Contacts of the strand formed by residues 177 - 182 (chain B) in PDB entry 2BTU
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 VAL 177 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B GLY 3.4 1.0 + - - -
176B HIS* 1.3 72.5 - - - +
178B LEU* 1.3 67.2 + - - +
179B ILE* 4.1 6.7 - - + -
306B ALA* 3.4 1.1 - - - -
307B VAL* 2.5 49.7 + - - +
309B GLU* 3.4 43.3 - - - +
312B ALA* 3.6 26.0 - - + -
328B ILE* 3.3 31.0 - - + -
331B ARG* 3.3 9.4 - - + -
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B HIS 3.4 0.8 + - - -
177B VAL* 1.3 75.5 - - - +
179B ILE* 1.3 63.6 + - - +
256B ILE* 4.8 3.4 - - + -
259B MET* 3.4 20.6 - - + -
260B LEU* 5.6 0.2 - - + -
266B ALA* 3.8 23.3 - - + -
268B ILE* 3.9 19.3 - - + -
304B VAL* 3.3 25.4 - - + -
305B VAL 3.9 0.4 - - - -
306B ALA* 4.1 14.6 - - + -
328B ILE* 3.7 1.6 - - - -
329B ILE* 3.2 30.2 + - + -
330B GLY 3.0 17.7 + - - +
331B ARG 3.7 26.5 - - - +
332B THR* 4.3 8.3 - - - +
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Residues in contact with ILE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B VAL* 3.9 8.7 + - + -
178B LEU* 1.3 77.1 - - - +
180B GLY* 1.3 67.6 + - - +
181B LEU* 4.4 7.9 - - + -
303B MET 3.8 0.2 - - - +
304B VAL* 3.0 8.9 - - - +
305B VAL* 2.8 47.4 + - + +
307B VAL* 4.8 10.5 - - + -
312B ALA* 4.6 3.6 - - + +
315B ILE* 4.8 7.2 - - + -
316B VAL* 3.3 31.0 - - + -
319B LEU* 4.2 24.0 - - + -
326B ALA* 4.5 6.3 - - + -
327B ARG 3.0 24.0 - - - +
328B ILE* 3.4 15.0 - - + -
329B ILE* 4.7 0.9 - - - -
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Residues in contact with GLY 180 (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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178B LEU 4.1 0.6 + - - -
179B ILE* 1.3 74.5 - - - +
181B LEU* 1.3 63.9 + - - -
273B TRP* 6.0 0.2 - - - +
301B ILE* 4.5 7.8 - - - +
303B MET 3.3 6.7 - - - -
304B VAL* 4.4 0.9 - - - -
325B THR 3.2 12.5 - - - +
327B ARG* 3.0 27.7 + - - +
329B ILE* 4.0 25.6 - - - +
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ILE* 4.4 4.3 - - + -
180B GLY* 1.3 74.4 - - - +
182B ALA* 1.3 54.2 + - - +
228B TYR* 4.0 13.4 + - + -
232B ILE* 5.6 4.5 - - + -
301B ILE* 3.7 3.0 - - - -
302B GLY* 2.9 30.8 + - - -
303B MET* 2.7 33.7 + - + +
305B VAL* 3.9 28.0 - - + -
319B LEU* 3.6 34.3 - - + -
324B GLU* 3.3 46.4 - - + +
325B THR 3.5 4.3 - - - +
326B ALA* 4.7 4.3 - - + -
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Residues in contact with ALA 182 (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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180B GLY 4.0 0.4 + - - -
181B LEU* 1.3 70.9 - - - +
183B SER* 1.3 64.0 + - - +
226B LYS* 4.4 7.6 - - - +
228B TYR* 3.4 15.1 + - - -
300B GLY 4.0 7.9 - - - -
301B ILE* 4.7 2.9 - - - +
324B GLU* 3.8 7.2 + - - +
325B THR* 3.1 32.9 + - - -
327B ARG* 5.9 1.6 - - - +
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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