Contacts of the helix formed by residues 297 - 311 (chain B) in PDB entry 5D0A
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 LYS 297 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B ILE* 3.9 23.1 - - + +
279B SER 4.7 0.2 - - - +
280B ASN* 2.8 35.6 + - - +
283B PHE* 3.5 44.4 - - + -
296B GLY* 1.3 73.0 - - - -
298B LYS* 1.3 62.7 + - - +
299B PRO* 3.6 0.4 - - - -
300B ILE* 3.4 4.5 + - - +
301B GLN* 2.9 63.7 + - + +
329B ARG* 4.0 5.9 - - - +
30E G 5.6 0.6 - - - -
31E A 2.9 27.2 + - - -
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Residues in contact with LYS 298 (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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222B LYS* 3.2 40.5 + - + +
295B ARG 5.3 1.3 - - - +
296B GLY 3.4 0.4 - - - -
297B LYS* 1.3 79.5 - - - +
299B PRO* 1.4 64.9 - - + +
301B GLN* 3.1 3.6 + - - +
302B ARG* 2.8 28.2 + - + +
329B ARG* 3.9 36.1 - - - +
330B PRO* 6.3 0.6 - - - +
331B VAL* 3.8 27.6 - - + +
332B ILE* 4.1 8.6 - - + +
32E C 3.3 31.8 + - - +
33E U 5.2 5.7 + - - +
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Residues in contact with PRO 299 (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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219B THR 3.4 20.6 - - - +
220B GLN* 4.1 7.0 - - - +
221B THR 3.5 21.8 - - - +
222B LYS* 4.3 9.9 - - + -
238B TYR* 6.5 0.9 - - + -
295B ARG* 3.6 35.2 - - + +
296B GLY 3.7 5.2 - - - +
298B LYS* 1.4 96.2 - - + +
300B ILE* 1.3 59.5 + - + +
302B ARG* 3.3 6.6 + - + +
303B ASN* 2.9 38.2 + - - +
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Residues in contact with ILE 300 (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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96B PHE* 3.9 29.8 - - + -
237B LEU* 3.9 23.4 - - + +
238B TYR* 5.1 3.4 - - + -
275B LEU* 4.3 24.7 - - + -
283B PHE* 3.6 35.4 - - + -
287B PHE* 5.6 0.4 - - + -
292B GLY 3.4 25.8 - - - +
293B SER* 5.3 0.2 - - - -
296B GLY 3.7 9.2 - - - +
297B LYS* 3.4 7.6 + - - +
298B LYS 3.2 0.2 - - - -
299B PRO* 1.3 78.7 - - + +
301B GLN* 1.3 61.1 + - + +
303B ASN* 3.3 2.9 + - - +
304B ALA* 2.9 27.4 + - - +
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Residues in contact with GLN 301 (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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275B LEU* 2.9 32.6 + - + +
276B LEU* 3.8 18.4 + - + +
277B ALA 4.9 0.2 - - - -
278B ILE* 3.9 12.5 + - + +
297B LYS* 2.9 43.7 + - + +
298B LYS 3.1 3.1 + - - +
300B ILE* 1.3 74.8 - - + +
302B ARG* 1.3 66.9 + - - +
304B ALA* 3.3 8.1 + - - +
305B ILE* 3.1 28.5 + - + +
329B ARG* 2.8 39.9 + - - +
332B ILE* 4.4 11.7 - - + -
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Residues in contact with ARG 302 (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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218B LEU 2.8 24.9 + - - -
219B THR* 3.6 11.9 + - - +
221B THR* 2.9 32.1 + - - -
222B LYS 5.8 0.2 - - - -
223B GLY 3.0 27.6 + - - -
225B LEU* 3.7 36.2 - - - +
298B LYS* 2.8 16.3 + - + +
299B PRO* 3.6 4.0 + - + +
301B GLN* 1.3 78.4 - - - +
303B ASN* 1.3 83.3 + - - +
305B ILE* 3.4 8.8 + - - +
306B LEU* 3.1 24.8 + - + +
331B VAL* 4.0 10.3 - - + -
332B ILE* 3.9 14.3 - - + +
335B THR* 3.8 24.0 - - + +
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Residues in contact with ASN 303 (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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219B THR* 3.0 30.7 + - - +
233B ILE* 3.7 15.9 - - + +
234B GLY 5.2 0.3 - - - +
236B ARG 3.7 16.5 - - - +
237B LEU* 2.8 30.5 + - - -
299B PRO 2.9 16.3 + - - +
300B ILE 3.7 4.0 - - - +
302B ARG* 1.3 99.3 + - - +
304B ALA* 1.3 56.0 + - - +
306B LEU* 3.3 8.9 + - - +
307B ALA* 2.7 36.0 + - - +
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Residues in contact with ALA 304 (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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237B LEU* 3.5 15.4 - - + +
272B LEU* 3.9 17.1 - - + +
275B LEU* 4.2 16.6 - - + -
276B LEU* 4.3 12.8 - - + -
300B ILE 2.9 17.0 + - - +
301B GLN* 3.3 9.1 + - - +
303B ASN* 1.3 77.5 - - - +
305B ILE* 1.3 57.5 + - - +
307B ALA* 3.4 2.5 + - - +
308B LEU* 2.9 34.0 + - - +
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Residues in contact with ILE 305 (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 LEU* 3.6 19.5 - - + -
301B GLN* 3.1 16.4 + - + +
302B ARG* 3.6 7.4 - - - +
304B ALA* 1.3 75.2 - - - +
306B LEU* 1.3 58.3 + - - +
308B LEU* 3.2 8.6 + - - +
309B ALA* 3.0 26.5 + - - +
320B LEU* 3.7 15.0 - - + -
323B LEU* 4.4 5.4 - - + -
332B ILE* 3.9 42.2 - - + +
335B THR* 3.6 21.1 - - + +
336B ALA* 3.8 8.7 - - + +
339B ALA* 3.4 25.3 - - + +
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Residues in contact with LEU 306 (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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225B LEU* 3.6 38.1 - - + -
230B ARG* 3.9 24.1 - - + +
233B ILE* 4.4 15.5 - - + -
234B GLY 4.6 1.3 - - - -
302B ARG* 3.1 22.7 + - + +
303B ASN* 3.5 19.1 - - - +
305B ILE* 1.3 79.8 - - - +
307B ALA* 1.3 56.1 + - - +
309B ALA* 3.3 6.4 + - - +
310B HIS* 2.9 27.4 + - - +
335B THR* 3.7 19.7 - - + -
338B TRP* 3.7 28.4 - - + -
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Residues in contact with ALA 307 (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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234B GLY 3.4 20.3 + - - +
235B ASN* 3.8 17.9 - - + +
236B ARG 5.5 0.2 - - - +
237B LEU* 4.9 0.7 - - + -
272B LEU* 3.7 23.1 - - + -
303B ASN 2.7 21.6 + - - +
304B ALA* 3.6 5.2 - - - +
305B ILE 3.3 0.2 - - - -
306B LEU* 1.3 71.6 - - - +
308B LEU* 1.3 64.8 + - - +
310B HIS* 3.2 2.9 + - - +
311B PHE* 3.0 30.3 + - - -
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Residues in contact with LEU 308 (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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92B ARG* 4.5 6.1 - - + -
272B LEU* 3.7 31.0 - - + -
273B LYS* 4.2 9.9 - - + -
276B LEU* 3.6 36.8 - - + -
304B ALA 2.9 18.4 + - - +
305B ILE* 3.2 9.2 + - - +
307B ALA* 1.3 75.3 - - - +
309B ALA* 1.3 61.5 + - - +
311B PHE* 3.2 4.4 + - - +
312B LYS 3.1 15.9 + - - -
313B ASP* 3.1 40.9 + - + +
316B ALA* 3.7 20.6 - - + -
320B LEU* 4.8 7.9 - - + -
343B ILE* 4.1 2.5 - - - +
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Residues in contact with ALA 309 (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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305B ILE 3.0 13.5 + - - +
306B LEU 3.6 7.4 - - - +
307B ALA 3.3 0.2 - - - -
308B LEU* 1.3 76.1 - - - +
310B HIS* 1.3 58.4 + - - +
312B LYS* 3.0 25.3 + - - +
338B TRP* 3.9 17.3 - - + -
339B ALA* 3.8 29.4 - - + +
342B LYS* 4.1 17.0 - - + +
343B ILE* 3.7 12.7 - - - +
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Residues in contact with HIS 310 (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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230B ARG 5.3 5.8 - - - +
231B THR* 5.4 9.2 + - - -
234B GLY* 3.9 39.9 - - - +
235B ASN* 4.7 1.0 + - - +
306B LEU 2.9 14.1 + - - +
307B ALA 3.2 7.8 + - - +
309B ALA* 1.3 76.9 - - - +
311B PHE* 1.3 90.1 + + - +
312B LYS* 3.2 5.4 + - - +
342B LYS* 6.5 0.7 - - - +
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Residues in contact with PHE 311 (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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87B SER* 4.5 5.8 - - - -
89B ARG* 5.4 3.6 + - - -
92B ARG* 3.7 68.8 + - + +
93B ARG 3.7 14.4 - - - -
235B ASN* 3.6 36.6 - - + -
272B LEU* 3.9 11.0 - - + -
307B ALA 3.0 23.3 + - - +
308B LEU* 3.2 4.9 + - - +
309B ALA 3.2 0.2 - - - -
310B HIS* 1.3 92.7 - + - +
312B LYS* 1.3 70.0 + - - +
313B ASP* 3.2 6.5 + - + +
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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