Contacts of the strand formed by residues 274 - 279 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLU* 3.7 19.1 - - + +
28D TRP* 4.2 17.7 - - + +
162D THR* 5.0 5.6 - - - -
165D ARG* 3.3 58.1 - - + +
166D ILE* 3.5 11.0 - - - +
167D THR* 3.2 26.5 + - - +
272D ASP 3.5 7.5 + - - +
273D ALA* 1.3 70.1 - - - +
275D VAL* 1.3 62.4 + - - +
276D VAL* 4.0 1.5 - - + +
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Residues in contact with VAL 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLU 2.5 22.8 + - - +
27D VAL* 3.6 13.8 - - + -
28D TRP* 3.1 26.1 + - - -
168D HIS* 3.6 13.7 - - + +
170D VAL* 3.9 15.9 - - + -
263D ALA* 3.8 32.3 - - + +
266D VAL* 4.0 16.4 - - + -
267D ALA* 4.5 5.4 - - + -
273D ALA* 3.7 23.3 - - + +
274D VAL* 1.3 76.2 - - - +
276D VAL* 1.3 66.9 - - - +
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Residues in contact with VAL 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU* 4.9 9.4 - - + -
28D TRP* 4.0 10.1 - - + +
30D LYS* 5.1 0.4 - - + -
158D ILE* 3.9 22.7 - - + -
162D THR* 4.1 17.5 - - + -
166D ILE* 3.4 31.0 - - + -
168D HIS 2.8 14.1 + - - +
169D PHE* 3.4 18.3 - - + -
170D VAL 2.9 27.3 + - - +
274D VAL* 4.0 3.6 - - + +
275D VAL* 1.3 82.2 - - - +
277D ALA* 1.3 68.7 - - - +
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Residues in contact with ALA 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D VAL* 4.8 1.1 - - + +
28D TRP 3.1 16.2 + - - +
29D LEU* 3.9 15.0 - - + -
30D LYS* 2.9 29.1 + - - +
170D VAL* 3.7 7.2 - - - +
259D ALA* 4.0 22.2 - - + +
260D VAL* 5.1 1.8 - - + -
263D ALA* 4.1 12.8 - - + -
275D VAL* 4.2 1.4 - - - +
276D VAL* 1.3 75.5 - - - +
278D ILE* 1.3 66.5 + - - +
279D ILE* 4.9 2.0 - - + -
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Residues in contact with ILE 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D LYS* 3.7 24.2 - - + -
32D GLU* 3.9 15.9 - - + +
40D VAL* 5.1 5.2 - - + -
154D THR* 4.4 9.6 - - + -
158D ILE* 3.8 9.2 - - + -
169D PHE* 3.3 41.3 - - + -
170D VAL 3.3 10.4 + - - +
171D SER* 4.5 8.1 - - - -
172D SER 5.9 0.4 - - - +
178D THR* 4.2 13.7 - - + -
256D SER* 4.6 1.2 - - - -
259D ALA* 3.9 19.9 - - + +
277D ALA* 1.3 74.5 - - - +
279D ILE* 1.3 80.4 + - - +
280D CYS* 4.1 16.1 + - - -
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Residues in contact with ILE 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D LEU* 3.7 39.0 - - + -
30D LYS 2.5 20.7 + - - +
31D LEU* 3.6 27.4 - - + -
32D GLU* 2.9 33.1 + - - +
33D GLY 6.1 0.2 - - - +
244D LEU* 5.4 0.2 - - + -
250D ILE* 5.3 1.3 - - + -
252D CYS* 3.5 23.1 - - + -
256D SER* 3.3 24.5 - - - +
260D VAL* 4.1 16.8 - - + -
277D ALA* 4.9 1.3 - - + -
278D ILE* 1.3 82.6 - - - +
280D CYS* 1.3 59.3 + - - +
281D ASP 3.5 4.2 + - - +
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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