Contacts of the strand formed by residues 261 - 271 (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 LYS 261 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246C THR 3.2 7.2 - - - +
247C GLN* 3.5 31.2 - - + +
259C ALA* 4.0 4.0 - - - +
260C ASN* 1.3 82.7 + - + +
262C THR* 1.3 70.5 + - - +
263C GLU* 6.4 0.7 - - + -
288C GLY* 3.5 1.0 - - - -
289C LYS* 2.9 45.8 + - + +
290C ASN* 4.2 17.6 + - - +
411C LDA 3.5 45.7 + - - +
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Residues in contact with THR 262 (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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118C THR 5.1 0.3 + - - -
245C GLN* 3.3 9.2 - - - +
246C THR* 3.0 52.0 + - + +
250C SER* 4.2 10.6 + - - -
259C ALA* 3.7 21.5 - - + -
261C LYS* 1.3 82.2 - - - +
263C GLU* 1.3 63.0 + - - +
264C ASN* 2.9 19.3 + - - +
286C SER* 4.1 7.6 - - - +
287C LYS 3.1 8.1 - - - +
289C LYS* 5.6 0.7 - - - -
300C LEU* 3.8 20.2 - - + -
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Residues in contact with GLU 263 (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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243C TYR* 3.6 24.2 - - + +
244C GLY 3.6 4.0 - - - -
245C GLN* 3.8 10.4 - - + +
261C LYS* 6.4 0.7 - - + -
262C THR* 1.3 75.2 - - - +
264C ASN* 1.3 60.7 + - - +
265C VAL* 5.5 1.7 - - + +
285C GLN* 3.9 1.2 - - - +
286C SER* 3.4 1.9 - - - -
287C LYS* 2.8 53.2 + - + +
289C LYS* 3.5 37.7 + - + +
411C LDA 4.7 11.5 - - - -
413C LDA 4.2 10.7 + - - -
414C LDA 4.2 13.4 + - - -
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Residues in contact with ASN 264 (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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118C THR* 3.0 32.9 + - - +
119C MET* 3.2 27.4 - - + +
242C MET* 4.6 2.7 - - + -
243C TYR* 3.1 10.9 - - - -
244C GLY 2.8 41.3 + - - +
262C THR* 2.9 21.9 + - - +
263C GLU* 1.3 74.9 + - - +
265C VAL* 1.3 62.8 + - - +
285C GLN 3.3 2.7 - - - -
286C SER* 2.7 40.8 + - - +
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Residues in contact with VAL 265 (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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242C MET 3.4 8.3 - - - +
243C TYR* 3.9 17.9 - - + -
263C GLU* 5.5 1.1 - - + -
264C ASN* 1.3 79.5 - - - +
266C GLU* 1.3 69.7 + - - +
267C LEU* 4.1 28.5 - - + -
283C TYR* 4.0 7.8 - - + +
284C ASN* 3.6 1.0 - - - -
285C GLN* 2.9 48.4 + - + +
414C LDA 4.5 23.1 - - + -
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Residues in contact with GLU 266 (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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105C ASN* 3.0 16.4 + - - +
108C THR* 2.5 43.3 + - + +
116C ALA* 3.5 15.1 + - - -
118C THR* 2.6 33.5 + - - +
241C ALA* 3.3 3.5 - - - -
242C MET* 2.8 48.7 + - + +
265C VAL* 1.3 81.3 - - - +
267C LEU* 1.3 64.7 + - - +
283C TYR 3.4 4.5 - - - +
284C ASN* 3.1 30.6 + - - +
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Residues in contact with LEU 267 (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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108C THR* 5.1 0.4 - - - -
111C PHE* 3.7 3.9 - - - -
240C ALA 3.4 4.9 - - - +
241C ALA* 3.6 22.4 - - + -
242C MET 4.8 0.7 - - - +
265C VAL* 4.1 18.4 - - + -
266C GLU* 1.3 83.1 - - - +
268C VAL* 1.3 64.4 + - - +
282C GLY* 3.3 1.1 - - - -
283C TYR* 2.8 63.6 + - + +
414C LDA 4.7 18.4 - - + -
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Residues in contact with VAL 268 (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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108C THR* 4.2 9.9 - - - -
110C VAL* 3.7 27.6 - - + -
111C PHE* 3.8 20.6 - - + -
238C TYR* 4.1 4.7 - - + -
239C LEU* 3.2 4.2 - - - +
240C ALA* 2.8 61.4 + - + +
267C LEU* 1.3 77.4 - - - +
269C ALA* 1.3 66.3 + - - +
270C GLN* 4.1 3.1 - - - +
280C SER* 3.8 19.5 - - - +
281C ILE 3.4 13.9 - - - +
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Residues in contact with ALA 269 (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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238C TYR 3.4 5.8 - - - -
239C LEU* 3.8 17.3 - - + -
268C VAL* 1.3 75.7 - - - +
270C GLN* 1.3 61.3 + - - +
280C SER* 3.4 1.4 + - - -
281C ILE* 2.8 50.1 + - + +
415C LDA 4.2 16.7 - - + +
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Residues in contact with GLN 270 (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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110C VAL* 3.4 41.3 + - - +
237C VAL* 3.7 5.0 - - - +
238C TYR* 2.8 66.2 + - + +
239C LEU* 4.7 0.6 - - - +
268C VAL* 4.1 2.0 - - + +
269C ALA* 1.3 77.5 - - - +
271C TYR* 1.3 58.7 + - - +
278C LYS* 3.4 36.4 - - + +
279C PRO 3.1 19.3 - - - +
280C SER* 2.8 27.3 + - - -
309C TYR* 4.2 1.8 - - - -
415C LDA 4.1 6.8 - - - +
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Residues in contact with TYR 271 (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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235C ASN 4.1 3.1 + - - -
236C ASN* 3.3 30.4 + - + +
237C VAL* 3.6 23.1 - - + -
270C GLN* 1.3 75.3 - - - +
272C LEU* 1.3 76.0 + - - +
273C PHE* 3.8 29.8 - + + -
278C LYS* 3.2 23.9 - - - -
279C PRO* 3.2 18.0 + - + +
415C LDA 3.6 46.6 + - + +
427C LDA 3.4 54.8 + - + +
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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