Contacts of the strand formed by residues 268 - 275 (chain D) in PDB entry 4NY0
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 ILE 268 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A LEU* 3.6 37.5 - - + -
268A ILE* 4.0 25.8 - - + -
270A VAL* 3.8 21.5 - - + -
282A TYR* 3.6 27.8 - - + -
293A LEU* 4.2 4.9 - - + -
261D ALA* 3.2 2.0 - - - -
262D LEU* 2.8 39.2 + - - +
266D TRP 3.3 15.5 + - - +
267D ILE* 1.3 77.1 - - - +
269D SER* 1.3 74.5 + - - +
270D VAL* 3.5 4.3 + - + +
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Residues in contact with SER 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A TYR* 3.2 29.6 + - - -
284A THR* 3.9 16.1 + - - -
291A THR* 4.9 1.7 + - - +
260D CYS 3.3 12.6 - - - -
261D ALA* 3.8 8.3 - - - +
267D ILE* 4.1 0.4 + - - -
268D ILE* 1.3 78.1 - - - +
270D VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ILE* 3.8 29.8 - - + -
258D PHE 3.8 0.2 - - - +
259D LYS* 3.7 3.9 - - - +
260D CYS* 2.8 37.9 + - - +
262D LEU* 3.8 30.7 - - + -
268D ILE* 4.1 7.4 - - + +
269D SER* 1.3 80.0 - - - +
271D GLU* 1.3 68.7 + - - +
272D LEU* 4.2 7.2 - - + +
282D TYR* 4.1 21.5 - - + -
283D LEU 5.0 3.6 - - - +
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Residues in contact with GLU 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ASP* 5.8 0.3 - - - +
257D CYS* 3.4 27.7 - - + +
258D PHE 3.4 18.2 - - - +
259D LYS* 3.8 29.7 - - + +
270D VAL* 1.3 78.2 - - - +
272D LEU* 1.3 61.9 + - - +
273D ALA 3.7 0.2 + - - -
282D TYR* 3.2 0.7 - - - -
283D LEU* 2.7 58.7 + - + +
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Residues in contact with LEU 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D GLU 3.7 0.5 - - - +
257D CYS* 3.1 7.3 - - - +
258D PHE* 2.9 38.5 + - + +
260D CYS* 3.9 15.3 - - - -
262D LEU* 4.3 12.8 - - + -
270D VAL* 4.0 3.6 - - + +
271D GLU* 1.3 72.6 - - - +
273D ALA* 1.3 59.2 + - - +
274D ILE* 4.1 12.6 - - + -
280D ILE* 4.0 24.0 - - + -
281D SER 3.1 18.8 - - - +
282D TYR* 4.2 9.6 - - + -
293D LEU* 4.2 10.3 - - + -
318D LEU* 6.4 0.9 - - + -
327D LEU* 6.1 0.2 - - + -
329D VAL* 4.5 13.5 - - + -
340D MET* 3.6 29.2 - - + -
344D ILE* 5.6 2.5 - - + -
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Residues in contact with ALA 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D LYS* 3.9 25.1 - - - -
256D GLU 3.5 4.5 - - - -
257D CYS* 4.1 2.2 - - - -
271D GLU 3.7 0.2 + - - -
272D LEU* 1.3 73.2 - - - +
274D ILE* 1.3 61.7 + - - +
278D GLU* 3.8 10.9 - - - +
279D GLY 3.2 3.8 - - - +
281D SER* 2.5 43.4 + - - +
283D LEU* 4.1 22.0 - - + -
290D PRO* 5.0 0.7 - - + -
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Residues in contact with ILE 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D LYS* 3.4 4.3 - - - +
256D GLU* 2.9 37.9 + - - +
258D PHE* 4.1 21.1 - - + -
272D LEU* 4.4 17.7 - - + -
273D ALA* 1.3 80.8 - - - +
275D GLY* 1.3 62.1 + - - +
278D GLU* 4.4 0.2 - - - -
279D GLY 3.4 4.3 - - - +
280D ILE* 4.6 9.2 - - + -
296D PHE* 3.8 25.1 - - + -
340D MET* 4.5 5.6 - - + +
343D LEU* 3.8 29.3 - - + +
344D ILE* 3.9 30.3 - - + -
347D TYR* 4.1 4.3 + - + -
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Residues in contact with GLY 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D ASP 4.0 2.7 - - - -
274D ILE* 1.3 80.4 - - - +
276D PRO* 1.3 71.6 - - - +
277D GLU 3.3 2.2 - - - -
278D GLU* 3.7 10.5 - - - +
279D GLY* 2.9 33.3 + - - -
296D PHE* 3.5 7.2 - - - -
347D TYR* 3.7 11.2 - - - -
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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