Contacts of the strand formed by residues 263 - 272 (chain A) in PDB entry 2PY5
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 LEU 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A GLN 4.0 2.5 - - - +
258A MET* 3.9 24.0 - - - +
261A ARG* 3.5 16.8 - - + +
262A LEU* 1.3 79.4 - - - +
264A PRO* 1.3 69.7 - - + +
265A TYR* 4.4 1.0 - - - -
283A LEU* 3.6 4.9 - - - -
355A ALA* 3.1 2.4 - - - -
356A THR* 2.9 37.2 + - - +
357A THR* 6.3 0.2 - - - -
359A LEU* 4.9 2.1 - - + +
360A PHE* 3.9 18.4 - - + -
429A MET* 3.7 24.9 - - + -
432A PHE* 3.9 22.4 - - + -
433A ILE* 4.1 10.8 - - + -
436A TRP* 3.7 20.4 - - + -
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Residues in contact with PRO 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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263A LEU* 1.3 89.4 - - + +
265A TYR* 1.3 65.0 + - - +
283A LEU* 3.8 10.1 - - + -
353A PHE* 3.8 28.0 - - + -
354A LYS 3.2 8.3 - - - +
359A LEU* 5.3 0.2 - - - -
426A TYR* 3.5 6.6 - - - -
428A PRO* 3.4 35.4 - - + +
429A MET* 3.4 23.3 - - - +
432A PHE* 3.7 25.8 - - + -
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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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210A VAL* 3.4 28.9 - - + +
211A PHE* 4.3 8.7 - - + -
264A PRO* 1.3 75.6 - - - +
266A GLY* 1.3 67.7 + - - +
267A GLU 5.0 0.2 - - - +
353A PHE* 4.4 2.8 - - - +
354A LYS* 3.0 61.1 + - + +
355A ALA* 3.6 37.1 + - - -
356A THR* 3.9 14.4 - - + -
359A LEU* 4.4 5.6 - - + -
426A TYR* 3.0 15.8 + - - -
9005A EDO 3.3 35.7 - - - -
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Residues in contact with GLY 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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209A LYS 4.9 2.2 - - - -
210A VAL* 2.7 22.1 + - - -
212A PRO* 3.5 13.1 - - - +
265A TYR* 1.3 80.4 - - - +
267A GLU* 1.3 64.8 + - - -
268A PRO* 3.5 3.6 - - - +
353A PHE* 4.7 0.2 - - - -
354A LYS* 4.2 8.3 - - - -
426A TYR* 2.6 30.7 + - - -
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Residues in contact with GLU 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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212A PRO* 3.6 21.9 - - + +
213A THR 4.4 5.2 - - - +
214A LEU* 3.9 13.0 - - - +
215A SER 5.6 0.3 + - - -
218A LEU* 4.1 14.7 - - - +
265A TYR 5.0 1.0 - - - +
266A GLY* 1.3 70.6 - - - -
268A PRO* 1.3 90.0 - - - +
269A ILE* 4.7 0.9 - - - +
281A TYR* 3.9 18.4 + - - -
354A LYS* 4.6 9.3 + - - +
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Residues in contact with PRO 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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214A LEU* 3.5 35.4 - - + -
218A LEU* 4.3 9.2 - - + +
266A GLY 3.5 5.8 - - - +
267A GLU* 1.3 105.3 - - - +
269A ILE* 1.3 63.9 + - - +
270A VAL* 4.3 2.1 + - + +
351A LEU* 4.3 20.0 - - + -
352A LYS 3.3 15.0 - - - +
353A PHE* 3.6 29.4 - - + -
426A TYR* 4.9 0.2 - - - +
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Residues in contact with ILE 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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267A GLU 4.7 0.9 - - - +
268A PRO* 1.3 78.8 - - - +
270A VAL* 1.3 74.5 + - - +
271A PHE* 3.9 1.5 + - + -
281A TYR* 3.3 30.3 - - + +
351A LEU* 3.4 2.6 - - - -
352A LYS* 2.8 55.5 + - + +
9011A EDO 3.3 33.9 - - - +
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Residues in contact with VAL 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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218A LEU* 3.9 32.3 - - + -
221A GLU* 5.4 4.0 - - - +
268A PRO 4.3 2.4 + - - +
269A ILE* 1.3 86.7 - - - +
271A PHE* 1.3 71.2 + - - +
272A GLU* 4.1 13.0 - - + +
349A SER* 5.7 1.6 - - - -
350A GLY 3.5 12.1 - - - +
351A LEU* 4.5 7.2 - - + +
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Residues in contact with PHE 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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269A ILE* 4.1 3.1 - - + -
270A VAL* 1.3 75.5 - - - +
272A GLU* 1.3 71.3 + - - +
273A GLY 3.5 18.2 - - - -
274A LYS 4.2 0.9 - - - -
275A TYR* 3.4 55.0 - + + -
276A VAL 5.8 0.2 - - - -
284A HIS* 4.1 2.5 - + + -
285A ILE 3.9 7.0 - - - -
286A GLN* 3.7 7.0 - - - -
349A SER* 3.4 5.5 - - - -
350A GLY* 2.9 51.3 + - - +
351A LEU 3.3 26.0 - - - -
352A LYS* 3.8 19.7 - - + -
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Residues in contact with GLU 272 (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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270A VAL* 4.1 11.6 - - - +
271A PHE* 1.3 91.3 - - - +
273A GLY* 1.3 65.1 + - - +
274A LYS 3.8 3.8 + - - +
348A ILE 4.0 4.4 - - - +
349A SER* 3.7 12.0 - - - -
220B LYS* 4.0 7.8 + - - -
224B TYR* 2.4 45.9 + - + +
325B ASP* 6.1 2.5 - - - +
327B TRP* 6.3 0.2 - - - +
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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