Contacts of the helix formed by residues 268 - 283 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266B ASP* 3.2 3.4 + - - +
267B LYS* 1.3 84.0 - - + +
269B PHE* 1.3 67.3 + - - +
270B ASN* 4.1 17.3 - - + +
271B LYS* 3.4 30.6 + - + +
272B VAL* 3.3 22.3 + - - +
291B CYS* 3.9 1.6 - - - -
69D C 3.4 39.9 - - + +
70D C 3.6 40.2 - - + +
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Residues in contact with PHE 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B LYS 3.9 0.2 + - - -
268B ILE* 1.3 71.5 - - - +
270B ASN* 1.3 80.3 + - - +
272B VAL* 2.8 23.1 + - + +
273B GLU* 2.9 47.5 + - + +
291B CYS* 3.6 28.9 - - + -
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Residues in contact with ASN 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ILE* 3.6 9.8 - - + +
269B PHE* 1.3 93.5 - - - +
271B LYS* 1.3 58.2 + - + +
273B GLU* 3.2 9.7 + - - +
274B LYS* 2.9 26.2 + - - +
68D C 5.1 5.0 + - - +
69D C 3.7 20.5 + - - +
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Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ALA* 3.5 27.0 + - + +
245B PRO* 5.6 1.2 - - + +
266B ASP* 3.6 17.5 - - - +
268B ILE* 3.4 32.2 + - + +
270B ASN* 1.3 76.5 - - + +
272B VAL* 1.3 59.6 + - - +
274B LYS* 3.0 10.4 + - - +
275B ILE* 2.9 28.9 + - - +
70D C 3.3 33.4 + - - -
71D U 4.5 11.4 + - - -
72D C 4.2 17.0 + - - -
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ALA* 4.8 0.2 - - - +
266B ASP* 3.6 16.8 - - + +
268B ILE 3.4 13.7 - - - +
269B PHE* 2.8 11.5 + - + +
271B LYS* 1.3 76.6 - - - +
273B GLU* 1.3 67.1 + - - +
275B ILE* 3.0 13.3 + - + +
276B LYS* 2.9 35.6 + - + +
289B ALA* 3.8 21.8 - - + +
290B PHE 3.6 30.7 - - - +
291B CYS* 3.7 15.5 - - + +
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Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B PHE* 2.9 52.3 + - + +
270B ASN* 3.3 11.9 - - - +
271B LYS 3.2 0.2 - - - -
272B VAL* 1.3 78.4 - - - +
274B LYS* 1.3 56.4 + - - +
276B LYS* 3.4 30.3 + - - +
277B GLN* 2.9 48.4 + - - +
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Residues in contact with LYS 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PRO* 3.7 24.5 - - + -
270B ASN 2.9 12.9 + - - +
271B LYS* 3.0 13.4 + - - +
273B GLU* 1.3 75.2 - - - +
275B ILE* 1.3 58.6 + - - +
277B GLN* 3.4 25.7 + - + +
278B ASN* 2.9 50.1 + - - +
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Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ALA* 3.7 15.7 - - + -
244B ALA* 3.5 27.1 - - + +
245B PRO 3.3 24.2 + - - -
246B GLY* 3.9 8.5 - - - +
249B THR* 4.9 2.7 - - + -
250B THR* 5.1 1.8 - - + +
264B ALA* 4.3 15.5 - - + -
265B LEU 4.7 0.4 - - - +
266B ASP* 4.7 7.4 - - + -
271B LYS 2.9 16.0 + - - +
272B VAL* 3.2 16.6 - - + +
274B LYS* 1.3 76.3 - - - +
276B LYS* 1.3 58.5 + - - +
278B ASN* 3.1 4.2 + - - +
279B ALA* 2.9 27.5 + - - +
287B ILE* 4.5 11.9 - - + -
289B ALA* 3.8 19.1 - - + -
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Residues in contact with LYS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B VAL* 2.9 23.1 + - - +
273B GLU* 3.7 30.3 + - - +
275B ILE* 1.3 75.5 - - - +
277B GLN* 1.3 57.5 + - + +
279B ALA* 3.3 6.7 + - - +
280B LEU* 2.9 32.3 + - - +
287B ILE* 6.2 0.7 - - - -
289B ALA* 3.4 41.8 + - + +
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Residues in contact with GLN 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B GLU* 2.9 40.8 + - - +
274B LYS* 3.6 30.9 + - + +
275B ILE 3.3 0.2 - - - -
276B LYS* 1.3 76.2 - - + +
278B ASN* 1.3 57.6 + - - +
280B LEU* 3.5 6.0 + - - +
281B LEU* 2.9 30.8 + - - +
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Residues in contact with ASN 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B PHE* 4.1 26.0 - - + -
245B PRO* 2.9 36.0 + - - +
246B GLY 4.8 0.4 - - - +
250B THR* 4.2 13.7 - - + -
274B LYS* 2.9 34.4 + - - +
275B ILE 3.1 4.7 + - - +
277B GLN* 1.3 73.9 - - - +
279B ALA* 1.3 60.1 + - - +
281B LEU* 3.2 16.0 + - - +
282B LEU* 2.9 36.5 + - + +
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Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B THR* 4.0 10.9 - - + +
275B ILE* 2.9 16.1 + - + +
276B LYS* 3.7 7.0 - - - +
278B ASN* 1.3 76.1 - - - +
280B LEU* 1.3 63.8 + - - +
282B LEU* 3.5 1.0 + - - -
283B GLY 3.1 4.2 + - - -
284B LEU* 3.0 38.2 + - - +
287B ILE* 3.8 37.5 - - + +
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B LYS 2.9 17.5 + - - +
277B GLN* 3.9 6.1 - - - +
279B ALA* 1.3 76.5 - - - +
281B LEU* 1.3 66.1 + - - +
283B GLY* 3.5 9.7 + - - -
284B LEU 4.9 1.6 - - - -
285B ASN* 5.5 7.4 - - - +
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LEU* 4.2 2.6 - - - +
213B PRO* 3.3 36.3 - - + +
214B ARG* 4.0 33.7 + - + +
277B GLN 2.9 19.7 + - - +
278B ASN* 3.2 17.9 + - - +
280B LEU* 1.3 83.2 - - - +
282B LEU* 1.3 63.8 + - + +
283B GLY* 3.2 1.3 + - - -
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Residues in contact with LEU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ARG* 4.3 6.3 - - - +
58B ASN* 2.7 37.7 + - + +
60B HIS* 4.8 1.6 + - - -
61B LEU* 3.2 12.3 - - - +
213B PRO 3.6 24.0 - - - +
214B ARG 3.6 14.1 - - - +
216B LEU 3.8 13.5 - - - +
217B PHE* 4.1 20.9 - - + -
250B THR* 3.7 31.2 - - + +
278B ASN* 2.9 18.8 + - + +
281B LEU* 1.3 79.6 - - + +
283B GLY* 1.3 60.3 + - - +
284B LEU* 3.5 17.3 - - + +
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Residues in contact with GLY 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B HIS* 3.7 14.9 - - - -
61B LEU* 4.5 11.1 - - - +
258B ASP* 3.5 8.8 - - - +
279B ALA 3.1 5.3 + - - -
280B LEU* 3.5 7.8 + - - -
281B LEU 3.2 4.2 + - - -
282B LEU* 1.3 80.2 - - - +
284B LEU* 1.3 63.3 + - - +
285B ASN* 3.8 11.5 + - - +
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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