3.4 5.4 - - - +
241A ALA* 3.6 22.0 - - + -
242A MET 4.8 1.8 - - - +
265A VAL* 5.3 7.0 - - + -
266A GLU* 1.3 86.8 - - - +
268A VAL* 1.3 64.8 + - - +
282A GLY* 3.3 1.3 - - - -
283A TYR* 2.8 55.8 + - + +
401A LDA 4.0 32.1 - - + -
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Residues in contact with VAL 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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108A THR* 4.2 9.0 - - - -
110A VAL* 3.7 28.7 - - + -
111A PHE* 3.8 20.2 - - + -
238A TYR* 4.1 4.9 - - + -
239A LEU* 3.2 4.5 - - - +
240A ALA* 2.8 61.7 + - + +
267A LEU* 1.3 77.6 - - - +
269A ALA* 1.3 66.6 + - - +
270A GLN* 4.1 2.9 - - - +
280A SER* 3.7 19.1 - - - +
281A ILE 3.4 14.4 - - - +
401A LDA 4.3 3.3 - - - +
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Residues in contact with ALA 269 (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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238A TYR 3.3 4.9 - - - -
239A LEU* 3.5 20.2 - - + -
268A VAL* 1.3 75.6 - - - +
270A GLN* 1.3 62.1 + - - +
280A SER* 3.4 1.6 + - - -
281A ILE* 2.8 51.6 + - + +
401A LDA 4.0 8.6 - - + +
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Residues in contact with GLN 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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110A VAL* 3.4 37.8 + - - +
236A ASN 3.9 0.2 - - - +
237A VAL* 3.6 4.5 - - - +
238A TYR* 2.8 65.9 + - + +
239A LEU* 4.6 0.8 - - - +
268A VAL* 4.1 1.5 - - + +
269A ALA* 1.3 77.3 - - - +
271A TYR* 1.3 59.0 + - - +
278A LYS* 3.4 37.5 - - + +
279A PRO 3.1 18.2 - - - +
280A SER* 2.8 27.2 + - - -
309A TYR* 4.3 1.7 - - - -
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Residues in contact with TYR 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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235A ASN 4.1 8.4 + - - -
236A ASN* 3.3 23.1 + - + +
237A VAL* 3.6 24.2 - - + -
270A GLN* 1.3 75.5 - - - +
272A LEU* 1.3 72.6 + - - +
273A PHE* 3.5 43.5 - + + -
278A LYS* 3.2 23.8 - - - -
279A PRO* 3.2 19.4 + - + +
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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