Contacts of the strand formed by residues 267 - 276 (chain B) in PDB entry 5BUG
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 LYS 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B GLN* 6.0 0.9 - - - +
258B PHE* 4.1 40.2 - - + -
259B HIS 3.7 6.5 - - - +
260B LYS* 4.8 6.1 - - + +
265B LEU 3.6 1.4 + - - +
266B LYS* 1.3 83.3 - - + +
268B ASP* 1.3 65.7 + - - +
269B LYS* 3.6 2.3 + - - +
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Residues in contact with ASP 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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206B PHE* 4.7 11.3 - - + +
258B PHE* 3.1 5.6 - - - -
259B HIS* 2.6 68.5 + - + +
261B GLN* 5.1 8.3 - - - +
266B LYS* 3.4 36.2 + - - +
267B LYS* 1.3 71.4 - - - +
269B LYS* 1.3 59.0 + - - +
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Residues in contact with LYS 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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206B PHE* 3.8 11.5 - - - -
256B GLU* 2.9 30.9 + - + +
257B PHE 4.7 1.6 - - - +
258B PHE* 3.9 17.7 - - + -
266B LYS* 5.8 0.6 - - - +
267B LYS 3.6 2.3 + - - +
268B ASP* 1.3 73.9 - - - +
270B MET* 1.3 65.1 + - - +
271B PHE* 4.7 3.4 - - - +
272B HIS* 5.2 6.7 - - + -
327B LYS* 3.6 40.3 + - + +
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Residues in contact with MET 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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200B PHE* 4.3 11.4 - - + -
204B PRO* 3.4 42.2 - - + -
206B PHE* 3.6 27.1 - - + -
211B CYS* 3.8 12.6 - - + -
213B PRO* 4.4 11.0 - - + -
257B PHE* 2.9 18.3 + - - +
258B PHE 3.6 24.5 - - - +
259B HIS* 3.7 18.8 - - + +
268B ASP 3.7 0.2 + - - -
269B LYS* 1.3 74.2 - - - +
271B PHE* 1.3 78.1 + - + +
327B LYS* 3.7 16.9 - - - +
328B ALA 4.1 0.3 + - - -
337B PHE* 3.8 13.2 - - + -
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Residues in contact with PHE 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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200B PHE* 3.8 16.8 - + - -
256B GLU* 3.7 2.1 - - - +
257B PHE* 2.8 64.0 + + + +
269B LYS* 4.7 2.2 - - - +
270B MET* 1.3 93.5 - - + +
272B HIS* 1.3 70.2 + - - +
273B PHE* 4.0 8.7 - + - -
325B LEU* 3.8 27.1 - - + -
327B LYS* 4.2 9.6 - - - +
328B ALA* 3.9 22.2 - - + +
337B PHE* 3.9 14.6 - + - -
341B PHE* 4.0 11.4 - + - -
343B VAL* 3.7 31.6 - - + -
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Residues in contact with HIS 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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93B HIS* 4.9 10.3 - - + -
94B ASN* 5.5 1.3 - - - -
168B ILE* 5.6 0.7 - - + -
254B LYS* 3.5 28.7 + - - -
255B VAL 3.2 14.8 - - - +
256B GLU* 3.8 24.7 - - + -
269B LYS* 5.2 5.2 - - + -
271B PHE* 1.3 81.5 - - - +
273B PHE* 1.3 69.4 + - - +
274B TRP* 4.7 4.4 - + - -
325B LEU* 3.8 1.7 - - - -
326B ASP* 2.8 66.2 + - + +
327B LYS* 4.4 10.1 + - + +
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Residues in contact with PHE 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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170B SER* 3.8 7.6 - - - +
173B ARG* 4.3 11.2 - - - +
198B MET* 4.4 0.4 - - - -
253B ILE 5.2 0.2 - - - -
254B LYS* 3.3 4.6 - - - +
255B VAL* 2.9 75.1 + - + +
257B PHE* 4.8 1.1 - + - -
271B PHE* 4.0 16.2 - + - -
272B HIS* 1.3 78.9 - - - +
274B TRP* 1.3 64.3 + - - +
275B VAL* 3.8 18.2 - - + -
320B LEU* 3.7 17.0 - - + -
324B ASP 4.6 3.6 - - - +
325B LEU* 3.8 24.5 - - + -
326B ASP* 4.3 1.1 - - - -
343B VAL* 4.8 5.8 - - + -
345B LEU* 3.6 43.7 - - + -
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Residues in contact with TRP 274 (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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94B ASN* 3.7 26.5 - - + -
95B PRO* 3.5 39.7 - - + +
170B SER* 3.1 19.0 + - - +
173B ARG* 2.8 28.2 + - - -
174B TYR* 4.2 15.0 - - + -
220B LEU* 4.0 31.9 - - + -
252B ASP* 4.1 26.0 - - + -
253B ILE 3.2 22.4 - - - -
254B LYS* 3.3 47.7 - - + +
272B HIS* 4.7 1.5 - + - -
273B PHE* 1.3 76.0 - - - +
275B VAL* 1.3 63.5 + - - +
326B ASP* 4.4 5.4 - - - -
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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
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173B ARG* 4.2 8.1 - - - +
174B TYR* 3.8 5.3 + - - -
177B TYR* 3.6 12.1 - - - +
252B ASP* 3.7 1.7 - - - -
253B ILE* 2.8 49.2 + - + +
273B PHE* 3.8 21.1 - - + -
274B TRP* 1.3 80.6 - - - +
276B ASN* 1.3 61.1 + - - +
277B THR* 5.2 0.9 - - + +
280B ILE* 4.4 17.3 - - + -
318B LEU* 3.9 23.1 - - + -
320B LEU* 4.3 6.1 - - + -
345B LEU* 4.4 12.8 - - + -
347B PHE* 5.0 4.7 - - + -
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Residues in contact with ASN 276 (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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98B LEU* 3.7 11.5 - - - +
174B TYR* 4.1 0.4 - - + +
177B TYR* 3.1 26.5 + - + -
188B TYR* 3.3 25.2 + - - -
251B GLY 3.3 8.4 - - - +
252B ASP* 2.7 31.5 + - - +
275B VAL* 1.3 75.6 - - - +
277B THR* 1.3 60.0 + - - +
278B PHE* 2.9 27.0 + - - +
279B PHE* 2.9 34.7 + - + +
280B ILE* 3.9 7.4 - - - +
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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