Contacts of the helix formed by residues 379 - 390 (chain B) in PDB entry 5H1Y
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 PRO 379 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A ARG* 5.8 7.6 - - - +
347B ASP* 5.9 0.2 - - + -
377B THR* 3.5 17.0 - - - +
378B MET* 1.4 96.6 - - - +
380B LYS* 1.3 66.3 + - - +
381B LYS* 3.2 7.2 + - + +
382B ILE* 3.3 26.9 + - + +
383B GLN* 3.0 18.2 + - - +
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Residues in contact with LYS 380 (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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379B PRO* 1.3 74.7 - - - +
381B LYS* 1.3 56.6 + - - +
383B GLN* 3.3 14.1 + - + +
384B ASN* 2.8 47.6 + - - +
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Residues in contact with LYS 381 (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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350B ILE* 3.9 30.8 + - + +
355B GLU* 4.3 14.4 - - - +
379B PRO* 3.2 6.8 - - + +
380B LYS* 1.3 77.9 - - - +
382B ILE* 1.3 61.6 + - + +
384B ASN* 3.3 10.3 + - - +
385B PHE* 3.0 28.7 + - + +
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Residues in contact with ILE 382 (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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346B ALA* 4.3 1.6 - - + +
347B ASP* 3.7 23.3 - - + +
350B ILE* 3.5 40.4 - - + -
351B ASP* 5.9 0.9 - - - +
373B LEU* 4.2 13.2 - - + +
375B SER* 4.1 14.6 - - - +
377B THR 4.2 0.2 - - - +
378B MET* 3.6 26.9 - - + -
379B PRO* 3.3 31.6 + - + +
381B LYS* 1.3 76.5 - - + +
383B GLN* 1.3 58.1 + - - +
385B PHE* 3.4 6.2 + - + +
386B ALA* 2.9 28.8 + - - +
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Residues in contact with GLN 383 (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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172B GLU* 5.4 6.1 + - - -
378B MET* 3.7 33.5 - - - +
379B PRO 3.0 12.3 + - - +
380B LYS* 3.4 19.0 - - + +
382B ILE* 1.3 78.9 - - - +
384B ASN* 1.3 63.7 + - - +
386B ALA* 3.5 4.5 + - - +
387B LYS* 3.1 22.7 + - - +
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Residues in contact with ASN 384 (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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359B ARG* 5.9 0.2 - - - -
380B LYS* 2.8 44.4 + - - +
381B LYS* 3.6 8.2 - - - +
383B GLN* 1.3 73.9 - - - +
385B PHE* 1.3 63.6 + - - +
387B LYS* 3.4 9.0 + - - +
388B SER* 3.2 21.3 + - - -
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Residues in contact with PHE 385 (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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343B LEU* 4.1 20.6 - - + -
346B ALA* 5.3 4.7 - - + -
350B ILE* 4.3 22.4 - - + -
355B GLU* 3.8 36.6 - - + +
358B ILE* 3.6 33.2 - - + -
359B ARG* 4.3 24.7 - - + +
362B PHE* 4.1 13.5 - + - -
373B LEU* 3.8 19.5 - - + -
381B LYS 3.0 16.3 + - - +
382B ILE* 3.7 7.9 - - + +
384B ASN* 1.3 73.3 - - - +
386B ALA* 1.3 61.2 + - - +
388B SER* 3.0 8.5 + - - -
389B ALA* 2.8 30.4 + - + +
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Residues in contact with ALA 386 (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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222B ILE* 3.9 33.0 - - + -
373B LEU* 4.3 18.8 - - + -
378B MET* 5.3 2.0 - - - -
382B ILE 2.9 17.6 + - - +
383B GLN* 3.6 7.6 - - - +
385B PHE* 1.3 75.7 - - - +
387B LYS* 1.3 56.9 + - - +
389B ALA* 2.9 3.0 + - - +
390B LEU* 2.8 42.1 + - + +
393B PRO* 5.8 0.9 - - - -
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Residues in contact with LYS 387 (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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383B GLN 3.1 14.2 + - - +
384B ASN* 3.7 8.3 - - - +
385B PHE 3.3 0.2 - - - -
386B ALA* 1.3 78.9 - - - +
388B SER* 1.3 59.8 + - - +
390B LEU* 3.6 13.3 - - - +
393B PRO* 6.1 4.3 - - - -
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Residues in contact with SER 388 (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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359B ARG* 3.3 37.3 + - - -
362B PHE* 5.4 2.9 - - - -
369B ARG* 5.4 1.2 + - - -
384B ASN 3.2 11.3 + - - -
385B PHE* 3.0 9.5 + - - -
387B LYS* 1.3 77.8 - - - +
389B ALA* 1.3 62.0 + - - +
390B LEU 3.6 0.8 - - - +
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Residues in contact with ALA 389 (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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343B LEU* 5.1 2.9 - - + -
362B PHE* 3.7 32.8 - - + -
369B ARG* 3.6 18.9 + - - +
371B THR* 4.1 7.8 + - - +
373B LEU* 5.4 0.9 - - + -
385B PHE* 2.8 28.5 + - + +
386B ALA* 3.9 3.4 - - - +
388B SER* 1.3 79.5 - - - +
390B LEU* 1.3 72.7 + - + +
391B VAL* 5.6 0.5 - - - +
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Residues in contact with LEU 390 (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 ASP* 3.2 13.5 - - + +
221B MET 3.8 11.2 - - - +
222B ILE* 3.4 35.0 - - + -
343B LEU* 5.7 0.4 - - + -
371B THR* 3.5 44.2 - - + +
372B LEU 4.5 0.9 - - - +
373B LEU* 4.3 13.0 - - + -
386B ALA* 2.8 22.6 + - + +
387B LYS* 3.6 15.8 - - - +
388B SER 4.8 0.5 - - - -
389B ALA* 1.3 86.7 - - + +
391B VAL* 1.3 65.1 + - - +
392B LYS 4.1 1.5 + - - -
393B PRO* 3.8 17.5 - - + +
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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