Contacts of the strand formed by residues 303 - 308 (chain B) in PDB entry 3BUW
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 TRP 303 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247B LEU* 2.9 45.8 + - + +
248B PHE* 3.6 41.3 - + - -
261B LEU 5.4 0.4 - - - -
268B TYR* 3.7 28.5 - + - -
293B PHE* 3.7 22.9 - + + -
294B ARG 3.4 26.5 - - - -
295B LEU* 4.0 8.1 - - + -
301B GLY 5.3 0.4 - - - -
302B GLN* 1.3 75.7 - - - +
304B ALA* 1.3 60.4 + - - +
305B ILE* 4.5 4.0 - - + -
318B ILE* 3.2 15.0 - - - +
319B PRO* 3.1 30.9 - - + +
324B LEU* 3.4 49.5 - - + +
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Residues in contact with ALA 304 (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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323A PTR 3.9 17.3 - - + -
277B VAL* 5.9 0.7 - - - +
293B PHE* 3.4 2.6 - - - -
294B ARG* 2.9 73.4 + - - +
296B SER* 4.2 9.2 - - - -
302B GLN 4.1 0.4 + - - -
303B TRP* 1.3 73.0 - - - +
305B ILE* 1.3 62.5 + - - +
306B GLY 4.0 0.5 + - - -
316B GLN* 4.6 2.8 + - + +
317B THR 3.5 4.7 - - - -
318B ILE* 4.3 0.7 - - + -
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Residues in contact with ILE 305 (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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291B TYR* 4.3 9.2 - - + -
292B ILE 3.6 8.1 - - - +
293B PHE* 3.1 30.7 - - + -
303B TRP* 4.5 3.6 - - + -
304B ALA* 1.3 75.1 - - - +
306B GLY* 1.3 64.0 + - - +
307B TYR* 4.8 2.4 - - - -
315B LEU 3.7 0.9 - - - +
316B GLN* 3.1 3.5 - - - -
317B THR* 2.8 45.2 + - - +
319B PRO* 4.3 17.3 - - + -
324B LEU* 3.6 27.4 - - + -
327B ALA* 5.5 1.3 - - + -
328B LEU* 4.3 5.2 - - + -
337B TYR* 3.5 48.5 - - + +
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Residues in contact with GLY 306 (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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277B VAL* 4.2 12.6 - - - +
281B LEU* 3.6 7.2 - - - -
291B TYR* 3.1 7.1 - - - +
292B ILE 2.8 36.0 + - - -
304B ALA 4.0 1.4 + - - -
305B ILE* 1.3 74.1 - - - +
307B TYR* 1.3 61.1 + - - -
315B LEU 3.2 9.0 - - - -
316B GLN* 3.7 13.9 - - - +
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Residues in contact with TYR 307 (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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327A LEU* 5.7 4.5 - - - +
281B LEU* 3.7 6.7 - - - +
290B SER 3.2 12.1 - - - +
291B TYR* 3.8 4.7 - - + -
305B ILE 4.8 2.5 - - - -
306B GLY* 1.3 77.5 - - - +
308B VAL* 1.3 74.0 + - - +
309B THR* 3.7 28.0 + - + +
313B ASN 3.5 1.4 - - - +
314B ILE* 3.4 3.6 - - - -
315B LEU* 2.9 62.1 + - + +
317B THR* 4.8 11.9 - - + -
336B PHE* 3.4 65.1 - + + +
337B TYR* 3.8 21.8 - + + -
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Residues in contact with VAL 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 4.0 26.0 - - + +
284B PHE 3.5 20.9 - - - +
285B ILE* 3.6 28.7 - - + +
287B LYS 3.9 7.6 - - - +
288B PRO* 3.9 8.0 - - + +
289B GLY 3.0 23.7 + - - -
290B SER* 2.9 22.2 + - - +
307B TYR* 1.3 82.6 - - - +
309B THR* 1.3 72.7 + - - +
312B GLY* 5.0 0.7 - - - -
313B ASN 3.5 7.4 - - - +
314B ILE* 4.5 5.8 - - + -
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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