Contacts of the helix formed by residues 272 - 283 (chain B) in PDB entry 5C16
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 272 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270B SER 3.5 7.7 + - - +
271B VAL* 1.3 81.0 - - - +
273B ASP* 1.3 65.9 + - - +
274B ASP* 3.1 11.4 - - + +
275B ASP* 3.1 40.5 + - - +
276B LEU* 3.2 9.9 + - - +
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Residues in contact with ASP 273 (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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247B LYS* 4.2 12.1 + - - -
249B SER* 5.2 4.1 + - - -
251B ILE* 4.0 28.7 + - + +
271B VAL 4.2 6.4 - - - +
272B LYS* 1.3 75.6 - - - +
274B ASP* 1.3 63.3 + - - +
275B ASP 3.4 0.2 - - - -
276B LEU* 3.5 13.9 + - - +
277B SER* 3.0 27.9 + - - -
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Residues in contact with ASP 274 (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 LYS* 3.1 9.4 - - + +
273B ASP* 1.3 82.3 - - - +
275B ASP* 1.3 65.7 + - - +
277B SER* 3.6 7.8 + - - -
278B LYS* 3.2 29.0 + - - +
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Residues in contact with ASP 275 (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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271B VAL* 4.2 11.1 - - + +
272B LYS* 3.1 40.7 + - - +
274B ASP* 1.3 81.4 - - - +
276B LEU* 1.3 59.1 + - - +
278B LYS* 3.1 10.1 + - - +
279B VAL* 2.9 33.0 + - + +
319B GLU* 3.7 32.6 - - + +
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Residues in contact with LEU 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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247B LYS* 5.9 0.4 - - - -
249B SER* 5.0 1.8 - - - +
251B ILE* 4.5 20.6 - - + -
257B PHE* 3.6 17.7 - - + -
265B ILE* 5.2 0.9 - - + -
267B VAL* 4.3 19.5 - - + -
271B VAL* 3.7 30.1 - - + -
272B LYS 3.2 8.3 + - - +
273B ASP* 3.7 15.9 - - - +
274B ASP 3.4 0.2 - - - -
275B ASP* 1.3 75.1 - - - +
277B SER* 1.3 52.9 + - - +
279B VAL* 3.0 9.7 + - + +
280B ALA 2.8 30.3 + - - -
288B VAL* 4.2 21.5 - - + -
323B TYR* 3.9 32.1 - - + +
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Residues in contact with SER 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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251B ILE* 4.3 9.2 - - - +
257B PHE* 3.8 12.9 - - - -
273B ASP 3.0 14.0 + - - -
274B ASP* 3.7 12.4 + - - -
275B ASP 3.3 0.2 - - - -
276B LEU* 1.3 76.9 - - - +
278B LYS* 1.3 58.6 + - - +
280B ALA* 3.3 4.8 + - - +
281B ALA* 3.1 24.4 + - - +
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Residues in contact with LYS 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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274B ASP* 3.2 18.6 - - - +
275B ASP* 3.1 14.3 + - - +
277B SER* 1.3 76.5 - - - +
279B VAL* 1.3 63.4 + - - +
281B ALA* 3.2 16.9 + - - +
282B PHE* 3.3 13.2 + - - +
317B CYS* 4.1 8.3 - - - -
319B GLU* 3.4 44.1 + - + +
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Residues in contact with VAL 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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275B ASP* 2.9 23.4 + - + +
276B LEU* 3.4 10.8 - - + +
278B LYS* 1.3 75.7 - - - +
280B ALA* 1.3 62.9 + - - +
282B PHE* 2.9 15.4 + - - +
283B ARG* 3.2 13.6 + - + +
288B VAL* 3.6 21.5 - - + -
289B PRO* 4.1 11.4 - - + -
317B CYS* 4.9 0.2 - - - -
319B GLU* 3.9 22.0 - - + +
320B ASP* 3.1 33.9 - - - +
323B TYR* 4.0 19.1 - - + -
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Residues in contact with ALA 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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257B PHE* 3.7 30.7 - - + +
276B LEU 2.8 13.1 + - - +
277B SER* 3.3 11.4 - - - +
278B LYS 3.2 0.2 - - - -
279B VAL* 1.3 76.9 - - - +
281B ALA* 1.3 60.6 + - - +
283B ARG 3.1 20.0 - - - +
286B GLY* 3.3 20.4 + - - +
288B VAL* 3.4 11.6 - - + +
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Residues in contact with ALA 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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277B SER 3.1 13.1 + - - +
278B LYS* 3.5 12.1 - - - +
279B VAL 3.2 0.6 - - - -
280B ALA* 1.3 75.2 - - - +
282B PHE* 1.3 57.2 + - - +
283B ARG 3.4 0.2 - - - -
309B LEU* 3.5 16.6 - - - +
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Residues in contact with PHE 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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278B LYS 3.3 9.8 + - - +
279B VAL 2.9 9.6 + - - +
281B ALA* 1.3 76.3 - - - +
283B ARG* 1.3 58.1 + - - +
308B PRO* 3.3 17.8 - - + +
309B LEU* 2.7 60.5 + - + -
310B VAL* 4.1 11.2 - - + -
315B LYS* 3.7 26.9 - - + -
316B ARG* 4.1 4.5 - - - -
317B CYS* 3.4 38.1 - - + -
320B ASP* 3.5 22.2 - - - +
364B TYR* 3.4 22.4 - + - -
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Residues in contact with ARG 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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279B VAL* 3.2 22.3 + - + +
280B ALA 3.1 8.5 + - - +
281B ALA 3.4 0.6 - - - -
282B PHE* 1.3 81.1 - - - +
284B ALA* 1.3 67.5 + - - +
285B LYS 3.3 0.5 + - - -
286B GLY 2.9 13.4 + - - -
287B ARG 3.9 20.2 - - - +
288B VAL* 4.4 4.3 - - - +
289B PRO* 4.4 8.2 - - - +
305B CYS* 3.6 13.4 - - - -
306B SER* 3.1 33.7 + - - +
307B GLN 3.5 4.9 - - - -
308B PRO* 3.4 19.6 - - - +
309B LEU* 3.6 7.5 - - - +
320B ASP* 2.8 38.9 + - - +
324B LEU* 3.9 15.6 - - - +
359B GLU* 2.7 35.9 + - - +
435B VAL* 6.1 0.2 - - - +
437B HIS* 4.2 0.8 - - - -
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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