Contacts of the strand formed by residues 263 - 271 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A GLY* 3.4 15.8 - - - -
260A LYS* 2.8 29.3 + - + +
261A PRO 3.0 20.6 + - - -
262A ASN* 1.3 84.5 - - - +
264A ALA* 1.3 63.5 + - - +
265A TYR* 3.5 26.8 + - + +
281A HIS* 3.6 11.9 + - - -
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Residues in contact with ALA 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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77A CYS* 3.4 11.9 - - - +
78A MET* 3.6 49.1 - - + +
81A CYS* 3.4 5.0 - - - -
145A TRP* 4.1 3.4 - - + +
258A GLY 3.1 12.8 - - - +
259A GLY* 4.3 1.1 - - - -
260A LYS 3.7 1.1 + - - -
263A ASN* 1.3 75.2 - - - +
265A TYR* 1.3 60.3 + - - +
280A PRO* 3.4 10.2 - - - +
281A HIS* 3.1 18.6 - - - -
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Residues in contact with TYR 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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81A CYS* 3.3 10.4 - - - -
257A LEU* 3.9 1.9 - - - -
258A GLY 2.8 29.9 + - - +
259A GLY* 4.9 3.4 - - - -
263A ASN* 3.5 36.1 + - + +
264A ALA* 1.3 78.2 - - - +
266A TYR* 1.3 61.2 + - - +
267A PHE* 3.8 27.4 + + + -
277A PHE* 3.5 39.5 - + + -
278A LEU 3.9 1.1 - - - -
279A ASP* 3.4 34.9 + - - -
281A HIS* 3.7 10.6 + + - -
309A MET* 4.5 15.0 - - - -
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Residues in contact with TYR 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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32A LEU* 4.0 5.0 - - + +
52A ARG* 5.7 3.1 - - + -
53A LEU 5.5 0.9 - - - -
81A CYS* 3.5 9.9 - - + -
84A MET* 3.5 48.5 - - + -
85A MET* 3.8 22.9 - - + -
88A GLN* 3.7 23.8 - - + +
254A LEU* 2.6 33.6 + - - -
256A ALA 3.5 11.4 - - - -
257A LEU* 4.2 10.1 - - + -
265A TYR* 1.3 72.3 - - - +
267A PHE* 1.3 63.3 + - - +
268A ILE* 3.4 26.5 + - + +
277A PHE* 3.2 3.1 - - - -
278A LEU* 2.8 50.0 + - + +
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Residues in contact with PHE 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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244A PHE* 5.3 0.9 - + + -
248A PHE* 3.8 20.2 - - + -
255A GLY* 3.2 5.4 - - - -
256A ALA* 2.9 47.5 + - + +
257A LEU 4.5 0.4 - - - -
258A GLY* 3.8 23.6 - - - -
259A GLY 4.8 0.2 - - - -
265A TYR* 3.8 23.1 - + + -
266A TYR* 1.3 73.0 - - - +
268A ILE* 1.3 61.1 + - - +
269A GLY 3.7 0.7 - - - -
275A LEU* 3.8 27.1 - - + -
276A ILE 3.5 4.7 - - - +
277A PHE* 3.8 18.8 - - + -
309A MET* 3.8 23.1 - - + -
314A LEU* 2.9 42.2 - - + -
318A VAL* 5.8 0.4 - - + -
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Residues in contact with ILE 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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31A ILE* 3.3 11.5 - - + -
32A LEU* 2.8 50.3 + - + +
49A ILE* 4.0 37.2 - - + -
52A ARG* 4.7 6.3 - - + -
248A PHE* 3.7 6.6 - - - -
266A TYR* 3.4 41.5 - - + +
267A PHE* 1.3 74.8 - - - +
269A GLY* 1.3 58.8 + - - +
276A ILE* 2.9 29.9 + - + +
277A PHE* 4.2 4.3 - - - -
278A LEU* 4.2 17.9 - - + -
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Residues in contact with GLY 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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30A TRP 3.0 14.4 - - - -
31A ILE* 4.2 3.1 - - - -
248A PHE* 3.6 18.7 - - - -
267A PHE* 5.2 0.2 - - - +
268A ILE* 1.3 81.6 - - - +
270A PHE* 1.3 65.3 + - - +
275A LEU* 3.4 9.9 - - - +
276A ILE* 2.8 27.4 + - - +
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Residues in contact with PHE 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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28A LEU 5.4 2.7 - - - -
29A VAL* 3.7 2.8 - - - +
30A TRP* 3.0 60.6 + + + +
245A LYS* 3.4 54.3 - - + -
248A PHE* 4.1 10.3 - + + -
249A LYS* 3.6 25.4 - - + -
269A GLY* 1.3 74.4 - - - +
271A LEU* 1.3 67.1 + - - +
272A GLY 3.6 21.5 - - - +
274A GLU 3.2 14.1 - - - +
275A LEU* 4.1 14.1 - - + +
276A ILE* 4.2 6.8 - - - +
311A ILE* 5.2 0.9 - - + -
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Residues in contact with LEU 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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27A GLU* 3.2 44.0 - - + +
28A LEU 3.8 11.2 - - - +
29A VAL* 3.9 22.2 - - + -
38A LEU* 3.6 20.0 - - + -
45A LEU* 5.8 0.2 - - + -
270A PHE* 1.3 77.1 - - - +
272A GLY* 1.3 64.3 + - - +
273A ASP 3.2 0.3 + - - -
274A GLU* 2.8 37.8 + - + +
276A ILE* 4.4 8.5 - - + -
308A ARG* 3.6 37.7 - - - +
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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