Contacts of the helix formed by residues 269 - 286 (chain A) in PDB entry 3J8B
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 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A PRO 3.3 5.1 - - - +
268A LYS* 1.3 71.2 - - - +
270A GLN* 1.3 61.6 + - - +
272A MET* 3.8 8.0 - - + +
273A ALA* 3.0 27.5 + - - +
302A LEU* 5.7 8.5 - - + +
306A MET* 5.5 12.1 - - + -
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Residues in contact with GLN 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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268A LYS* 3.1 7.8 - - + +
269A PRO* 1.3 82.4 - - - +
271A LEU* 1.3 62.9 + - - +
272A MET 3.2 0.2 + - - -
273A ALA* 3.4 4.8 + - - +
274A ASN* 3.3 18.9 + - - +
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Residues in contact with LEU 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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234A LEU* 5.2 12.7 - - + +
267A PRO* 5.8 3.1 - - + -
268A LYS* 3.1 17.4 + - + +
270A GLN* 1.3 78.8 - - - +
272A MET* 1.3 61.0 + - - +
274A ASN* 3.7 8.7 + - - +
275A TYR* 3.3 18.9 + - - +
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Residues in contact with MET 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A PRO* 4.4 14.5 - - + +
268A LYS 3.0 16.2 + - - +
269A PRO* 3.8 8.7 - - + +
270A GLN 3.1 0.2 - - - -
271A LEU* 1.3 77.0 - - - +
273A ALA* 1.3 64.7 + - - +
274A ASN 3.2 0.2 - - - -
275A TYR* 3.1 22.9 - - - +
276A TYR* 3.1 9.0 + - - +
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Residues in contact with ALA 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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269A PRO 3.0 17.3 + - - +
270A GLN* 3.8 4.5 - - - +
272A MET* 1.3 73.3 - - - +
274A ASN* 1.3 65.8 + - - +
276A TYR* 3.4 7.8 + - - +
277A ASN* 3.0 23.6 + - - +
299A LEU* 4.7 9.8 - - + +
302A LEU* 4.7 23.2 - - + +
303A SER* 5.6 3.8 - - - +
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Residues in contact with ASN 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 GLN 3.3 11.0 + - - +
271A LEU* 3.8 11.2 - - - +
272A MET 3.2 0.8 - - - -
273A ALA* 1.3 76.3 - - - +
275A TYR* 1.3 64.6 + - - +
277A ASN* 3.1 9.7 + - - +
278A LYS* 3.0 21.7 + - - +
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Residues in contact with TYR 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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234A LEU* 5.6 11.0 - - + +
237A LEU* 6.4 2.7 - - + -
271A LEU 3.3 11.3 + - - +
272A MET* 3.1 14.3 + - - +
274A ASN* 1.3 79.5 - - - +
276A TYR* 1.3 57.4 + - - +
278A LYS* 3.0 23.3 + - - +
279A VAL* 3.1 12.0 + - - +
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Residues in contact with TYR 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 MET 3.1 9.2 + - - +
273A ALA* 3.9 7.6 - - - +
274A ASN 3.3 0.2 - - - -
275A TYR* 1.3 78.9 - - - +
277A ASN* 1.3 61.3 + - - +
279A VAL* 3.1 19.5 + - - +
280A SER* 3.2 12.1 + - - -
295A THR* 3.9 24.9 - - - +
298A ARG* 4.5 9.2 - - + -
299A LEU* 4.0 17.2 - - + +
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Residues in contact with ASN 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 ALA 3.0 18.0 + - - +
274A ASN* 3.1 9.8 + - - +
276A TYR* 1.3 77.5 - - - +
278A LYS* 1.3 58.8 - - - +
280A SER* 3.9 12.6 + - - +
281A THR* 3.9 10.0 + - - -
299A LEU* 4.7 7.6 - - + +
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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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237A LEU* 5.2 12.3 - - + +
238A ASP* 5.3 7.4 - - + -
241A ILE* 4.9 18.3 - - + +
274A ASN 3.0 9.6 + - - +
275A TYR* 3.0 13.6 + - - +
277A ASN* 1.3 75.5 - - - +
279A VAL* 1.3 64.7 + - - +
280A SER 3.1 1.8 - - - -
281A THR* 3.1 8.7 + - - -
282A VAL* 3.0 22.6 + - - +
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Residues in contact with VAL 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 TYR 3.1 10.9 + - - +
276A TYR* 3.1 11.8 + - - +
278A LYS* 1.3 76.6 - - - +
280A SER* 1.3 63.0 + - - +
282A VAL* 3.8 7.0 - - - +
283A PHE* 3.0 28.9 + - - +
295A THR* 3.7 16.6 - - - -
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Residues in contact with SER 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 TYR 3.2 11.5 + - - -
277A ASN* 4.1 11.0 - - - -
278A LYS 3.1 0.8 - - - -
279A VAL* 1.3 77.4 - - - +
281A THR* 1.3 60.2 + - - +
283A PHE* 4.1 0.9 - - - +
284A TRP* 3.2 23.7 + - - +
292A HIS* 4.4 20.3 - - - +
295A THR* 3.8 8.7 - - - -
296A LEU* 4.7 10.5 - - - -
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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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241A ILE* 5.5 8.3 - - - -
277A ASN 3.9 7.0 + - - -
278A LYS* 3.1 12.0 + - - -
280A SER* 1.3 76.5 - - - +
282A VAL* 1.3 66.3 + - - +
284A TRP* 3.1 7.9 + - - +
285A LYS* 3.0 23.3 + - - +
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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
----------------------------------------------------------
241A ILE* 6.1 2.2 - - + +
246A TRP* 5.8 7.0 - - + +
249A ALA* 5.0 17.5 - - + -
250A PHE* 5.8 4.5 - - + +
278A LYS 3.0 15.1 + - - +
279A VAL* 3.8 7.9 - - - +
281A THR* 1.3 78.8 - - - +
283A PHE* 1.3 51.3 + - + +
285A LYS* 3.2 7.6 + - - +
286A SER* 2.8 34.3 + - - -
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Residues in contact with PHE 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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279A VAL* 3.0 17.1 + - + +
282A VAL* 1.3 73.1 - - + +
284A TRP* 1.3 63.7 + - - +
286A SER* 3.6 9.6 - - - -
287A GLY* 3.2 15.2 + - - -
288A ASN* 3.2 21.4 + - + +
289A ALA* 5.0 0.2 - - - -
291A PHE* 4.1 10.8 - - + -
292A HIS* 3.7 31.7 - - - +
295A THR* 6.0 0.2 - - - -
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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
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280A SER 3.2 18.9 + - - +
281A THR* 3.1 8.1 + - - +
283A PHE* 1.3 75.9 - - - +
285A LYS* 1.3 63.9 - - - +
286A SER 3.4 0.3 + - - -
287A GLY* 3.4 10.0 + - - -
292A HIS* 4.5 6.7 - - + +
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Residues in contact with LYS 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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246A TRP* 5.1 13.2 - - + -
281A THR 3.0 11.9 + - - +
282A VAL* 3.5 10.3 - - - +
284A TRP* 1.3 79.2 - - - +
286A SER* 1.3 59.1 + - - +
287A GLY* 3.4 0.7 + - - -
517C LEU 3.5 9.0 - - - +
518C GLY* 4.6 1.1 - - - -
519C PRO* 4.2 24.8 - - + +
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Residues in contact with SER 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 2.8 17.6 + - - -
283A PHE* 3.7 12.3 - - - -
284A TRP 3.2 0.4 - - - -
285A LYS* 1.3 77.5 - - - +
287A GLY* 1.3 61.8 + - - +
288A ASN* 3.6 11.3 + - - +
516C LEU* 6.0 3.8 - - - -
517C LEU* 3.4 31.8 + - - +
518C GLY* 5.3 0.7 - - - -
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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