Contacts of the strand formed by residues 290 - 295 (chain B) in PDB entry 3BUN
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 SER 290 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281B LEU* 4.2 3.0 - - - +
284B PHE* 3.5 30.0 - - - +
287B LYS* 2.8 41.2 + - - +
288B PRO 3.6 0.2 + - - -
289B GLY* 1.3 78.2 - - - +
291B TYR* 1.3 58.3 + - - +
307B TYR* 3.2 2.9 - - - +
308B VAL* 2.9 33.8 + - - +
339B PHE* 3.3 12.7 - - - +
342B GLY* 3.7 7.7 - - - -
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Residues in contact with TYR 291 (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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265B HIS* 3.3 16.4 + + - -
267B GLY* 4.5 0.4 - - - -
281B LEU* 4.3 4.4 - - - +
289B GLY 3.5 4.0 - - - +
290B SER* 1.3 74.6 - - - +
292B ILE* 1.3 70.0 + - - +
293B PHE* 3.9 17.9 - + - -
305B ILE* 4.3 7.4 - - + -
306B GLY 3.2 14.4 - - - +
307B TYR* 3.7 10.8 - - + +
328B LEU* 3.7 24.8 - - + +
337B TYR* 3.4 50.0 - + + -
338B LEU 3.7 1.1 - - - -
339B PHE 3.0 10.4 + - - -
340B PRO* 3.3 24.4 - - + +
341B ASP 2.8 24.0 + - - +
346B ASN* 2.5 27.2 + - - -
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Residues in contact with ILE 292 (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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267B GLY 3.4 15.0 - - - +
269B MET* 3.9 17.7 - - + -
272B LEU* 5.1 1.3 - - + -
277B VAL* 3.0 51.6 - - + +
280B ARG* 5.0 6.1 - - + +
281B LEU* 3.8 23.1 - - + -
291B TYR* 1.3 88.1 - - - +
293B PHE* 1.3 68.0 + - - +
305B ILE* 3.5 2.4 - - - +
306B GLY 2.8 28.2 + - - +
341B ASP* 3.5 35.4 - - + +
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Residues in contact with PHE 293 (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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261B LEU* 3.2 28.5 - - - -
265B HIS* 3.6 32.1 - + - -
267B GLY* 2.9 22.6 + - - +
268B TYR* 3.5 21.3 - + + -
269B MET* 2.8 32.3 + - - +
291B TYR* 3.9 14.6 - + - -
292B ILE* 1.3 77.9 - - - +
294B ARG* 1.3 60.5 + - - +
303B TRP* 3.8 18.6 - + + -
304B ALA 3.3 11.7 - - - +
305B ILE* 4.0 15.7 - - + -
324B LEU* 3.8 21.8 - - + -
328B LEU* 4.1 17.7 - - + -
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Residues in contact with ARG 294 (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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53A PTR 3.2 30.3 + - - -
268B TYR* 4.7 1.1 - - - -
269B MET* 3.4 24.5 - - + +
270B ALA 5.4 0.2 - - - +
272B LEU 3.1 28.1 + - - +
273B THR 3.6 5.0 - - - -
274B TYR* 3.0 23.3 - - - +
277B VAL* 3.3 25.7 - - + +
293B PHE* 1.3 79.5 - - - +
295B LEU* 1.3 78.0 + - - +
296B SER* 3.5 1.6 - - - +
297B CYS* 4.0 0.4 - - - +
303B TRP* 3.4 18.7 - - - -
304B ALA* 2.9 51.4 + - - +
316B GLN* 2.8 27.1 - - - +
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Residues in contact with LEU 295 (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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156B LEU* 6.0 1.0 - - - +
160B HIS* 5.2 7.3 - - + +
227B THR* 5.4 2.9 - - + +
230B LEU* 4.1 34.1 - - + -
243B ILE* 4.5 3.1 - - + -
247B LEU* 3.5 36.1 - - + -
248B PHE* 5.2 3.6 - - + -
268B TYR* 4.0 21.1 - - + +
269B MET 4.9 1.0 + - - -
270B ALA 5.5 6.4 + - - +
272B LEU 4.4 4.0 - - - +
294B ARG* 1.3 91.2 + - - +
296B SER* 1.3 69.2 + - - +
297B CYS* 3.4 1.7 + - - +
300B LEU* 4.8 7.2 - - + -
301B GLY 5.7 1.1 - - - +
302B GLN 4.0 4.3 - - - +
303B TRP* 4.0 19.5 - - + -
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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