Contacts of the helix formed by residues 274 - 291 (chain A) in PDB entry 6KJV
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 TRP 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ASN* 3.1 39.9 + - - -
185A ALA* 4.3 13.0 - - + -
186A SER* 3.9 26.5 - - - -
189A LEU* 4.8 14.6 - - + -
235A TYR* 2.4 61.6 + + - +
236A CYS* 5.8 1.1 - - - -
239A ALA* 3.9 20.4 - - + -
243A TRP* 3.1 29.9 - + - +
270A VAL* 3.3 17.7 + - + +
273A GLY* 1.3 75.2 - - - +
275A GLY* 1.3 64.9 + - - +
276A VAL 3.7 0.4 - - - -
277A PRO* 3.9 1.6 - - - -
278A LEU* 4.0 4.7 + - - +
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Residues in contact with GLY 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A VAL 3.6 3.4 + - - -
271A ALA* 3.1 19.7 + - - -
274A TRP* 1.3 77.6 - - - +
276A VAL* 1.3 64.1 + - - +
278A LEU* 3.1 25.6 + - - +
279A LEU* 3.5 6.7 + - - +
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Residues in contact with VAL 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A TYR* 3.9 31.4 - - + +
271A ALA 3.1 13.7 + - - +
272A ILE* 3.5 25.6 - - + +
275A GLY* 1.3 71.7 - - - +
277A PRO* 1.3 68.3 - - + +
279A LEU* 2.8 32.9 + - + +
280A PHE* 3.3 12.7 - - + -
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Residues in contact with PRO 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A TYR* 3.8 18.6 - - + -
238A ALA* 3.6 37.5 - - + +
239A ALA* 3.9 2.5 - - - +
242A TYR* 4.2 5.8 - - + -
272A ILE 3.2 15.9 - - - +
273A GLY 3.2 21.3 - - - +
274A TRP* 3.9 1.6 - - - +
275A GLY 3.6 2.5 - - - -
276A VAL* 1.3 89.0 - - + +
278A LEU* 1.3 57.3 + - - +
279A LEU 3.0 0.7 + - - -
280A PHE* 3.3 14.2 + - + -
281A VAL* 2.9 35.9 + - - +
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A TYR* 3.7 22.3 - - + +
274A TRP 4.0 9.9 - - - +
275A GLY* 3.1 18.4 + - - +
277A PRO* 1.3 78.1 - - - +
279A LEU* 1.3 57.8 + - - +
280A PHE 3.4 0.6 + - - -
281A VAL* 4.2 0.7 - - - -
282A VAL* 3.4 50.7 + - + +
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLY 3.5 3.3 + - - +
276A VAL* 2.8 31.2 + - + +
278A LEU* 1.3 79.7 - - - +
280A PHE* 1.3 63.0 + - + +
282A VAL* 5.4 0.2 - - - -
283A PRO* 3.7 15.3 - - - +
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Residues in contact with PHE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ALA* 3.6 30.7 - - + -
242A TYR* 3.8 22.2 - + - -
276A VAL* 3.3 24.0 - - + -
277A PRO* 3.6 6.5 - - + -
279A LEU* 1.3 82.1 - - + +
281A VAL* 1.3 68.8 + - + +
283A PRO* 3.5 12.9 - - - +
284A TRP* 3.7 13.7 + - - +
308A ILE* 3.7 21.4 - - + +
309A ILE* 3.9 25.2 - - + +
312A PRO* 3.6 39.9 - - + -
313A ILE* 4.5 5.6 - - + -
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 3.6 35.1 - - + +
234A GLN* 4.4 7.4 - - + +
235A TYR* 4.2 28.5 - - + +
238A ALA* 4.3 6.5 - - + -
277A PRO 2.9 25.0 + - - +
278A LEU* 4.8 2.5 - - - -
280A PHE* 1.3 87.0 - - + +
282A VAL* 1.3 63.7 + - + +
284A TRP* 3.2 8.4 + - + +
285A GLY 3.0 22.0 + - - -
309A ILE* 3.8 21.5 - - + -
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 5.2 9.6 - - + -
278A LEU* 3.4 43.3 + - + +
279A LEU 5.3 0.4 - - - +
281A VAL* 1.3 78.9 - - + +
283A PRO* 1.3 73.5 - - + +
285A GLY* 3.2 3.5 + - - +
286A ILE* 2.9 39.5 + - + +
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Residues in contact with PRO 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU 3.7 16.8 - - - +
280A PHE* 3.5 19.1 - - - +
282A VAL* 1.3 101.1 - - + +
284A TRP* 1.3 55.2 + - - +
286A ILE* 3.2 12.4 + - + +
287A VAL* 2.9 36.7 + - + +
308A ILE* 4.4 6.7 - - + -
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Residues in contact with TRP 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PHE* 3.3 38.8 - + - -
231A LEU* 3.5 28.9 - - + -
234A GLN* 4.3 24.2 - - + -
280A PHE 3.7 12.0 + - - +
281A VAL 3.2 9.1 + - - +
282A VAL 3.2 0.4 - - - -
283A PRO* 1.3 77.9 - - - +
285A GLY* 1.3 71.9 + - - +
287A VAL* 3.2 1.6 - - - +
288A LYS* 2.9 64.8 + - + +
297A TRP* 3.9 16.2 - + + -
300A ASN* 5.6 5.7 - - + +
305A TYR* 3.1 28.8 + - + -
306A TRP* 5.2 1.4 - - - +
308A ILE* 3.7 17.1 - - + +
309A ILE* 4.1 28.2 - - + +
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Residues in contact with GLY 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 4.2 14.8 - - - -
281A VAL 3.0 13.1 + - - -
282A VAL 3.2 3.7 + - - -
284A TRP* 1.3 89.0 - - - +
286A ILE* 1.3 57.3 + - - +
288A LYS* 3.4 3.3 + - - +
289A TYR* 2.9 31.9 + - - +
297A TRP* 4.4 10.1 - - - -
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Residues in contact with ILE 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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282A VAL* 2.9 27.7 + - + +
283A PRO* 3.6 14.4 - - + +
284A TRP 3.2 0.2 - - - -
285A GLY* 1.3 76.2 - - - +
287A VAL* 1.3 64.1 + - + +
289A TYR* 3.2 5.0 + - - +
290A LEU* 3.0 48.3 + - + +
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PRO* 2.9 20.9 + - + +
284A TRP* 3.2 21.3 - - - +
286A ILE* 1.3 81.8 - - + +
288A LYS* 1.3 58.7 + - - +
291A TYR* 2.9 42.8 + - + +
292A GLU* 3.4 4.5 + - - +
305A TYR* 3.6 45.4 - - + -
308A ILE* 3.8 10.3 - - + -
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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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284A TRP* 2.9 49.9 + - + +
285A GLY 4.0 1.8 - - - +
287A VAL* 1.3 78.4 - - + +
289A TYR* 1.3 59.8 + - - +
292A GLU* 2.5 72.5 + - + +
293A ASP* 3.3 0.7 + - - -
297A TRP* 3.2 52.0 + - + +
299A ARG 3.7 4.9 + - - -
300A ASN* 3.5 27.6 - - + +
305A TYR* 4.2 13.5 - - + -
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Residues in contact with TYR 289 (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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224A LEU* 4.3 25.7 - - + +
227A ARG* 5.3 3.6 - - - -
285A GLY 2.9 19.4 + - - +
286A ILE* 3.2 4.7 + - - +
288A LYS* 1.3 79.8 - - - +
290A LEU* 1.3 80.4 + - + +
293A ASP* 3.7 27.0 - - - +
297A TRP* 4.0 20.8 - + + +
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Residues in contact with LEU 290 (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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286A ILE* 3.0 34.0 + - + +
289A TYR* 1.3 100.6 - - + +
291A TYR* 1.3 92.6 + - + +
293A ASP* 5.8 0.2 - - - -
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Residues in contact with TYR 291 (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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287A VAL* 2.9 28.9 + - + +
290A LEU* 1.3 110.2 - - + +
292A GLU* 1.3 68.8 + - - +
293A ASP 4.1 1.1 - - - -
302A ASN* 4.8 2.9 + - - -
305A TYR* 4.0 27.1 - - + +
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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
------------------------------------------------------------
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