Contacts of the helix formed by residues 337 - 344 (chain B) in PDB entry 6HYI
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 ARG 337 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280B ASN* 3.4 38.2 + - + +
313B LEU* 3.5 29.3 + - + +
316B ASP* 3.2 26.3 + - - -
336B ASP* 1.3 74.8 - - - +
338B ASP* 1.3 72.6 + - - +
340B TYR* 3.2 3.0 + - - +
341B ARG* 2.8 63.3 + - - +
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Residues in contact with ASP 338 (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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220B TYR* 3.7 21.1 - - + +
336B ASP* 3.2 9.0 + - - +
337B ARG* 1.3 96.0 + - - +
339B THR* 1.3 59.4 + - - +
341B ARG* 3.8 3.5 - - - +
342B ASN* 2.8 42.5 + - - +
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Residues in contact with THR 339 (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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220B TYR* 2.7 23.9 + - - -
222B ALA* 4.0 8.5 - - + -
223B PRO* 3.4 9.0 - - - +
256B VAL* 4.5 7.2 - - + -
259B ALA* 4.2 4.0 - - + +
335B LEU* 3.7 24.0 - - + -
336B ASP* 2.6 33.3 + - - -
338B ASP* 1.3 74.0 - - - +
340B TYR* 1.3 63.5 + - - +
343B LEU* 2.9 47.7 + - + +
344B VAL* 3.6 1.6 + - - +
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Residues in contact with TYR 340 (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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244B LEU* 4.3 13.6 + - + +
282B LEU* 4.0 22.9 - - + -
310B GLU* 4.8 3.5 + - + -
313B LEU* 3.7 43.3 - - + -
314B MET* 3.4 30.6 - - - +
335B LEU* 4.0 9.5 - - + +
336B ASP 3.1 14.9 + - - +
337B ARG 3.6 6.1 - - - +
339B THR* 1.3 76.7 - - - +
341B ARG* 1.3 66.8 + - + +
344B VAL* 2.9 43.2 + - + -
345B MET* 2.9 63.1 + - + +
348B ALA* 4.9 0.3 - - - +
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Residues in contact with ARG 341 (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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313B LEU* 3.7 12.2 + - + +
314B MET 5.1 0.8 + - - -
316B ASP* 3.1 28.1 + - - -
337B ARG* 2.8 67.2 + - + +
338B ASP* 4.0 4.5 - - - +
340B TYR* 1.3 82.5 - - + +
342B ASN* 1.3 64.3 + - - +
345B MET* 3.5 47.1 + - + +
346B GLY 4.7 3.1 + - - -
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Residues in contact with ASN 342 (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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216B LYS* 4.7 1.2 - - - +
217B ALA* 3.5 42.3 + - + +
220B TYR* 3.6 41.5 - - + +
338B ASP* 2.8 36.0 + - - +
341B ARG* 1.3 82.6 - - - +
343B LEU* 1.3 61.8 + - + +
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Residues in contact with LEU 343 (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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217B ALA* 4.5 11.2 - - + +
220B TYR* 4.1 20.4 - - + +
222B ALA* 3.9 9.0 - - + +
248B LEU* 3.2 23.0 - - - +
252B ASP* 5.2 16.9 - - - +
255B VAL* 3.8 29.8 - - + -
256B VAL* 4.2 15.3 - - + -
339B THR* 2.9 30.2 + - + +
342B ASN* 1.3 87.8 - - + +
344B VAL* 1.3 62.0 + - - +
346B GLY* 5.2 1.6 - - - -
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Residues in contact with VAL 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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244B LEU 3.5 25.2 - - - +
245B PHE* 3.8 27.8 - - + -
248B LEU* 4.2 13.1 - - + +
256B VAL* 3.8 24.9 - - + -
335B LEU* 4.1 6.5 - - + -
339B THR 4.0 1.6 - - - +
340B TYR* 2.9 44.9 + - + +
343B LEU* 1.3 81.6 - - - +
345B MET* 1.3 69.6 + - - +
346B GLY* 3.2 4.3 + - - -
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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