Contacts of the helix formed by residues 268 - 283 (chain A) in PDB entry 5WWT
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 ILE 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A ASP* 3.3 2.8 + - - +
267A LYS* 1.3 84.6 - - + +
269A PHE* 1.3 67.3 + - - +
270A ASN* 4.1 13.7 - - + +
271A LYS* 3.4 31.0 - - + +
272A VAL* 3.3 19.8 + - - +
291A CYS* 3.9 1.6 - - - -
69C C 3.4 45.5 - - + +
70C C 3.4 42.8 - - + +
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Residues in contact with PHE 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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267A LYS 3.9 0.2 + - - -
268A ILE* 1.3 70.8 - - - +
270A ASN* 1.3 77.9 + - - +
272A VAL* 2.8 27.2 + - + +
273A GLU* 2.9 47.6 + - + -
291A CYS* 3.6 27.8 - - + -
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Residues in contact with ASN 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ILE* 3.6 8.8 - - + +
269A PHE* 1.3 94.2 - - - +
271A LYS* 1.3 56.7 + - + +
273A GLU* 3.3 9.2 + - - +
274A LYS* 2.9 26.7 + - - +
68C C 5.2 1.7 + - - +
69C C 3.6 20.3 + - - +
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Residues in contact with LYS 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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244A ALA* 3.4 28.3 + - + +
245A PRO* 5.6 0.8 - - - +
266A ASP* 3.5 18.2 - - - +
268A ILE* 3.4 31.1 + - + +
269A PHE 3.1 0.6 - - - -
270A ASN* 1.3 75.5 - - + +
272A VAL* 1.3 60.1 + - - +
274A LYS* 3.0 10.9 + - - +
275A ILE* 2.9 28.8 + - - +
70C C 3.2 35.8 + - - -
71C U 4.5 11.8 + - - -
72C C 4.2 16.2 + - - -
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Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ASP* 3.6 17.5 - - + +
268A ILE 3.3 13.9 + - - +
269A PHE* 2.8 14.6 + - + +
271A LYS* 1.3 72.0 - - - +
273A GLU* 1.3 67.4 + - - +
275A ILE* 3.0 13.6 + - + +
276A LYS* 3.0 32.8 + - - +
289A ALA* 3.7 23.3 - - + -
290A PHE 3.6 31.2 - - - +
291A CYS* 3.7 16.8 - - + +
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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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269A PHE* 2.9 51.7 + - + +
270A ASN* 3.4 11.7 - - - +
272A VAL* 1.3 78.9 - - - +
274A LYS* 1.3 57.4 + - - +
276A LYS* 3.4 35.2 + - - +
277A GLN* 2.9 50.3 + - - +
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Residues in contact with LYS 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PRO* 3.7 26.0 - - + -
270A ASN 2.9 12.9 + - - +
271A LYS* 3.0 13.6 + - - +
273A GLU* 1.3 74.6 - - - +
275A ILE* 1.3 59.4 + - - +
277A GLN* 3.6 24.6 + - + +
278A ASN* 2.9 49.8 + - - +
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Residues in contact with ILE 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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243A ALA* 3.6 16.2 - - + -
244A ALA* 3.5 38.1 - - + +
245A PRO 3.4 13.2 + - - -
246A GLY* 4.6 8.5 - - - -
249A THR* 4.8 2.7 - - + -
250A THR* 5.1 1.9 - - + +
264A ALA* 4.2 15.5 - - + -
265A LEU 4.7 0.9 - - - +
266A ASP* 4.6 7.0 - - + -
271A LYS 2.9 16.6 + - - +
272A VAL* 3.2 16.6 - - + +
274A LYS* 1.3 75.6 - - - +
276A LYS* 1.3 58.5 + - - +
278A ASN* 3.1 4.2 + - - +
279A ALA* 2.9 26.7 + - - +
287A ILE* 4.4 13.0 - - + -
289A ALA* 3.8 18.6 - - + -
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Residues in contact with LYS 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 VAL* 3.0 21.0 + - - +
273A GLU* 3.6 35.9 + - - +
275A ILE* 1.3 76.0 - - - +
277A GLN* 1.3 58.6 + - + +
279A ALA* 3.3 6.4 + - - +
280A LEU* 2.9 31.2 + - - +
287A ILE* 6.0 0.9 - - - -
289A ALA* 3.5 39.6 + - + +
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Residues in contact with GLN 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 41.9 + - - +
274A LYS* 3.6 32.7 + - + +
275A ILE 3.3 0.2 - - - -
276A LYS* 1.3 75.8 - - + +
278A ASN* 1.3 57.3 + - - +
280A LEU* 3.5 5.4 + - - +
281A LEU* 2.9 31.0 + - - +
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Residues in contact with ASN 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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217A PHE* 4.0 26.3 - - + -
245A PRO* 2.8 36.5 + - - +
246A GLY 4.9 0.4 - - - +
250A THR* 4.3 14.1 - - + -
274A LYS* 2.9 34.7 + - - +
275A ILE 3.5 4.5 - - - +
277A GLN* 1.3 74.6 - - - +
279A ALA* 1.3 59.1 + - - +
281A LEU* 3.2 17.1 + - - +
282A LEU* 2.9 35.9 + - + +
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Residues in contact with ALA 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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250A THR* 4.1 10.0 - - - +
275A ILE 2.9 15.2 + - - +
276A LYS* 3.7 7.2 - - - +
278A ASN* 1.3 75.8 - - - +
280A LEU* 1.3 62.3 - - - +
282A LEU* 3.9 0.6 - - - -
283A GLY 3.0 4.5 + - - -
284A LEU* 3.0 39.6 + - - +
287A ILE* 3.7 37.7 - - + +
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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 LYS 2.9 17.0 + - - +
277A GLN* 3.9 6.5 - - - +
279A ALA* 1.3 76.2 - - - +
281A LEU* 1.3 64.9 + - - +
283A GLY* 3.5 10.5 + - - -
284A LEU 4.9 2.7 - - - -
285A ASN* 5.4 7.9 - - - +
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Residues in contact with LEU 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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61A LEU* 4.1 2.6 - - - +
213A PRO* 3.4 37.0 - - + +
214A ARG* 3.8 34.6 + - + +
277A GLN 2.9 20.0 + - - +
278A ASN* 3.4 18.4 - - - +
280A LEU* 1.3 82.1 - - - +
282A LEU* 1.3 64.5 + - + +
283A GLY* 3.4 0.9 + - - -
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Residues in contact with LEU 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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56A ARG* 4.4 6.1 - - - +
58A ASN* 2.7 44.6 + - + +
60A HIS* 4.8 2.1 + - - -
61A LEU* 3.2 12.8 - - - +
213A PRO 3.5 19.7 - - - +
214A ARG 3.5 11.0 - - - +
216A LEU 3.8 13.2 - - - +
217A PHE* 4.2 20.9 - - + -
250A THR* 3.8 33.4 - - + +
278A ASN* 2.9 15.9 + - + +
281A LEU* 1.3 80.8 - - + +
283A GLY* 1.3 60.4 + - - +
284A LEU* 3.5 18.0 - - + +
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Residues in contact with GLY 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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60A HIS* 3.7 14.8 - - - -
61A LEU* 4.5 11.2 - - - +
258A ASP* 3.6 9.2 - - - +
279A ALA 3.0 5.6 + - - -
280A LEU* 3.5 7.4 + - - -
281A LEU 3.2 4.4 + - - -
282A LEU* 1.3 80.0 - - - +
284A LEU* 1.3 63.4 + - - +
285A ASN* 3.8 10.9 + - - +
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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