Contacts of the strand formed by residues 237 - 247 (chain C) 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 VAL 237 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232C PHE* 3.5 22.9 - - + +
233C ASP* 3.5 4.9 - - - +
234C ALA 2.8 29.3 + - - +
235C ASN 3.5 13.7 - - - +
236C ASN* 1.3 81.4 - - - +
238C TYR* 1.3 63.2 + - - +
239C LEU* 3.8 24.0 - - + -
270C GLN 3.7 5.4 - - - +
271C TYR* 3.6 19.3 - - + -
415C LDA 4.0 34.1 - - + -
416C LDA 4.5 10.8 - - + +
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Residues in contact with TYR 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C TRP* 2.6 42.2 + - - +
110C VAL* 3.9 23.2 - - + +
231C LYS* 3.6 22.6 + - + +
232C PHE 3.2 4.7 - - - -
233C ASP* 3.4 38.6 - - + +
236C ASN 4.2 0.2 + - - -
237C VAL* 1.3 75.3 - - - +
239C LEU* 1.3 65.0 + - - +
240C ALA* 3.7 14.1 - - + -
268C VAL* 4.1 3.1 - - + -
269C ALA* 3.4 3.3 - - - -
270C GLN* 2.8 70.3 + - + +
278C LYS* 6.2 1.1 - - + -
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Residues in contact with LEU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C LYS* 3.1 5.8 - - - +
232C PHE* 2.8 46.5 + - + +
237C VAL* 3.8 20.0 - - + -
238C TYR* 1.3 88.1 - - - +
240C ALA* 1.3 65.0 + - - +
268C VAL 3.2 5.4 - - - +
269C ALA* 3.8 20.9 - - + -
270C GLN 4.7 1.3 - - - +
414C LDA 6.0 8.1 - - + -
415C LDA 4.7 11.4 - - + -
416C LDA 3.7 29.4 - - + -
418C LDA 4.8 8.5 - - + -
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Residues in contact with ALA 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C TRP* 3.4 31.4 - - + +
108C THR* 4.1 3.5 - - + +
230C GLY 3.3 11.4 - - - +
231C LYS* 3.9 6.5 - - + +
238C TYR* 3.7 9.0 - - + -
239C LEU* 1.3 77.5 - - - +
241C ALA* 1.3 62.7 + - - +
266C GLU 4.0 0.2 - - - +
267C LEU* 3.4 3.8 - - - +
268C VAL* 2.8 39.6 + - + +
414C LDA 6.4 0.4 - - - -
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Residues in contact with ALA 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C TRP* 5.3 1.7 - - - +
108C THR* 4.0 3.4 - - - +
229C GLY* 3.1 3.6 - - - -
230C GLY 3.0 31.6 + - - +
240C ALA* 1.3 76.1 - - - +
242C MET* 1.3 61.8 + - - +
266C GLU 3.3 5.2 - - - -
267C LEU* 3.6 21.5 - - + -
413C LDA 4.4 12.8 - - + -
414C LDA 3.8 28.9 - - + -
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Residues in contact with MET 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C THR* 4.6 10.5 - - + +
105C ASN* 3.6 36.6 - - - +
108C THR* 3.8 14.3 - - + +
118C THR* 4.0 12.6 - - - +
119C MET* 3.9 29.2 - - + -
227C ASN* 3.7 21.5 - - + +
228C VAL 3.3 13.5 - - - +
229C GLY* 4.1 1.6 - - - -
241C ALA* 1.3 76.8 - - - +
243C TYR* 1.3 62.7 + - - +
244C GLY 4.3 8.7 - - - +
264C ASN* 4.0 4.7 - - + +
265C VAL* 3.4 6.5 - - - +
266C GLU* 2.8 46.1 + - + +
267C LEU* 5.8 0.2 - - - -
413C LDA 5.6 0.9 - - - -
414C LDA 6.2 0.7 - - - -
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Residues in contact with TYR 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C TRP* 3.7 21.0 - + - -
227C ASN* 3.1 4.7 - - - +
228C VAL* 2.8 38.0 + - + +
242C MET* 1.3 77.4 - - - +
244C GLY* 1.3 60.0 + - - +
245C GLN* 2.7 34.6 + - + +
263C GLU* 3.6 11.9 - - + +
264C ASN 3.1 26.2 - - - -
265C VAL* 3.9 13.9 - - + -
413C LDA 3.6 63.9 - - + +
414C LDA 3.6 39.3 + - + -
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Residues in contact with GLY 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C MET* 3.4 17.7 - - - -
226C TRP* 3.2 13.9 - - - -
227C ASN* 3.8 2.7 - - - -
242C MET* 4.3 1.6 - - - +
243C TYR* 1.3 80.9 - - - +
245C GLN* 1.3 66.0 + - - +
263C GLU* 3.6 0.2 - - - -
264C ASN* 2.8 42.6 + - - +
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Residues in contact with GLN 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C MET* 3.6 3.1 - - - +
224C GLN* 4.6 0.4 - - - -
225C ALA* 3.4 2.8 - - - -
226C TRP* 2.9 73.5 + - + +
243C TYR* 2.7 26.9 + - + +
244C GLY* 1.3 79.3 - - - +
246C THR* 1.3 65.7 + - - +
262C THR 3.3 12.3 - - - +
263C GLU* 3.8 8.9 - - + +
411C LDA 3.7 33.5 + - - +
413C LDA 3.3 22.8 + - - -
429C LDA 5.1 2.4 - - - -
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Residues in contact with THR 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C MET* 4.1 12.1 - - - +
127C THR* 5.2 0.9 - - - +
224C GLN* 3.3 5.6 - - - -
225C ALA* 4.1 12.3 - - - +
245C GLN* 1.3 78.4 + - - +
247C GLN* 1.3 64.5 + - - +
248C ASN 4.4 0.7 - - - +
249C THR* 3.7 22.0 - - - +
250C SER* 3.6 29.8 + - - +
259C ALA 4.6 2.9 - - - +
261C LYS* 3.2 8.5 - - - +
262C THR* 3.0 53.6 + - + +
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Residues in contact with GLN 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C ARG 4.7 3.4 - - - +
223C ALA* 3.3 0.2 - - - -
224C GLN* 2.7 56.9 + - + +
246C THR* 1.3 76.7 - - - +
248C ASN* 1.3 80.0 + - - +
249C THR* 2.9 13.2 + - - -
260C ASN 3.3 11.9 - - - +
261C LYS* 3.5 31.0 - - + +
411C LDA 4.4 3.2 + - - -
429C LDA 3.7 21.3 + - - -
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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