Contacts of the strand formed by residues 268 - 273 (chain B) in PDB entry 2AY6
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 GLY 268 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B PHE* 3.7 12.0 - - - -
83B MET* 5.4 0.2 - - - -
104B ALA* 3.7 0.5 - - - +
105B THR* 3.0 28.2 + - - +
107B GLY* 3.7 8.4 - - - -
254B ALA 3.1 17.0 - - - -
255B SER* 4.4 0.9 - - - -
256B CYS* 4.4 8.3 - - - -
267B THR* 1.3 77.8 + - - +
269B CYS* 1.3 65.2 + - - +
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Residues in contact with CYS 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B PHE* 3.7 13.5 - - + -
83B MET* 3.9 35.7 - - - -
87B ILE* 5.0 0.2 - - - -
102B THR* 4.2 6.3 - - + -
103B LEU 3.0 21.3 - - - +
105B THR* 3.5 5.6 + - - -
111B ALA* 3.6 6.3 - - - +
252B ILE 3.7 0.9 - - - +
254B ALA* 2.9 33.9 + - - +
268B GLY* 1.3 75.9 - - - +
270B LEU* 1.3 58.3 + - - +
271B LEU* 3.8 26.5 - - - -
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Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B THR* 3.5 2.6 - - - -
103B LEU* 2.8 33.1 + - + +
105B THR* 4.4 4.5 - - + +
111B ALA* 4.1 13.9 - - + +
114B GLN* 4.1 11.4 - - + +
115B ALA* 3.6 45.8 - - + +
118B LEU* 4.4 12.1 - - + -
220B LEU* 4.8 0.2 - - + -
251B LEU* 4.3 8.3 - - + -
252B ILE 3.4 27.4 - - - +
253B ALA* 4.3 2.0 - - - +
269B CYS* 1.3 75.2 - - - +
271B LEU* 1.3 67.0 + - - +
272B ALA* 5.5 0.2 - - + -
287B MET* 3.4 28.8 - - + +
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B GLY* 4.6 16.8 - - - +
87B ILE* 3.3 36.8 - - + -
88B LEU* 4.4 11.2 - - + -
100B THR* 4.5 6.3 - - + -
101B ALA 3.5 4.0 - - - +
102B THR* 3.9 22.9 - - + +
250B VAL 3.7 1.7 - - - +
251B LEU* 3.3 4.9 - - - -
252B ILE* 2.8 59.2 + - + +
269B CYS* 3.8 23.8 - - - +
270B LEU* 1.3 76.5 - - - +
272B ALA* 1.3 60.2 + - - +
273B LEU* 3.8 11.5 - - + +
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Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.4 13.0 - - + -
99B THR 3.6 1.4 - - - +
100B THR* 3.3 5.0 - - - -
101B ALA* 2.9 39.9 + - + +
118B LEU* 4.6 3.8 - - + -
250B VAL 3.7 3.6 - - - -
251B LEU* 4.1 16.6 - - + -
271B LEU* 1.3 70.8 - - - +
273B LEU* 1.3 63.9 + - - +
274B CYS* 3.6 2.2 + - - -
283B ALA* 4.4 5.2 - - + -
287B MET* 3.9 26.6 - - + +
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.7 1.0 - - - +
88B LEU* 4.0 21.5 - - + -
91B GLY 5.6 4.5 - - - +
96B LYS* 5.9 2.5 - - + +
99B THR* 3.9 4.7 - - - +
100B THR* 4.0 16.2 - - + +
244B ALA* 4.4 17.3 - - + +
248B PRO 4.1 4.3 - - - +
249B GLU* 3.3 12.3 - - - +
250B VAL* 2.8 59.3 + - + +
252B ILE* 4.1 20.2 - - + -
271B LEU* 3.8 17.7 - - + +
272B ALA* 1.3 75.5 - - - +
274B CYS* 1.3 61.4 + - - +
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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