Contacts of the helix formed by residues 266 - 280 (chain A) in PDB entry 2WTJ
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 PRO 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A ILE* 5.5 3.1 - - + -
252A SER 4.3 6.7 - - - +
253A LYS* 3.5 32.5 - - + +
267A ALA* 1.3 68.8 + - + +
268A LEU* 3.1 5.9 + - - -
269A ASN* 3.3 11.1 + - + +
270A VAL* 3.1 30.8 + - + +
297A TYR* 4.2 15.0 - - + -
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Residues in contact with ALA 267 (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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266A PRO* 1.3 80.7 - - + +
268A LEU* 1.3 57.3 + - - +
270A VAL* 3.9 0.4 - - - +
271A GLU* 2.8 28.9 + - - -
297A TYR* 3.4 26.6 + - - +
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Residues in contact with LEU 268 (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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266A PRO 3.2 3.6 - - - -
267A ALA* 1.3 79.8 - - - +
269A ASN* 1.3 70.0 + - - +
271A GLU* 3.8 0.9 - - - +
272A THR* 3.1 31.8 + - + +
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Residues in contact with ASN 269 (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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266A PRO* 3.3 11.2 + - + +
268A LEU* 1.3 81.9 - - - +
270A VAL* 1.3 58.6 + - + +
272A THR* 3.4 6.4 + - - -
273A GLU* 3.1 32.1 + - - +
370A GLY* 3.2 29.0 + - - +
371A HIS* 4.2 10.7 + - - -
1519A EDO 3.5 27.9 + - - -
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Residues in contact with VAL 270 (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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251A ILE* 3.8 27.1 - - + -
266A PRO 3.1 18.0 + - - +
267A ALA* 3.9 3.6 - - - +
269A ASN* 1.3 75.8 - - + +
271A GLU* 1.3 66.8 + - - +
273A GLU* 3.4 6.4 + - - +
274A ILE* 3.0 30.7 + - + +
291A PHE* 3.8 31.2 - - + -
297A TYR* 3.7 36.8 - - + -
299A ILE* 4.6 4.3 - - + -
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Residues in contact with GLU 271 (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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267A ALA 2.8 18.4 + - - -
268A LEU 3.3 1.5 + - - -
270A VAL* 1.3 77.6 - - - +
272A THR* 1.3 59.7 + - - +
274A ILE* 3.7 6.2 + - - +
275A GLU* 3.2 24.1 + - - +
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Residues in contact with THR 272 (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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268A LEU* 3.1 18.8 + - + +
269A ASN* 3.4 10.6 + - - -
271A GLU* 1.3 72.9 - - - +
273A GLU* 1.3 72.3 + - - +
275A GLU* 3.2 4.1 + - - +
276A ILE* 2.9 38.5 + - - +
369A PHE 4.4 4.3 + - - -
370A GLY 4.3 6.6 + - - -
372A SER 4.6 10.2 + - - +
374A ILE* 5.3 11.4 - - + -
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Residues in contact with GLU 273 (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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249A LYS* 2.8 32.3 + - - +
251A ILE* 4.2 11.4 - - - +
269A ASN* 3.1 14.0 + - - +
270A VAL* 3.6 6.2 - - - +
272A THR* 1.3 83.5 + - - +
274A ILE* 1.3 58.5 + - + +
276A ILE* 3.5 2.5 - - - +
277A LEU* 2.9 46.5 + - + +
299A ILE* 4.0 16.5 - - + +
368A ASP* 4.1 2.3 + - - -
369A PHE* 3.9 34.0 + - + +
370A GLY* 3.5 20.2 - - - -
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Residues in contact with ILE 274 (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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270A VAL* 3.0 22.2 + - + +
271A GLU* 4.0 5.6 - - - +
273A GLU* 1.3 78.8 - - + +
275A GLU* 1.3 59.2 + - + +
277A LEU* 3.3 5.4 + - + +
278A LYS* 2.9 60.4 + - + +
288A ILE* 3.7 20.1 - - + +
291A PHE* 3.9 29.2 - - + -
299A ILE* 3.3 39.9 - - + -
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Residues in contact with GLU 275 (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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271A GLU 3.2 16.2 + - - +
272A THR* 3.2 5.8 + - - +
274A ILE* 1.3 82.9 - - + +
276A ILE* 1.3 61.8 + - + +
278A LYS* 3.8 7.3 + - - +
279A LYS* 3.5 22.5 + - - +
374A ILE* 6.3 3.4 - - + -
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Residues in contact with ILE 276 (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 THR* 2.9 27.6 + - - +
273A GLU* 3.5 4.7 - - - +
275A GLU* 1.3 77.4 - - + +
277A LEU* 1.3 67.6 + - + +
279A LYS* 3.1 4.7 + - - +
280A LEU* 3.1 46.8 + - + +
343A ILE* 3.8 22.7 - - + -
369A PHE* 4.1 19.3 - - + +
372A SER* 3.6 32.3 - - - +
374A ILE* 4.5 25.4 - - + -
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Residues in contact with LEU 277 (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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273A GLU* 2.9 40.0 + - + +
274A ILE* 4.0 5.6 - - + +
276A ILE* 1.3 78.6 - - + +
278A LYS* 1.3 62.7 + - - +
279A LYS 3.3 0.5 + - - -
280A LEU* 3.5 17.7 + - + +
285A ILE* 4.3 5.8 - - + -
286A ILE* 3.2 46.0 - - + +
287A LYS* 5.2 2.3 - - - +
288A ILE* 4.2 25.1 + - + +
299A ILE* 5.2 5.2 - - + -
301A LEU* 4.4 16.2 - - + -
367A THR* 5.6 1.6 - - - +
368A ASP 5.8 0.4 - - - +
369A PHE* 3.8 28.5 - - + -
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Residues in contact with LYS 278 (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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274A ILE* 2.9 45.9 + - + +
275A GLU* 4.0 7.4 - - - +
277A LEU* 1.3 77.9 - - - +
279A LYS* 1.3 59.3 + - - +
280A LEU 4.2 2.8 - - - +
288A ILE* 3.8 19.5 - - + -
291A PHE* 5.6 4.5 - - - +
1517A EDO 3.0 34.9 + - - -
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Residues in contact with LYS 279 (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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275A GLU 3.5 14.2 + - - +
276A ILE* 3.1 5.8 + - - +
278A LYS* 1.3 78.5 - - + +
280A LEU* 1.3 66.6 + - + +
281A ASN* 3.9 3.1 + - - +
337A TYR* 4.5 2.1 + - - -
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Residues in contact with LEU 280 (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 ILE* 3.1 37.1 + - + +
277A LEU* 3.5 13.9 - - - +
278A LYS 3.4 3.5 - - - +
279A LYS* 1.3 85.3 - - + +
281A ASN* 1.3 61.4 + - - +
282A HIS 4.2 0.9 - - - -
285A ILE* 4.5 21.3 - - + -
287A LYS* 5.0 8.1 + - - +
337A TYR* 3.5 26.7 - - + +
338A LEU* 3.5 27.6 - - + -
341A ASN* 4.2 14.1 - - + +
343A ILE* 3.6 19.3 - - + -
369A PHE* 4.5 1.8 - - + -
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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