Contacts of the strand formed by residues 326 - 332 (chain B) 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 THR 326 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264B SER* 4.1 1.4 + - - -
321B SER* 3.6 4.3 - - - -
322B LEU* 3.0 16.7 + - + -
323B GLY 2.9 33.7 + - - -
324B LYS* 2.9 12.6 + - - +
325B GLY* 1.3 77.1 - - - +
327B ALA* 1.3 66.1 + - - +
347B GLN* 3.4 33.2 - - + +
348B VAL 3.1 11.2 - - - +
349B SER* 4.4 7.6 - - - +
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ILE* 4.3 11.4 - - + -
264B SER* 5.0 5.2 - - - -
272B ILE* 6.5 0.9 - - + -
274B PHE* 5.0 7.4 - - + -
320B GLY 3.2 14.6 - - - +
321B SER* 3.7 9.0 - - - -
322B LEU* 3.5 7.9 - - - +
325B GLY 5.3 0.9 - - - +
326B THR* 1.3 76.2 - - - +
328B LEU* 1.3 61.4 + - - +
329B VAL* 5.3 0.9 - - + -
347B GLN* 3.5 7.1 - - - +
348B VAL* 2.9 46.7 + - + +
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Residues in contact with LEU 328 (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* 4.9 8.5 - - + -
19B PHE* 5.2 12.3 - - + -
21B LEU* 4.9 9.2 - - + -
30B LEU* 5.9 6.1 - - + -
48B VAL* 5.8 3.1 - - + -
55B LEU* 4.8 17.5 - - + -
319B GLY* 2.9 2.3 - - - -
320B GLY 2.5 43.0 + - - +
322B LEU* 4.1 27.1 - - + +
327B ALA* 1.3 73.8 - - - +
329B VAL* 1.3 84.1 + - - +
345B PHE* 3.7 35.2 - - + -
346B TYR 3.5 11.0 - - - +
347B GLN* 4.9 1.6 - - + +
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Residues in contact with VAL 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ILE* 4.4 5.2 - - + -
274B PHE* 3.4 41.3 - - + -
307B TRP* 6.1 1.3 - - + -
311B ILE* 5.0 11.2 - - + -
317B TRP* 5.0 8.1 - - + -
318B PHE 3.2 15.7 - - - +
319B GLY* 3.7 6.1 - - - -
320B GLY 5.0 0.2 - - - +
327B ALA* 5.3 1.1 - - + -
328B LEU* 1.3 88.3 - - - +
330B ALA* 1.3 64.5 + - - +
331B ILE* 6.1 0.2 - - + -
345B PHE* 3.4 1.0 - - - -
346B TYR* 2.9 57.2 + - + +
348B VAL* 4.7 5.2 - - + -
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Residues in contact with ALA 330 (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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15B VAL* 6.0 0.7 - - + -
19B PHE* 6.0 1.8 - - + -
317B TRP* 3.2 24.9 - - - +
318B PHE* 3.0 33.6 + - + -
328B LEU* 5.9 0.2 - - + -
329B VAL* 1.3 78.4 - - - +
331B ILE* 1.3 64.2 + - - +
332B PRO* 3.8 2.0 - - - +
343B TYR* 4.3 11.0 - - + -
344B HIS 3.1 10.1 - - - +
345B PHE* 4.0 22.2 - - + -
346B TYR* 6.1 0.4 - - - -
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Residues in contact with ILE 331 (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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310B GLU* 5.1 15.7 - - + +
311B ILE* 3.5 43.7 - - + +
314B SER* 3.5 30.7 - - - +
317B TRP* 3.6 18.6 - - + -
329B VAL* 6.1 0.4 - - + -
330B ALA* 1.3 72.7 - - - +
332B PRO* 1.3 82.7 - - + +
333B SER* 4.2 6.3 - - - +
334B GLU* 4.5 2.7 - - - +
343B TYR* 3.0 24.5 - - - -
344B HIS* 2.9 21.4 + - + +
346B TYR* 4.4 12.3 - - + +
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Residues in contact with PRO 332 (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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314B SER* 4.2 3.8 - - - +
315B ARG* 5.7 0.7 - - + +
316B THR* 3.2 42.4 - - - +
317B TRP* 4.2 2.0 - - - -
318B PHE* 4.9 5.8 - - + -
330B ALA 3.8 6.3 - - - +
331B ILE* 1.3 86.8 - - + +
333B SER* 1.3 53.8 + - - +
334B GLU* 2.6 30.4 - - - +
342B ALA* 3.0 8.3 - - + +
343B TYR* 3.8 16.2 - - + -
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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