Contacts of the strand formed by residues 343 - 349 (chain D) in PDB entry 6DBV
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D GLY 5.0 7.6 - - - -
15D VAL* 3.7 27.4 + - + -
17D PRO* 3.8 23.1 - - + +
34D LYS* 4.7 8.3 + - - -
318D PHE* 3.4 39.7 - + - -
330D ALA* 5.1 0.9 - - + -
331D ILE 3.1 11.9 - - - +
332D PRO* 4.1 8.7 - - + -
333D SER* 3.2 3.2 + - - -
341D GLU* 2.6 40.2 + - - +
342D ALA* 1.3 110.7 - - + +
344D HIS* 1.3 62.0 + - - +
345D PHE* 3.1 27.2 - + + -
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Residues in contact with HIS 344 (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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6D LEU 5.3 1.1 - - - +
7D THR* 5.7 9.4 - - + -
310D GLU* 3.6 36.0 + - + +
330D ALA* 3.2 5.5 - - - -
331D ILE* 2.9 40.5 + - + +
333D SER* 3.5 24.4 + - - -
341D GLU* 4.8 3.4 - - - -
343D TYR* 1.3 77.9 - - - +
345D PHE* 1.3 61.8 + - - +
346D TYR* 4.9 4.9 + - + +
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Residues in contact with PHE 345 (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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5D PRO* 3.5 1.2 - - - +
6D LEU* 2.9 46.7 + - + +
7D THR* 5.4 1.1 - - - -
8D ALA* 5.2 13.7 - - + -
12D GLY* 6.4 0.7 - - - -
15D VAL* 4.6 27.8 - - + -
19D PHE* 5.8 1.8 - + - -
55D LEU* 4.8 22.0 - - + -
328D LEU* 3.4 37.2 - - + -
329D VAL 3.4 2.0 - - - -
330D ALA* 3.5 21.5 - - + -
341D GLU* 3.5 11.9 - - - -
343D TYR* 3.1 41.5 - - + -
344D HIS* 1.3 73.8 - - - +
346D TYR* 1.3 72.1 + - - +
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Residues in contact with TYR 346 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D LEU* 4.9 11.7 - - + -
4D GLN 3.5 4.3 - - - +
5D PRO* 3.4 35.9 - - + -
308D THR* 3.7 21.7 + - + +
310D GLU* 2.1 42.7 + - - +
311D ILE* 3.5 40.8 - - + -
328D LEU* 3.4 8.3 - - - -
329D VAL* 2.9 46.4 + - + +
331D ILE* 4.2 10.1 - - + -
344D HIS* 4.9 5.2 + - + -
345D PHE* 1.3 84.0 - - - +
347D GLN* 1.3 64.2 + - - +
348D VAL* 3.8 5.5 + - + +
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Residues in contact with GLN 347 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D LEU* 3.1 4.2 - - - -
4D GLN* 2.8 50.0 + - + +
6D LEU* 3.3 37.1 - - + +
50D ILE* 3.3 42.9 - - + +
53D GLY* 4.9 1.0 - - - -
322D LEU* 5.7 1.2 - - + +
326D THR* 5.6 10.3 - - - +
327D ALA 3.5 9.4 - - - +
328D LEU* 4.8 0.9 - - - +
346D TYR* 1.3 71.8 - - - +
348D VAL* 1.3 65.0 + - - +
349D SER* 6.2 1.6 - - - -
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Residues in contact with VAL 348 (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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2D SER 3.1 6.1 - - - +
3D LEU* 3.5 25.8 - - + -
4D GLN* 4.9 0.2 - - - -
274D PHE* 3.5 38.1 - - + -
305D PRO* 5.0 5.8 - - + -
307D TRP* 5.0 6.7 - - + -
325D GLY 3.6 2.3 - - - +
326D THR* 3.6 2.9 - - - -
327D ALA* 2.9 48.1 + - + +
328D LEU 4.3 0.7 - - - +
329D VAL* 4.5 16.2 - - + -
346D TYR* 4.1 9.6 - - + +
347D GLN* 1.3 83.0 - - - +
349D SER* 1.3 61.6 + - - +
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Residues in contact with SER 349 (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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1D MET* 2.4 41.0 + - - +
2D SER* 2.9 24.7 + - - -
4D GLN* 4.9 5.8 + - - -
272D ILE* 5.4 1.1 - - - -
274D PHE* 6.3 0.7 - - - -
305D PRO* 5.0 0.7 - - - +
325D GLY 4.1 5.8 - - - -
326D THR* 4.7 10.3 - - - +
347D GLN* 6.2 1.6 - - - -
348D VAL* 1.3 75.2 - - - +
350D PHE* 1.3 56.8 + - - +
351D GLN 5.3 2.6 - - - -
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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