Contacts of the strand formed by residues 343 - 349 (chain B) in PDB entry 6DBU
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 TYR 343 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B GLY 5.5 2.0 - - - -
15B VAL* 3.9 22.0 - - + -
16B GLN* 5.1 0.2 - - - -
17B PRO* 3.2 27.9 - - + +
34B LYS* 5.4 9.8 + - - -
318B PHE* 3.4 40.2 - + + -
330B ALA* 4.7 4.3 - - + -
331B ILE 3.3 5.6 - - - +
332B PRO* 3.9 28.9 - - + +
341B GLU* 2.8 39.6 + - - +
342B ALA* 1.3 86.5 - - + +
344B HIS* 1.3 64.4 + - - +
345B PHE* 3.5 21.3 - - + -
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Residues in contact with HIS 344 (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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6B LEU 5.9 2.7 - - - +
7B THR* 6.5 1.1 - - + -
310B GLU* 3.9 27.0 + - - +
330B ALA* 3.1 4.9 - - - -
331B ILE* 2.9 39.6 + - + +
333B SER* 3.6 28.2 + - - +
339B PRO* 5.7 3.4 - - - +
341B GLU* 4.9 9.4 + - - -
342B ALA 4.1 0.4 - - - -
343B TYR* 1.3 76.3 - - - +
345B PHE* 1.3 60.6 + - - +
346B TYR* 4.7 12.0 - - + +
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Residues in contact with PHE 345 (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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6B LEU* 2.9 43.0 + - + +
7B THR* 5.4 1.3 - - - +
8B ALA* 4.8 16.4 - - + -
12B GLY* 5.7 2.7 - - - -
15B VAL* 4.1 37.7 - - + -
19B PHE* 5.7 3.6 - + - -
55B LEU* 3.9 21.8 - - + -
318B PHE* 5.6 0.4 - + - -
328B LEU* 3.5 39.0 - - + -
329B VAL 3.4 1.1 - - - -
330B ALA* 3.5 23.1 - - + -
341B GLU* 4.0 11.7 - - - -
343B TYR* 3.5 22.4 - - + -
344B HIS* 1.3 71.7 - - - +
346B TYR* 1.3 70.8 + - - +
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Residues in contact with TYR 346 (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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3B LEU* 4.9 13.0 - - + -
4B GLN 3.5 6.7 - - - +
5B PRO* 3.6 24.9 - - + -
6B LEU* 4.4 0.2 - - - -
307B TRP* 5.8 0.9 - + - -
308B THR* 4.8 10.2 - - - +
310B GLU* 2.6 38.9 + - - +
311B ILE* 3.5 47.7 - - + +
328B LEU* 3.3 6.0 - - - +
329B VAL* 2.9 46.9 + - + +
331B ILE* 3.9 15.4 - - + +
344B HIS* 4.7 10.9 - - + +
345B PHE* 1.3 87.3 - - - +
347B GLN* 1.3 64.1 + - - +
348B VAL* 3.9 6.5 + - + -
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Residues in contact with GLN 347 (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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3B LEU* 3.2 4.0 - - - -
4B GLN* 2.9 67.1 + - + +
6B LEU* 3.7 16.7 - - + +
50B ILE* 3.6 29.4 - - + +
53B GLY* 5.7 0.2 - - - -
322B LEU* 3.7 22.5 - - + +
326B THR* 3.8 21.0 - - + +
327B ALA 3.5 11.9 - - - +
328B LEU* 4.7 1.3 - - + +
346B TYR* 1.3 74.1 - - - +
348B VAL* 1.3 64.9 + - - +
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Residues in contact with VAL 348 (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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2B SER 3.2 6.1 - - - +
3B LEU* 3.6 23.8 - - + +
274B PHE* 3.4 39.2 - - + -
305B PRO* 6.1 2.9 - - + -
307B TRP* 4.3 14.6 - - + -
325B GLY 3.5 1.9 - - - +
326B THR* 3.7 0.6 - - - -
327B ALA* 2.9 40.2 + - + +
329B VAL* 4.0 28.7 - - + -
346B TYR* 4.7 2.2 - - + -
347B GLN* 1.3 81.0 - - - +
349B SER* 1.3 61.8 + - - +
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Residues in contact with SER 349 (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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1B MET* 2.4 37.9 + - - -
2B SER* 2.9 19.8 + - - +
4B GLN* 4.4 12.7 + - - -
274B PHE* 5.4 2.9 - - - -
325B GLY 3.3 8.7 - - - -
326B THR* 4.2 18.8 - - - -
347B GLN* 5.7 0.2 - - - -
348B VAL* 1.3 77.0 - - - +
350B PHE* 1.3 57.1 + - - +
351B GLN 5.7 2.0 - - - -
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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