Contacts of the helix formed by residues 453 - 461 (chain B) in PDB entry 2QUH
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 453 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220B LYS* 5.6 0.2 - - - -
450B LYS 5.4 2.2 - - - +
451B GLU 3.1 14.3 + - - +
452B VAL* 1.3 74.6 - - - +
454B ASP* 1.3 65.4 + - - +
455B GLU* 3.7 9.1 + - - +
456B ILE* 2.9 33.4 + - + +
457B VAL* 2.9 17.9 + - - +
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Residues in contact with ASP 454 (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 LYS* 4.3 15.8 + - - -
453B THR* 1.3 73.5 - - - +
455B GLU* 1.3 63.3 + - - +
457B VAL* 3.4 7.5 + - - +
458B LYS* 3.0 26.3 + - - +
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Residues in contact with GLU 455 (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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453B THR* 3.1 9.0 + - - +
454B ASP* 1.3 79.7 - - - +
456B ILE* 1.3 65.7 + - + +
458B LYS* 3.5 10.3 + - - +
459B GLU* 3.1 23.8 + - - +
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Residues in contact with ILE 456 (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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223B ILE* 4.5 2.2 - - + -
229B ILE* 4.3 15.7 - - + -
451B GLU 5.0 1.6 - - - +
452B VAL* 4.3 17.3 - - + -
453B THR* 2.9 31.8 + - + +
455B GLU* 1.3 78.8 - - + +
457B VAL* 1.3 66.9 + - - +
459B GLU* 3.1 9.9 + - - +
460B PHE* 3.1 46.5 + - + -
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Residues in contact with VAL 457 (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 VAL* 3.9 18.8 - - + +
219B ALA* 4.2 2.0 - - + -
220B LYS* 3.8 23.3 - - + -
223B ILE* 4.0 19.3 - - + -
452B VAL* 3.7 11.4 - - + -
453B THR 2.9 22.2 + - - +
454B ASP* 3.5 12.1 - - - +
456B ILE* 1.3 74.2 - - - +
458B LYS* 1.3 62.6 + - - +
460B PHE* 3.2 3.3 + - - +
461B MET* 3.0 58.0 + - + +
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Residues in contact with LYS 458 (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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454B ASP 3.0 18.3 + - - +
455B GLU* 3.6 9.2 - - - +
457B VAL* 1.3 78.1 - - - +
459B GLU* 1.3 55.3 + - - +
461B MET* 3.3 7.6 + - - +
462B THR* 2.6 37.9 + - - +
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Residues in contact with GLU 459 (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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229B ILE* 3.3 36.6 - - + +
230B ASN* 4.8 5.7 - - - +
455B GLU 3.1 14.0 + - - +
456B ILE* 3.1 11.8 + - - +
458B LYS* 1.3 73.9 - - - +
460B PHE* 1.3 67.2 + - - +
462B THR* 2.9 17.7 + - - -
464B ARG* 2.9 29.8 + - - +
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Residues in contact with PHE 460 (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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223B ILE* 3.3 48.5 - - + -
227B PHE* 3.5 23.3 - - + -
228B ASP 4.2 0.7 - - - -
229B ILE* 3.4 42.6 - - + +
232B THR* 3.8 30.1 - - + -
233B PHE* 3.7 0.9 - - - -
234B ILE* 3.0 37.4 + - + -
456B ILE* 3.1 31.6 + - + -
457B VAL 3.6 7.4 - - - +
459B GLU* 1.3 77.9 - - - +
461B MET* 1.3 59.7 + - + +
462B THR 3.5 0.2 + - - -
464B ARG* 2.9 21.1 + - - +
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Residues in contact with MET 461 (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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195B MET* 5.6 1.8 - - - -
212B TYR* 5.5 2.5 - - - -
215B ALA 5.0 1.6 - - - +
216B VAL* 3.5 44.2 - - + -
219B ALA* 3.6 11.4 - - + -
233B PHE* 4.0 5.5 - - - -
234B ILE* 3.0 31.5 - - + +
235B PHE* 5.2 2.5 - - - +
236B SER* 5.2 14.6 - - - +
239B ASP* 6.1 1.2 - - - +
243B MET* 5.9 0.3 - - - +
457B VAL* 3.0 48.5 + - + +
458B LYS* 3.3 7.6 + - - +
459B GLU 3.0 0.4 - - - -
460B PHE* 1.3 78.7 - - + +
462B THR* 1.3 59.4 + - - +
463B PRO* 3.8 7.1 - - - +
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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