Contacts of the strand formed by residues 266 - 272 (chain B) in PDB entry 2H07
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 PHE 266 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B LEU* 4.1 2.5 - - + -
229B ILE* 3.3 43.1 - - + -
230B CYS* 3.9 15.0 - - - -
233B ALA* 3.8 15.3 - - + -
244B VAL* 3.7 22.4 - - + -
245B TYR 4.3 0.2 - - - -
246B ALA* 3.5 27.4 - - + -
261B ILE* 4.6 7.2 - - + -
264B ALA* 3.0 36.0 + - + +
265B CYS* 1.3 78.6 - - - +
267B GLU* 1.3 64.5 + - - +
268B ALA 3.9 9.6 - - - +
269B VAL* 3.8 22.2 - - + -
286B LYS* 4.1 22.4 - - + +
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Residues in contact with GLU 267 (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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243B ARG* 3.6 29.3 - - + +
244B VAL 2.8 18.5 + - - +
245B TYR* 3.2 39.0 - - + +
265B CYS 3.9 1.0 + - - -
266B PHE* 1.3 75.1 - - - +
268B ALA* 1.3 64.2 + - + +
286B LYS* 5.2 5.2 - - - +
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Residues in contact with ALA 268 (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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154B TRP* 5.0 0.2 - - + -
245B TYR* 3.6 26.6 - - + -
246B ALA 3.3 21.0 + - - +
266B PHE* 3.2 4.6 - - - +
267B GLU* 1.3 85.5 - - + +
269B VAL* 1.3 66.1 - - - +
270B VAL* 4.1 6.5 - - + -
286B LYS* 3.6 12.6 - - - +
288B GLN* 3.8 24.5 - - - +
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Residues in contact with VAL 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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229B ILE* 5.1 2.5 - - + -
246B ALA* 3.3 10.5 - - + +
248B LEU* 4.3 13.5 - - + -
253B PHE* 4.0 27.6 - - + -
261B ILE* 3.8 32.1 - - + -
266B PHE* 3.8 26.5 - - + -
268B ALA* 1.3 79.0 - - - +
270B VAL* 1.3 63.5 + - - +
271B VAL* 4.7 0.7 - - + -
286B LYS* 2.9 11.3 + - + +
287B ILE* 3.4 13.2 - - + +
288B GLN 3.1 24.1 + - - +
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Residues in contact with VAL 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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154B TRP* 3.5 47.1 - - + +
245B TYR* 5.2 1.1 - - + -
246B ALA 2.7 10.3 + - - +
247B ILE* 3.3 21.2 - - + +
248B LEU* 2.8 27.4 + - - +
268B ALA* 4.7 4.7 - - + -
269B VAL* 1.3 80.4 - - - +
271B VAL* 1.3 69.4 + - - +
288B GLN* 3.5 15.0 - - + +
290B ILE* 3.6 35.9 - - + -
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Residues in contact with VAL 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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248B LEU* 3.0 25.4 - - + +
251B GLY* 3.9 16.4 - - - +
253B PHE* 3.6 28.7 - - + -
269B VAL* 4.7 1.6 - - + -
270B VAL* 1.3 81.9 - - - +
272B THR* 1.3 72.0 + - - +
277B GLN* 3.8 30.1 - - + -
287B ILE* 4.3 4.9 - - + -
288B GLN 3.2 10.1 + - - +
289B VAL* 3.3 7.9 - - + -
290B ILE* 2.8 26.8 + - - +
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Residues in contact with THR 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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127B MET* 4.8 0.7 - - - -
147B ALA* 4.0 15.9 - - + -
150B ALA* 6.1 0.4 - - + -
151B VAL* 5.8 2.9 - - + -
248B LEU 4.7 0.7 - - - +
249B THR* 2.6 38.2 + - - +
251B GLY 4.9 0.7 + - - -
271B VAL* 1.3 89.6 - - - +
273B ASN* 1.3 60.5 + - - +
274B THR* 3.0 24.1 + - - +
275B ILE 4.5 0.7 + - - -
277B GLN* 3.9 8.1 - - - +
289B VAL* 4.0 2.8 - - - +
290B ILE* 3.1 22.0 - - + +
292B ILE* 3.8 27.1 - - + -
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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