Contacts of the strand formed by residues 274 - 279 (chain B) in PDB entry 2BHT
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 274 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLU* 3.7 14.8 - - - +
28B TRP* 4.3 13.0 - - + -
162B THR* 5.0 5.8 - - - -
165B ARG* 3.2 65.5 - - + +
166B ILE* 3.5 14.8 - - + +
167B THR* 2.6 35.7 + - - +
168B HIS 3.1 4.4 + - - -
272B ASP 4.6 4.5 - - - +
273B ALA* 1.3 77.7 - - - +
275B VAL* 1.3 62.4 + - - +
276B VAL* 4.9 3.1 - - + -
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Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER* 5.3 0.7 - - - -
26B GLU 3.1 7.4 + - - +
27B VAL* 4.3 12.3 - - + -
28B TRP* 2.7 31.7 + - - +
168B HIS* 3.3 19.3 - - + +
170B VAL* 3.9 24.2 - - + -
263B ALA* 3.9 19.5 - - + -
266B VAL* 3.9 20.6 - - + -
267B ALA* 4.4 15.0 - - + +
273B ALA* 4.1 16.8 - - + -
274B VAL* 1.3 75.9 - - - +
276B VAL* 1.3 64.9 + - - +
277B ALA 4.4 0.2 - - - -
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Residues in contact with VAL 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.9 15.7 - - + -
28B TRP* 2.8 28.9 - - + +
30B LYS* 4.3 9.6 - - + -
158B ILE* 4.4 13.7 - - + -
162B THR* 4.1 16.6 - - + -
166B ILE* 3.4 30.5 - - + -
168B HIS 3.0 7.3 + - - -
169B PHE* 3.7 8.5 - - + -
170B VAL 2.9 25.1 + - - +
274B VAL* 4.9 2.7 - - + -
275B VAL* 1.3 82.6 - - - +
277B ALA* 1.3 66.4 + - - +
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Residues in contact with ALA 277 (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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27B VAL* 5.4 0.4 - - - +
28B TRP 3.0 6.5 + - - -
29B LEU* 3.2 18.9 - - + +
30B LYS 2.9 23.3 + - - -
170B VAL* 3.4 17.0 - - + +
259B ALA* 4.0 32.5 - - + +
260B VAL* 4.6 0.7 - - + +
263B ALA* 4.2 11.1 - - + +
275B VAL* 5.1 0.2 - - - +
276B VAL* 1.3 75.5 - - - +
278B ILE* 1.3 62.9 + - - +
279B ILE* 3.6 0.8 + - + -
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Residues in contact with ILE 278 (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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30B LYS* 3.3 34.3 - - + -
32B GLU* 3.6 21.8 - - + -
40B VAL* 4.4 8.3 - - + -
154B THR* 4.3 11.0 - - + -
158B ILE* 4.3 8.3 - - + -
169B PHE* 3.8 32.1 - - + -
170B VAL 3.5 6.5 + - - +
171B SER* 5.3 6.3 - - - +
172B SER 5.6 1.5 + - - +
178B THR* 4.4 11.9 - - + -
256B SER* 4.4 0.3 + - - -
259B ALA* 3.7 18.8 - - - +
276B VAL* 5.5 0.2 - - + -
277B ALA* 1.3 71.5 - - - +
279B ILE* 1.3 62.7 + - - +
280B CYS* 3.5 28.4 + - - +
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Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 4.0 24.5 - - + -
30B LYS 3.0 12.8 + - - +
31B LEU* 4.1 19.7 - - + -
32B GLU* 2.8 27.5 + - - +
33B GLY* 3.3 2.4 + - - +
244B LEU* 4.6 1.8 - - + -
250B ILE* 4.8 6.5 - - + -
251B PHE 5.6 0.7 - - - +
252B CYS* 3.7 19.5 - - + -
256B SER* 3.5 31.9 - - - +
259B ALA* 5.0 0.7 - - + -
260B VAL* 3.9 19.1 - - + -
277B ALA 3.6 1.0 + - - +
278B ILE* 1.3 72.7 - - - +
280B CYS* 1.3 61.7 + - - +
281B ASP 3.1 23.1 + - - +
282B ARG* 5.6 1.1 - - + -
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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
------------------------------------------------------------
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