Contacts of the helix formed by residues 273 - 284 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B GLU 3.6 8.7 + - - -
5B GLU* 3.7 1.7 - - - +
6B GLY* 2.9 27.7 + - - -
7B LYS 3.2 24.3 + - - +
8B LEU* 4.1 4.6 - - + +
59B ASP* 3.1 22.6 + - - -
271B SER* 3.1 8.1 + - - +
272B PRO* 1.3 96.9 - - - +
274B LYS* 1.3 59.4 + - - +
275B GLU* 3.3 11.7 - - - -
276B LEU* 3.1 18.2 + - + +
277B ALA* 2.9 27.7 + - - +
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Residues in contact with LYS 274 (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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78B ALA* 3.8 24.2 - - + -
267B ILE* 4.1 25.7 - - + +
268B ASN 3.6 1.7 + - - +
269B ALA* 2.5 36.5 + - - +
270B ALA 3.9 0.6 - - - -
271B SER* 2.7 30.6 + - - +
272B PRO 3.7 1.4 - - - -
273B ASN* 1.3 76.0 - - - +
275B GLU* 1.3 68.5 + - - +
277B ALA* 3.1 4.9 + - - +
278B LYS* 3.0 21.9 + - - +
427B PRO* 4.3 6.5 - - - +
428B ALA 5.5 2.5 - - - +
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Residues in contact with GLU 275 (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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272B PRO 3.6 7.9 - - - +
273B ASN* 3.3 23.1 - - - -
274B LYS* 1.3 83.3 + - - +
276B LEU* 1.3 73.4 + - + +
278B LYS* 3.2 10.1 + - - +
279B GLU* 3.1 36.2 + - + +
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Residues in contact with LEU 276 (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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6B GLY* 4.7 6.3 - - - -
7B LYS 4.8 0.7 - - - +
8B LEU* 4.0 12.3 - - + +
28B PHE* 4.0 14.4 - - + -
34B ILE* 3.6 48.2 - - + -
273B ASN* 3.1 34.4 + - + +
275B GLU* 1.3 94.6 - - + +
277B ALA* 1.3 60.3 + - - +
279B GLU* 3.3 18.4 + - - +
280B PHE* 3.1 23.7 + - - +
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Residues in contact with ALA 277 (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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8B LEU* 4.0 8.9 - - + +
59B ASP* 5.1 1.3 - - + +
60B ILE* 3.6 31.0 - - + -
267B ILE* 3.7 24.2 - - + -
271B SER* 5.8 0.2 - - - +
273B ASN 2.9 12.7 + - - +
274B LYS 3.1 8.9 + - - +
276B LEU* 1.3 76.3 - - - +
278B LYS* 1.3 57.7 + - - +
280B PHE* 3.8 1.5 - - - +
281B LEU* 3.0 35.5 + - - +
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Residues in contact with LYS 278 (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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81B THR* 2.9 36.1 + - - +
82B PRO* 5.0 0.6 - - - +
83B ALA 5.4 1.0 - - - +
107B TYR* 3.7 19.1 - - - +
267B ILE* 4.2 6.9 - - + +
274B LYS 3.0 12.3 + - - +
275B GLU* 3.2 12.3 + - - +
277B ALA* 1.3 75.5 - - - +
279B GLU* 1.3 62.9 + - + +
281B LEU* 4.8 1.3 - - - -
282B GLU* 2.9 56.9 + - + +
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Residues in contact with GLU 279 (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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28B PHE* 4.3 12.0 - - + -
32B THR* 5.5 4.0 - - - +
275B GLU* 3.1 26.5 + - + +
276B LEU* 3.3 22.4 + - - +
278B LYS* 1.3 79.0 - - + +
280B PHE* 1.3 59.6 + - - +
283B ASN* 3.0 50.4 + - + +
284B TYR* 3.6 4.5 - - + -
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Residues in contact with PHE 280 (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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8B LEU* 4.1 11.4 - - + -
10B ILE* 4.5 15.5 - - + -
21B LEU* 4.2 27.4 - - + -
24B VAL* 3.7 36.1 - - + -
25B GLY* 3.8 15.7 - - - -
28B PHE* 3.7 32.2 - + + -
36B VAL* 4.6 7.6 - - + -
60B ILE* 4.2 9.6 - - + -
62B PHE* 5.4 1.3 - + - -
276B LEU 3.1 17.0 + - - +
277B ALA 3.8 2.9 - - - +
279B GLU* 1.3 78.3 - - - +
281B LEU* 1.3 78.5 + - + +
284B TYR* 3.1 10.3 + - + +
285B LEU* 2.8 30.9 + - + +
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Residues in contact with LEU 281 (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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60B ILE* 3.8 26.5 - - + -
62B PHE* 4.2 4.3 - - + -
107B TYR* 3.5 39.0 - - + -
109B ILE* 5.4 0.7 - - + -
265B ALA* 3.9 24.5 - - + +
267B ILE* 4.0 12.8 - - + -
277B ALA 3.0 20.7 + - - +
278B LYS 4.3 1.3 - - - +
280B PHE* 1.3 82.9 - - + +
282B GLU* 1.3 59.3 + - - +
285B LEU* 3.6 28.0 - - + -
286B LEU* 3.1 36.9 + - + +
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Residues in contact with GLU 282 (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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82B PRO* 3.7 13.7 - - - +
83B ALA* 5.1 1.7 + - - +
86B PHE* 3.6 46.4 - - + +
107B TYR* 2.6 43.2 + - + +
278B LYS* 2.9 42.9 + - + +
281B LEU* 1.3 78.2 - - - +
283B ASN* 1.3 71.1 + - - +
284B TYR 3.6 0.2 - - - -
286B LEU 3.7 13.0 - - - +
287B THR* 4.3 1.9 - - - +
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Residues in contact with ASN 283 (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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86B PHE* 5.9 0.3 - - - -
279B GLU* 3.0 31.8 + - - +
282B GLU* 1.3 90.7 - - - +
284B TYR* 1.3 73.5 + - + +
287B THR* 3.3 18.0 - - - +
289B GLU* 5.0 1.7 - - - +
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Residues in contact with TYR 284 (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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24B VAL* 3.6 12.8 - - + +
27B LYS* 4.1 11.0 - - + -
28B PHE* 3.5 53.4 - + + -
31B ASP* 3.1 32.4 - - + +
32B THR* 3.9 5.7 - - + +
279B GLU* 3.6 14.1 - - + -
280B PHE* 3.1 20.4 + - + +
283B ASN* 1.3 92.7 - - + +
285B LEU* 1.3 62.6 + - - +
287B THR* 3.1 18.7 + - - -
289B GLU* 5.1 1.4 - - - +
290B GLY* 3.3 11.4 - - - -
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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