Contacts of the strand formed by residues 263 - 271 (chain C) in PDB entry 2P82
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 ASN 263 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259C GLY* 3.3 15.9 - - - -
260C LYS* 2.8 25.6 + - + +
261C PRO 3.0 22.0 + - - -
262C ASN* 1.3 86.2 + - - +
264C ALA* 1.3 61.1 + - - +
265C TYR* 3.5 26.6 + - + -
281C HIS* 3.8 9.4 + - - -
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Residues in contact with ALA 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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77C CYS* 3.4 11.5 - - - +
78C MET* 3.7 48.0 - - + +
81C CYS* 3.5 4.5 - - - -
145C TRP* 4.1 4.0 - - + +
258C GLY 3.2 12.3 - - - +
259C GLY* 4.2 1.3 - - - -
260C LYS 3.7 0.8 + - - -
263C ASN* 1.3 76.2 - - - +
265C TYR* 1.3 62.3 + - - +
280C PRO* 3.5 7.6 - - - +
281C HIS* 3.0 21.5 - - - -
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Residues in contact with TYR 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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81C CYS* 3.3 11.0 - - - -
256C ALA 4.0 0.7 - - - +
257C LEU* 4.0 1.9 - - - -
258C GLY 2.9 28.2 + - - +
259C GLY* 5.1 1.1 - - - -
263C ASN* 3.5 36.3 + - + -
264C ALA* 1.3 77.4 - - - +
266C TYR* 1.3 61.2 + - - +
267C PHE* 3.7 19.4 - + + -
277C PHE* 3.4 38.6 - + + -
278C LEU 3.9 0.9 - - - -
279C ASP* 3.3 38.0 + - - -
281C HIS* 3.5 15.9 + + - -
309C MET* 3.7 31.9 - - + -
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Residues in contact with TYR 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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32C LEU* 3.9 5.0 - - + +
52C ARG* 5.4 2.5 - - + -
53C LEU 5.5 0.7 - - - -
81C CYS* 3.5 9.7 - - + -
84C MET* 3.5 48.9 - - + -
85C MET* 3.7 24.0 - - + -
88C GLN* 3.5 25.8 - - + +
254C LEU* 2.7 32.1 + - - -
256C ALA 3.6 10.8 - - - -
257C LEU* 4.2 10.1 - - + -
265C TYR* 1.3 72.1 - - - +
267C PHE* 1.3 65.9 + - - +
268C ILE* 3.4 26.9 + - + +
277C PHE* 3.2 2.5 - - - -
278C LEU* 2.8 48.5 + - + +
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Residues in contact with PHE 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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244C PHE* 5.7 0.2 - + - -
248C PHE* 3.8 18.6 - - + -
255C GLY* 3.1 5.4 - - - -
256C ALA* 2.9 47.7 + - + +
257C LEU 4.5 0.4 - - - -
258C GLY* 3.9 18.2 - - - -
259C GLY* 4.7 0.7 - - - -
265C TYR* 3.7 27.6 - + + -
266C TYR* 1.3 73.0 - - - +
268C ILE* 1.3 61.3 + - - +
269C GLY 3.7 0.7 - - - -
275C LEU* 3.8 31.2 - - + -
276C ILE 3.5 4.9 - - - +
277C PHE* 3.6 22.7 - + + -
309C MET* 3.8 29.4 - - + -
314C LEU* 3.3 32.5 - - + -
318C VAL* 6.1 0.4 - - + -
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Residues in contact with ILE 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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31C ILE* 3.3 12.7 - - + -
32C LEU* 2.7 49.2 + - + +
49C ILE* 4.1 29.6 - - + -
52C ARG* 4.8 6.1 - - + -
248C PHE* 3.7 6.9 - - - -
266C TYR* 3.4 43.7 - - + +
267C PHE* 1.3 75.9 - - - +
269C GLY* 1.3 58.1 + - - +
276C ILE* 2.9 37.1 + - + +
277C PHE* 4.4 2.9 - - - +
278C LEU* 4.2 18.4 - - + -
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Residues in contact with GLY 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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30C TRP 3.1 13.9 - - - -
31C ILE* 4.3 2.7 - - - -
248C PHE* 3.4 20.9 - - - -
268C ILE* 1.3 81.5 - - - +
270C PHE* 1.3 61.5 + - - +
275C LEU* 3.3 10.0 - - - +
276C ILE* 2.8 31.1 + - - +
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Residues in contact with PHE 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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28C LEU 4.6 2.1 - - - +
29C VAL* 3.8 2.6 - - - +
30C TRP* 3.1 64.3 + + + +
245C LYS* 3.4 55.2 - - + -
248C PHE* 4.0 12.3 - + + -
249C LYS* 3.8 17.9 - - + -
269C GLY* 1.3 74.2 - - - +
271C LEU* 1.3 65.0 + - - +
272C GLY* 3.6 20.6 - - - +
274C GLU 3.1 14.8 - - - +
275C LEU* 4.0 14.6 - - + +
276C ILE* 4.2 8.3 - - - +
311C ILE* 5.5 0.2 - - + -
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Residues in contact with LEU 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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27C GLU* 3.5 34.5 - - + +
28C LEU 3.6 14.4 - - - +
29C VAL* 3.8 14.6 - - + -
38C LEU* 3.8 31.2 - - + -
270C PHE* 1.3 76.7 - - - +
272C GLY* 1.3 70.0 - - - +
273C ASP 3.3 0.3 + - - -
274C GLU* 2.9 28.5 + - + +
276C ILE* 4.4 10.7 - - + +
308C ARG* 5.1 14.1 - - - -
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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