Contacts of the helix formed by residues 278 - 288 (chain B) in PDB entry 2Y0N
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 GLU 278 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191B ILE* 3.4 28.0 - - + +
197B LEU* 3.8 25.0 - - + +
198B VAL* 5.1 2.9 + - - +
274B LEU* 3.8 17.2 - - + +
275B TYR* 2.8 39.8 + - - +
277B TYR* 1.3 69.8 - - - +
279B GLN* 1.3 62.0 + - - +
280B ALA 3.5 0.9 - - - -
281B GLN* 3.5 15.2 + - - +
282B TYR* 3.3 19.2 + - - +
451B TYR* 5.2 0.9 + - - -
455B HIS* 3.0 17.0 + - - -
458B ARG* 2.6 34.0 + - - -
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Residues in contact with GLN 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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270B PRO 5.0 6.5 + - - +
274B LEU* 3.5 37.0 - - - +
275B TYR 3.9 4.0 + - - -
276B PRO* 3.2 23.6 - - + +
277B TYR 3.1 2.0 - - - -
278B GLU* 1.3 75.2 - - - +
280B ALA* 1.3 66.6 + - - +
282B TYR* 3.2 9.2 + - - +
283B LYS* 3.2 25.4 + - + +
588F ASN* 4.2 15.7 + - - +
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Residues in contact with ALA 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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277B TYR 4.1 6.3 + - - +
278B GLU 3.5 0.4 - - - -
279B GLN* 1.3 77.4 - - - +
281B GLN* 1.3 62.7 + - - +
283B LYS* 3.6 10.3 + - - +
284B LYS* 3.1 38.2 + - - +
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Residues in contact with GLN 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU* 3.8 40.4 - - + +
198B VAL* 3.0 27.1 + - - +
199B LYS* 4.9 0.6 - - - +
200B LEU* 3.5 35.6 - - + +
277B TYR 4.9 0.8 + - - +
278B GLU* 3.5 20.8 + - - +
279B GLN 3.2 0.4 - - - -
280B ALA* 1.3 77.9 - - - +
282B TYR* 1.3 57.7 + - - +
284B LYS* 3.3 7.7 + - - +
285B VAL* 2.9 37.4 + - + +
451B TYR* 4.9 4.0 + - - +
455B HIS* 5.6 0.9 + - - -
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Residues in contact with TYR 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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269B LEU* 3.9 19.1 - - + -
270B PRO* 3.3 38.4 - - + +
274B LEU* 3.7 23.8 - - + -
278B GLU 3.3 1.8 + - - +
279B GLN* 3.2 12.4 + - - +
281B GLN* 1.3 75.3 - - - +
283B LYS* 1.3 73.0 + - + +
285B VAL* 3.2 3.1 + - + -
286B THR* 3.1 58.6 + - + +
447B PRO* 4.5 11.5 - - + +
451B TYR* 3.7 24.4 + + - +
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Residues in contact with LYS 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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279B GLN* 3.2 12.4 + - + +
280B ALA* 3.7 12.6 - - - +
281B GLN 3.4 0.2 - - - -
282B TYR* 1.3 86.5 - - + +
284B LYS* 1.3 63.7 + - + +
286B THR* 3.6 5.7 + - - -
287B SER* 3.3 23.9 + - - -
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Residues in contact with LYS 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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280B ALA* 3.1 26.5 + - + +
281B GLN* 3.7 5.8 - - - +
282B TYR 3.3 0.2 - - - -
283B LYS* 1.3 80.7 - - + +
285B VAL* 1.3 63.5 + - + +
287B SER* 3.6 11.8 + - - -
288B SER* 3.6 13.5 + - - -
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Residues in contact with VAL 285 (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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200B LEU* 4.1 33.0 - - + +
201B PRO* 6.1 1.1 - - + -
281B GLN* 2.9 24.5 + - + +
282B TYR* 3.2 4.2 + - - +
284B LYS* 1.3 77.7 - - + +
286B THR* 1.3 67.5 + - + +
287B SER 3.5 0.3 + - - -
288B SER* 3.5 19.3 + - - +
445B PRO* 5.0 1.0 - - - +
450B ILE* 3.5 42.5 - - + +
451B TYR* 4.9 6.5 - - + +
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Residues in contact with THR 286 (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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282B TYR* 3.1 56.3 + - + +
283B LYS* 3.6 5.4 + - - -
285B VAL* 1.3 79.4 - - + +
287B SER* 1.3 63.5 + - - +
288B SER 3.3 6.4 - - - +
444B PRO* 3.9 30.2 - - + +
445B PRO* 4.5 16.2 - - - +
447B PRO* 5.7 3.6 - - + -
450B ILE* 4.9 4.5 - - + -
451B TYR* 6.2 0.4 - - + -
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Residues in contact with SER 287 (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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283B LYS 3.3 20.3 + - - -
284B LYS* 3.8 7.4 - - - -
285B VAL 3.3 0.4 - - - -
286B THR* 1.3 79.0 + - - +
288B SER* 1.3 58.9 + - - +
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Residues in contact with SER 288 (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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284B LYS 3.6 9.9 + - - -
285B VAL* 3.5 13.8 + - - +
286B THR 3.3 9.8 - - - +
287B SER* 1.3 81.5 + - - +
443B GLN 5.1 0.9 - - - +
445B PRO* 3.9 20.8 - - - +
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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