Contacts of the helix formed by residues 484 - 494 (chain A) in PDB entry 2YHS
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 LYS 484 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A ASP* 2.8 29.6 + - - -
285A PRO* 3.8 22.5 - - + +
482A PRO* 3.4 11.1 + - + +
483A PHE* 1.3 83.6 - - - +
485A ALA* 1.3 65.4 + - - +
486A ASP* 3.4 1.8 - - + +
487A ASP* 3.4 25.2 + - + +
488A PHE* 3.0 12.0 + - - +
1499A EDO 2.8 29.2 + - - +
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Residues in contact with ALA 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A GLY 4.7 2.0 - - - +
279A LEU* 3.7 40.4 - - + +
280A ALA* 3.7 12.1 - - + +
283A ASP* 2.8 19.2 + - + +
483A PHE* 3.7 15.7 - - + -
484A LYS* 1.3 70.6 - - - +
486A ASP* 1.3 65.7 + - - +
488A PHE* 3.3 2.1 + - - +
489A ILE* 2.9 29.1 + - - +
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Residues in contact with ASP 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A GLY* 5.4 4.0 - - - +
280A ALA* 5.3 6.2 - - - +
283A ASP* 4.5 1.0 + - - -
484A LYS* 3.4 1.8 - - + +
485A ALA* 1.3 78.9 - - - +
487A ASP* 1.3 62.8 + - - +
489A ILE* 3.5 6.5 + - - +
490A GLU* 2.9 36.9 + - + +
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Residues in contact with ASP 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LYS* 5.2 3.3 - - - -
195A PHE* 4.7 12.2 - - + -
196A PHE* 3.3 37.9 - - + -
199A LEU* 4.0 0.8 - - - +
484A LYS* 3.4 24.7 + - + +
485A ALA 3.3 0.6 - - - -
486A ASP* 1.3 77.0 - - - +
488A PHE* 1.3 66.1 + - - +
490A GLU* 4.4 0.9 - - - +
491A ALA* 3.0 21.5 + - - +
1499A EDO 4.0 15.0 + - - -
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Residues in contact with PHE 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A LEU* 4.5 5.2 - - + -
203A LEU* 3.9 29.1 - - + +
206A THR* 5.9 1.8 - - + -
279A LEU* 3.4 29.4 - - + -
448A LEU* 3.6 32.1 - - + -
454A GLY 5.3 2.9 - - - -
457A ILE* 3.9 20.2 - - + -
458A PHE* 4.2 0.9 - + - -
471A ILE* 3.7 18.6 - - + -
483A PHE* 3.8 10.1 - + + -
484A LYS 3.0 18.3 + - - +
485A ALA 3.3 3.3 + - - +
487A ASP* 1.3 76.0 - - - +
489A ILE* 1.3 59.1 + - - +
491A ALA* 3.3 3.5 + - - +
492A LEU* 2.9 51.8 + - + +
1499A EDO 3.6 10.9 - - - +
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Residues in contact with ILE 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LYS* 3.5 38.8 - - + +
275A MET 3.8 6.7 - - - -
276A GLY* 3.6 34.8 - - - +
279A LEU* 3.9 20.6 - - + -
458A PHE* 4.1 8.5 - - + -
485A ALA 2.9 21.0 + - - +
486A ASP* 3.8 5.8 - - - +
488A PHE* 1.3 77.0 - - - +
490A GLU* 1.3 62.4 + - - +
492A LEU* 3.2 3.9 + - + -
493A PHE* 2.9 41.1 + - + +
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Residues in contact with GLU 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LYS* 6.4 0.7 - - - -
196A PHE* 3.7 19.1 - - + -
272A LYS* 2.8 34.7 + - - +
486A ASP* 2.9 25.8 + - + +
487A ASP* 3.6 5.8 - - - +
489A ILE* 1.3 74.9 - - - +
491A ALA* 1.3 58.4 + - - +
493A PHE 3.8 0.2 - - - -
494A ALA* 2.8 38.0 + - - +
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Residues in contact with ALA 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A PHE* 4.0 8.4 - - + -
199A LEU* 3.6 30.3 - - + -
200A LYS* 3.6 24.8 - - + +
203A LEU* 4.2 7.6 - - + -
207A LYS* 2.8 28.8 + - - +
487A ASP 3.0 15.7 + - - +
488A PHE 3.7 3.1 - - - +
490A GLU* 1.3 75.1 - - - +
492A LEU* 1.3 59.8 + - - +
493A PHE 3.4 0.2 + - - -
494A ALA* 3.7 1.5 + - - -
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Residues in contact with LEU 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LEU* 4.4 11.2 - - + +
206A THR* 3.7 29.8 - - + -
207A LYS* 2.9 34.1 + - + +
210A LEU* 4.2 15.5 - - + +
211A GLY* 3.4 10.5 - - - +
212A SER* 3.0 14.0 + - - -
275A MET* 5.3 0.4 - - + -
458A PHE* 3.7 35.7 - - + -
488A PHE* 2.9 30.7 + - + +
489A ILE* 3.2 5.1 + - + +
491A ALA* 1.3 76.4 - - - +
493A PHE* 1.3 71.7 + - + +
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Residues in contact with PHE 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLY* 3.7 19.5 - - - -
212A SER* 3.7 8.8 - - - +
214A PHE* 3.8 29.2 - + - -
268A TYR* 2.5 53.1 + + + +
271A LEU 4.0 0.9 - - - -
272A LYS* 3.4 52.7 - - + -
275A MET* 4.0 13.7 - - - -
489A ILE* 2.9 40.3 + - + +
492A LEU* 1.3 96.9 - - + +
494A ALA* 1.3 63.4 + - - +
495A ARG* 3.3 2.9 + - - +
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Residues in contact with ALA 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A PHE* 6.5 0.2 - - + -
200A LYS* 3.7 27.2 - - + +
207A LYS* 2.6 29.1 + - - -
212A SER* 4.1 0.2 - - - -
268A TYR* 4.5 1.8 - - - -
272A LYS* 5.9 0.2 - - - +
490A GLU* 2.8 22.5 + - - +
491A ALA* 3.7 1.3 + - - +
492A LEU 3.5 0.6 - - - -
493A PHE* 1.3 75.9 - - - +
495A ARG* 1.3 63.0 + - - +
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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