Contacts of the helix formed by residues 277 - 288 (chain A) in PDB entry 4X4W
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 GLN 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A VAL* 1.3 72.9 - - - +
278A ASP* 1.3 61.0 + - - +
280A VAL* 2.8 29.7 + - - +
281A THR* 3.4 8.9 + - + +
298A LEU* 3.9 39.3 - - + +
301A VAL* 3.6 16.9 - - + +
302A LYS* 3.9 29.3 - - - +
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Residues in contact with ASP 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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276A VAL* 3.2 15.6 - - + +
277A GLN* 1.3 79.7 - - - +
279A ASP* 1.3 59.3 + - - +
281A THR* 3.3 15.2 + - - +
282A LYS* 2.9 43.8 + - + +
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Residues in contact with ASP 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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242A GLY 5.2 0.5 - - - +
244A PRO* 4.1 25.4 - - + +
274A PHE* 3.5 26.9 - - + -
275A LYS* 2.9 31.0 + - - +
276A VAL* 3.0 22.0 + - - +
278A ASP* 1.3 76.1 - - - +
280A VAL* 1.3 61.6 + - - +
282A LYS* 3.9 21.5 + - - +
283A LEU* 3.0 26.9 + - - +
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Residues in contact with VAL 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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267A VAL* 6.1 0.2 - - + -
274A PHE* 3.4 34.1 - - + -
276A VAL 4.6 0.2 - - - +
277A GLN* 2.8 13.2 + - - +
279A ASP* 1.3 76.4 - - - +
281A THR* 1.3 66.0 + - - +
283A LEU* 3.0 5.1 + - + +
284A ASP* 2.9 22.7 + - - +
289A ILE* 5.1 4.5 - - + -
293A GLU 5.3 0.2 - - - +
294A LYS* 3.5 39.3 - - + +
297A GLY* 3.8 22.9 - - - +
298A LEU* 3.7 15.7 - - + +
301A VAL* 4.1 8.3 - - + -
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Residues in contact with THR 281 (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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277A GLN* 3.6 15.5 - - + +
278A ASP* 3.3 19.8 + - - +
279A ASP 3.3 0.2 - - - -
280A VAL* 1.3 77.0 - - + +
282A LYS* 1.3 65.0 + - - +
284A ASP* 3.4 8.4 + - - +
285A LEU* 3.1 23.4 + - - +
294A LYS* 5.8 6.3 - - + -
298A LEU* 4.4 14.6 - - + -
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Residues in contact with LYS 282 (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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242A GLY* 4.9 3.2 - - - +
278A ASP* 2.9 30.2 + - + +
279A ASP* 3.9 21.9 + - - +
281A THR* 1.3 79.3 + - - +
283A LEU* 1.3 63.5 + - - +
285A LEU* 3.4 9.6 + - + +
286A ARG* 3.4 20.6 + - - +
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Residues in contact with LEU 283 (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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213A TRP* 5.0 2.9 - - + -
242A GLY 3.3 28.0 + - - +
243A LEU* 4.0 11.7 - - + -
267A VAL* 5.7 2.5 - - + -
270A LEU* 3.9 31.0 - - + -
274A PHE* 4.0 17.7 - - + -
279A ASP 3.0 16.6 + - - +
280A VAL* 3.0 6.3 + - + +
282A LYS* 1.3 76.5 - - - +
284A ASP* 1.3 51.3 + - - +
286A ARG* 3.3 3.5 + - - +
287A LEU* 2.7 56.2 + - + +
289A ILE* 4.0 31.2 - - + -
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Residues in contact with ASP 284 (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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280A VAL 2.9 12.9 + - - +
281A THR* 3.5 12.8 - - - +
283A LEU* 1.3 76.2 - - - +
285A LEU* 1.3 61.1 + - - +
288A LYS* 2.7 32.2 + - - +
289A ILE* 3.0 46.4 + - + +
294A LYS* 3.4 27.5 + - + +
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Residues in contact with LEU 285 (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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281A THR 3.1 16.1 + - - +
282A LYS* 3.7 10.1 - - + +
283A LEU 3.3 0.4 - - - -
284A ASP* 1.3 77.1 - - - +
286A ARG* 1.3 60.2 + - - +
288A LYS* 3.5 18.9 - - - +
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Residues in contact with ARG 286 (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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204A LEU 2.9 22.8 + - - -
205A ALA* 3.7 13.6 + - - +
207A ILE 3.1 17.8 + - - -
208A SER* 4.7 0.2 - - - +
209A GLY* 3.3 35.7 + - - +
212A ILE* 3.2 12.9 - - - +
239A PRO 5.6 0.2 + - - -
240A TYR 2.8 30.5 + - - -
242A GLY* 3.7 26.7 - - - +
282A LYS 3.4 8.8 + - - +
283A LEU 3.3 6.4 + - - +
284A ASP 3.1 0.2 - - - -
285A LEU* 1.3 82.1 - - - +
287A LEU* 1.3 68.2 + - + +
288A LYS* 3.5 4.7 + - - +
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Residues in contact with LEU 287 (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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209A GLY* 3.6 28.3 - - - +
210A GLU* 4.1 2.1 + - - +
212A ILE* 3.6 27.6 - - + -
213A TRP* 3.7 37.5 - - + +
216A LEU* 4.0 9.9 - - + -
241A ILE 3.6 22.9 - - - +
283A LEU* 2.7 38.8 + - + +
286A ARG* 1.3 86.0 - - + +
288A LYS* 1.3 70.7 + - - +
289A ILE* 3.4 12.8 + - + +
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Residues in contact with LYS 288 (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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209A GLY* 5.0 1.8 - - - +
210A GLU* 3.9 35.2 + - + +
213A TRP* 5.1 1.4 - - - -
284A ASP* 2.7 24.5 + - - +
285A LEU* 3.5 26.0 - - - +
286A ARG 4.1 6.7 - - - +
287A LEU* 1.3 75.7 - - - +
289A ILE* 1.3 64.3 + - - +
290A ALA 4.0 0.2 + - - -
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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