Contacts of the helix formed by residues 278 - 288 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191D ILE* 3.4 29.5 - - + +
197D LEU* 3.8 25.0 - - + +
198D VAL* 5.0 2.3 + - - +
274D LEU* 3.8 16.7 - - + +
275D TYR* 2.8 39.4 + - + +
277D TYR* 1.3 69.8 - - - +
279D GLN* 1.3 62.7 + - - +
280D ALA 3.5 0.7 - - - -
281D GLN* 3.4 15.2 + - - +
282D TYR* 3.3 19.8 + - - +
451D TYR* 5.2 0.5 + - - -
455D HIS* 3.0 17.1 + - - -
458D ARG* 2.5 34.6 + - - -
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Residues in contact with GLN 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D PRO 5.0 6.6 + - - +
274D LEU* 3.5 37.0 + - - +
275D TYR 3.8 4.6 + - - -
276D PRO* 3.2 24.0 - - + +
277D TYR 3.1 1.6 - - - -
278D GLU* 1.3 76.2 - - - +
280D ALA* 1.3 67.0 + - - +
282D TYR* 3.2 8.8 + - - +
283D LYS* 3.2 26.1 + - + +
588H ASN* 4.3 13.5 + - - -
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Residues in contact with ALA 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D TYR 4.1 7.2 + - - +
278D GLU 3.5 0.2 - - - -
279D GLN* 1.3 78.4 - - - +
281D GLN* 1.3 61.9 + - - +
283D LYS* 3.6 10.6 + - - +
284D LYS* 3.1 39.5 + - + +
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Residues in contact with GLN 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D LEU* 3.9 41.0 - - + +
198D VAL* 3.0 28.7 + - - +
199D LYS* 4.9 0.6 - - - +
200D LEU* 3.5 34.2 - - + +
277D TYR 4.9 0.8 + - - -
278D GLU* 3.4 20.9 + - - +
279D GLN 3.2 0.2 - - - -
280D ALA* 1.3 78.7 - - - +
282D TYR* 1.3 58.6 + - - +
284D LYS* 3.3 7.2 + - - +
285D VAL* 2.9 36.5 + - + +
451D TYR* 4.9 4.0 + - - +
455D HIS* 5.6 1.2 + - - -
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Residues in contact with TYR 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D LEU* 3.8 18.2 - - + -
270D PRO* 3.3 39.2 - - + +
274D LEU* 3.7 21.5 - - + -
278D GLU 3.3 2.2 + - - +
279D GLN* 3.2 12.6 + - - +
281D GLN* 1.3 75.3 - - - +
283D LYS* 1.3 73.7 + - + +
285D VAL* 3.2 3.4 + - + +
286D THR* 3.1 58.2 + - + +
447D PRO* 4.6 12.3 - - + +
451D TYR* 3.7 24.6 + + - +
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Residues in contact with LYS 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D GLN* 3.2 12.6 + - + +
280D ALA* 3.7 12.3 - - - +
282D TYR* 1.3 86.1 - - + +
284D LYS* 1.3 63.7 + - + +
286D THR* 3.6 5.0 + - - -
287D SER* 3.3 23.4 + - - -
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Residues in contact with LYS 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D ALA* 3.1 29.6 + - + +
281D GLN* 3.7 6.3 - - - +
283D LYS* 1.3 78.0 - - + +
285D VAL* 1.3 65.7 + - + +
287D SER* 3.6 10.7 + - - -
288D SER* 3.7 13.5 + - - -
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Residues in contact with VAL 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D LEU* 4.1 34.3 - - + +
201D PRO* 6.1 0.9 - - + -
281D GLN* 2.9 23.8 + - + +
282D TYR* 3.2 3.6 + - - +
284D LYS* 1.3 78.7 - - + +
286D THR* 1.3 68.3 + - + +
288D SER* 3.4 20.1 + - - +
445D PRO* 5.1 1.4 - - - +
450D ILE* 3.5 41.7 - - + +
451D TYR* 5.0 4.9 - - + +
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Residues in contact with THR 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282D TYR* 3.1 55.7 + - + +
283D LYS* 3.6 5.0 + - - -
285D VAL* 1.3 80.9 - - + +
287D SER* 1.3 64.8 + - - +
288D SER 3.3 7.4 + - - +
444D PRO* 3.9 30.5 - - + +
445D PRO* 4.5 17.0 - - - +
447D PRO* 5.8 2.7 - - + -
450D ILE* 4.8 4.3 - - + -
451D TYR* 6.2 0.4 - - + -
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Residues in contact with SER 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D LYS 3.3 20.3 + - - -
284D LYS* 3.8 8.1 - - - -
285D VAL 3.3 0.2 - - - -
286D THR* 1.3 79.2 + - - +
288D SER* 1.3 60.8 + - - +
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Residues in contact with SER 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D LYS 3.7 10.9 + - - -
285D VAL 3.4 13.5 + - - +
286D THR 3.3 8.9 - - - +
287D SER* 1.3 81.8 + - - +
443D GLN 5.0 1.4 - - - +
445D PRO* 3.9 21.5 - - - +
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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