Contacts of the strand formed by residues 246 - 250 (chain B) in PDB entry 6DGD
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 GLN 246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B TRP* 4.7 5.4 - - + -
240B VAL* 4.1 0.5 - - - +
244B GLY 5.1 1.1 - - - +
245B ARG* 1.3 76.7 - - - +
247B ALA* 1.3 63.8 + - - +
291B ALA* 2.9 26.9 + - - +
294B GLY* 3.4 20.3 - - - +
296B ALA 3.1 24.2 + - - +
297B ALA* 3.3 11.9 - - - +
310B PHE* 3.6 17.1 - - + -
311B LYS* 2.8 28.2 + - - +
312B ASP 2.9 22.2 + - - +
313B LEU* 3.7 11.6 - - + -
314B GLY* 2.8 26.9 + - - -
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Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LEU* 3.6 30.7 - - + -
240B VAL* 4.8 1.8 - - + -
241B LEU* 4.3 5.2 - - + -
246B GLN* 1.3 77.7 - - - +
248B LEU* 1.3 60.8 - - - +
249B VAL* 5.1 1.1 - - + -
297B ALA 3.0 6.3 + - - -
298B ILE* 3.2 34.1 - - + +
299B VAL* 3.2 5.5 + - - +
310B PHE* 4.7 5.6 - - - -
313B LEU* 4.7 1.6 - - - -
315B VAL* 3.5 19.1 - - + +
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Residues in contact with LEU 248 (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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247B ALA* 1.3 72.7 - - - +
249B VAL* 1.3 62.7 + - - +
250B MET* 5.0 4.9 - - + -
299B VAL* 3.2 26.9 - - + +
305B SER* 3.3 40.2 - - - +
306B LEU* 3.8 15.9 - - + -
308B THR* 4.0 9.4 - - - +
310B PHE* 3.8 27.4 - - + -
313B LEU* 4.8 3.4 - - + +
315B VAL 3.5 5.5 + - - -
316B ILE* 3.4 25.3 - - + +
317B VAL* 3.0 25.1 + - - +
343B ARG* 4.4 8.3 - - - +
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Residues in contact with VAL 249 (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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233B TYR* 5.9 2.0 - - + -
237B LEU* 4.2 24.2 - - + -
247B ALA* 4.1 3.1 - - + +
248B LEU* 1.3 79.6 - - - +
250B MET* 1.3 69.7 + - - +
251B VAL* 4.7 9.4 - - + -
264B PHE* 4.6 20.9 - - + -
298B ILE* 5.5 5.6 - - + -
299B VAL 3.1 13.4 + - - +
300B ILE* 3.3 14.8 - - + +
301B GLY 3.1 21.0 + - - -
317B VAL* 3.3 36.8 - - + +
319B ASP* 5.6 2.9 - - + -
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Residues in contact with MET 250 (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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248B LEU* 5.0 8.7 - - + +
249B VAL* 1.3 76.3 - - - +
251B VAL* 1.3 68.6 - - - +
301B GLY 3.2 9.0 - - - +
302B THR 3.2 26.2 - - - +
303B ARG* 3.7 16.6 - - - +
305B SER* 3.4 12.1 - - - +
306B LEU* 4.0 20.9 - - + +
316B ILE* 5.3 2.5 - - + -
317B VAL 3.0 14.4 + - - +
318B ILE* 3.6 31.2 - - + -
319B ASP* 3.1 26.9 + - - +
326B TYR* 3.3 9.0 + - + -
336B ALA* 4.8 8.3 - - + -
340B ALA* 4.5 4.7 - - - -
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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