Contacts of the strand formed by residues 269 - 275 (chain c) in PDB entry 3J7Y
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 269 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K TRP* 3.9 10.3 - - + +
12K ALA* 3.7 29.2 - - - +
15K ALA* 3.4 30.7 - - + +
132b PRO* 4.5 4.9 - - + -
133b PHE* 3.6 29.2 - - + -
259c ARG 3.6 1.0 - - - +
260c GLN* 3.4 15.7 + - - -
261c SER* 2.8 24.9 + - - +
267c LEU 5.3 0.2 - - - +
268c PRO* 1.3 72.7 - - - +
270c TYR* 1.3 65.6 + - - +
271c PHE* 3.3 23.6 + - + +
285c PRO* 4.1 13.2 - - + -
286c GLY 3.7 3.8 - - - +
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Residues in contact with TYR 270 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257c LEU* 4.5 3.4 - - + -
259c ARG 3.6 2.9 - - - -
260c GLN* 3.4 37.7 - - + -
263c GLY* 3.3 24.7 - - - -
268c PRO* 3.5 17.6 - - + +
269c LEU* 1.3 70.4 - - - +
271c PHE* 1.3 59.5 + - - +
272c VAL* 3.9 5.2 - - + -
285c PRO* 3.3 2.6 - - - +
286c GLY 2.8 40.2 + - - +
287c GLU 3.2 28.7 - - - -
288c THR* 3.5 21.8 - - + +
289c VAL* 3.6 25.1 - - + -
292c ALA* 3.5 15.3 - - + +
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Residues in contact with PHE 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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4K PHE* 3.8 25.6 - + - -
12K ALA* 4.0 14.1 - - + -
131b HIS* 4.0 32.3 - + + -
133b PHE* 4.1 20.0 - + + -
257c LEU* 3.5 1.1 - - - +
258c THR* 2.5 45.8 + - - +
259c ARG* 2.6 32.6 + - + +
269c LEU* 3.3 16.1 + - + +
270c TYR* 1.3 70.9 - - - +
272c VAL* 1.3 53.4 + - - +
283c GLU* 3.1 33.7 - - - -
284c GLY 3.3 13.0 - - - -
285c PRO* 3.6 20.9 - - + -
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Residues in contact with VAL 272 (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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255c SER 4.9 2.0 - - - +
256c ARG 3.4 13.9 - - - +
257c LEU* 3.5 27.1 - - + -
258c THR 4.1 0.7 - - - +
270c TYR* 4.4 1.8 - - + -
271c PHE* 1.3 72.8 - - - +
273c GLY* 1.3 67.7 + - - +
283c GLU* 3.4 3.6 - - - -
284c GLY 2.8 39.8 + - - +
289c VAL* 4.3 15.5 - - + +
292c ALA* 3.4 28.5 - - + -
293c GLU* 3.6 32.8 - - + +
296c ALA* 3.5 4.9 - - - +
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Residues in contact with GLY 273 (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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255c SER* 3.9 3.6 - - - -
256c ARG 2.8 21.3 + - - +
258c THR* 3.8 15.0 - - - +
272c VAL* 1.3 83.0 - - - +
274c LEU* 1.3 72.4 + - - +
275c TYR* 4.3 8.7 - - - -
282c ALA 3.5 9.4 - - - -
283c GLU* 3.9 8.5 - - - -
296c ALA* 4.4 0.4 - - - -
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Residues in contact with LEU 274 (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 MET* 4.4 15.5 - - + -
241c LEU* 3.5 16.2 - - + -
253c PRO* 4.6 11.2 - - + -
254c GLU 3.5 13.2 - - - +
255c SER* 3.8 16.2 - - - -
272c VAL* 5.9 0.2 - - + -
273c GLY* 1.3 82.4 - - - +
275c TYR* 1.3 57.8 + - - +
276c CYS* 5.1 0.2 - - - -
280c LEU* 3.3 1.1 - - - -
281c ILE* 2.8 46.0 + - + +
282c ALA 2.8 13.9 + - - +
293c GLU* 4.6 3.8 - - + +
296c ALA* 3.6 12.3 - - + +
297c ALA* 3.4 39.0 - - + +
300c ALA* 4.3 5.2 - - + -
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Residues in contact with TYR 275 (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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253c PRO* 3.3 3.8 - - - +
254c GLU* 2.8 57.1 + - + +
256c ARG* 3.9 34.1 - - + -
258c THR* 4.1 17.1 - - + +
273c GLY* 4.3 13.0 - - - -
274c LEU* 1.3 79.7 - - - +
276c CYS* 1.3 61.0 + - - +
277c ASP 4.1 0.8 + - - -
278c LYS* 4.2 9.9 - - - -
279c LYS* 3.5 15.5 - - - +
280c LEU* 3.6 42.8 - - + +
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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