Contacts of the helix formed by residues 273 - 284 (chain C) in PDB entry 5YGP
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 ASN 273 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323B GLU* 4.1 1.0 - - - +
327B LYS* 3.4 18.3 + - - +
6C GLY 3.5 22.0 + - - +
7C LYS 2.8 28.7 + - - -
8C LEU* 3.8 16.5 - - + +
59C ASP* 3.9 8.9 + - - +
271C SER* 3.2 11.0 + - - +
272C PRO* 1.3 102.0 - - - +
274C LYS* 1.3 65.0 + - - +
275C GLU 3.4 2.2 - - - -
276C LEU* 3.8 17.4 - - + +
277C ALA* 3.0 21.5 + - - +
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Residues in contact with LYS 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ALA* 3.7 21.3 - - + -
267C ILE* 4.1 23.2 - - + +
268C ASN 3.1 7.8 + - - +
269C ALA* 2.6 41.4 + - - +
271C SER 3.6 17.1 + - - +
272C PRO 3.7 1.4 - - - -
273C ASN* 1.3 76.0 - - - +
275C GLU* 1.3 71.4 + - - +
277C ALA* 3.1 4.7 + - - +
278C LYS* 3.0 27.4 + - - +
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Residues in contact with GLU 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B PRO* 3.9 25.7 - - - +
257B LYS* 3.6 25.3 + - - -
326B GLN* 3.5 25.9 - - - +
327B LYS* 4.1 22.7 - - + +
274C LYS* 1.3 89.1 + - - +
276C LEU* 1.3 62.8 + - - +
278C LYS* 3.4 8.6 + - - +
279C GLU* 3.1 24.9 + - - +
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Residues in contact with LEU 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B GLU* 3.8 21.8 - - - +
326B GLN* 3.4 31.0 - - + +
327B LYS* 3.8 30.7 - - + -
7C LYS 5.2 2.9 - - - +
8C LEU* 3.6 13.9 - - + +
28C PHE* 4.0 5.6 - - + -
34C ILE* 4.0 32.8 - - + -
273C ASN* 3.4 34.0 + - + +
274C LYS 3.3 0.6 - - - -
275C GLU* 1.3 77.8 - - - +
277C ALA* 1.3 57.8 + - - +
279C GLU* 3.8 0.7 + - - +
280C PHE* 3.2 26.9 + - - +
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Residues in contact with ALA 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 4.1 8.5 - - + +
59C ASP* 5.0 2.2 - - + +
60C ILE* 3.7 29.6 - - + -
267C ILE* 3.7 23.1 - - + -
273C ASN 3.0 14.5 + - - +
274C LYS 3.1 8.2 + - - +
276C LEU* 1.3 75.9 - - - +
278C LYS* 1.3 59.3 + - - +
280C PHE* 3.8 0.3 - - - +
281C LEU* 2.9 34.8 + - - +
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Residues in contact with LYS 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C THR* 2.3 46.3 + - - +
82C PRO* 4.4 1.3 - - - -
83C ALA 5.1 1.3 - - - +
107C TYR* 3.3 19.0 + - - +
267C ILE* 4.1 9.8 - - + +
274C LYS 3.0 15.1 + - - +
275C GLU* 3.8 7.9 - - - +
277C ALA* 1.3 74.8 - - - +
279C GLU* 1.3 59.7 + - - +
281C LEU* 4.7 2.0 - - - -
282C GLU* 2.8 64.0 + - - +
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Residues in contact with GLU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B PHE* 6.0 1.6 - - - -
326B GLN* 3.6 36.3 + - + +
28C PHE* 4.2 6.5 - - + -
275C GLU 3.1 16.1 + - - +
276C LEU 4.1 3.6 - - - +
278C LYS* 1.3 76.9 - - - +
280C PHE* 1.3 62.3 + - - +
282C GLU* 5.1 0.2 - - - -
283C ASN* 3.0 56.7 + - - +
284C TYR* 3.6 11.1 - - + -
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Residues in contact with PHE 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 3.8 10.3 - - + -
10C ILE* 3.6 29.8 - - + -
21C LEU* 4.6 13.9 - - + -
24C VAL* 3.9 37.0 - - + -
25C GLY* 3.9 16.4 - - - -
28C PHE* 3.7 33.1 - + + -
36C VAL* 4.3 6.1 - - + -
60C ILE* 4.0 18.4 - - + -
62C PHE* 5.6 0.7 - + - -
276C LEU 3.2 19.3 + - - +
277C ALA 3.8 2.7 - - - +
278C LYS 3.2 0.2 - - - -
279C GLU* 1.3 78.2 - - - +
281C LEU* 1.3 72.6 + - + +
284C TYR* 3.2 10.2 - - + +
285C LEU* 3.1 25.8 + - + -
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Residues in contact with LEU 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ILE* 4.1 20.2 - - + -
62C PHE* 4.0 4.9 - - + -
107C TYR* 3.5 37.2 - - + -
109C ILE* 5.0 0.2 - - + -
265C ALA* 3.8 26.9 - - + +
267C ILE* 4.2 13.9 - - + -
277C ALA 2.9 20.5 + - - +
278C LYS 4.0 1.6 - - - +
280C PHE* 1.3 85.7 - - + +
282C GLU* 1.3 58.3 + - - +
285C LEU* 3.7 28.0 - - + -
286C LEU* 3.1 41.1 + - + +
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Residues in contact with GLU 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C PRO* 3.4 13.9 - - - +
83C ALA* 5.2 1.6 + - - +
86C PHE* 3.6 43.1 - - + +
107C TYR* 2.5 43.4 + - + +
278C LYS* 2.8 46.9 + - - +
281C LEU* 1.3 74.8 - - - +
283C ASN* 1.3 74.2 + - - +
284C TYR 3.4 0.9 + - - -
286C LEU* 3.9 13.5 - - - +
287C THR* 4.3 1.6 - - - +
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Residues in contact with ASN 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 5.4 3.4 - - - -
279C GLU* 3.0 50.9 + - - +
282C GLU* 1.3 92.7 + - - +
284C TYR* 1.3 73.1 + - + +
287C THR* 3.9 12.0 - - - +
289C GLU* 5.4 0.7 - - - +
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Residues in contact with TYR 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B TYR* 6.0 0.3 - - - -
326B GLN* 5.7 0.2 - - - -
24C VAL* 3.8 15.7 - - + +
27C LYS* 3.7 25.6 - - + -
28C PHE* 3.6 49.4 - + + -
31C ASP* 3.1 34.6 + - - +
32C THR* 4.2 7.8 - - + +
279C GLU* 3.6 21.5 - - + -
280C PHE* 3.2 16.2 + - + +
282C GLU 3.4 1.4 + - - -
283C ASN* 1.3 100.1 - - + +
285C LEU* 1.3 61.9 + - - +
286C LEU 3.7 0.2 - - - -
287C THR* 2.8 24.0 + - - -
289C GLU* 5.1 1.2 - - - +
290C GLY* 3.4 9.5 - - - -
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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