Contacts of the helix formed by residues 272 - 282 (chain B) in PDB entry 3A2C
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 SER 272 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B SER* 4.0 13.2 + - - -
266B ASN* 3.0 35.6 + - - -
273B PRO* 1.3 76.5 - - - +
274B GLY 3.2 1.9 - - - +
275B MET* 3.3 21.5 + - - +
276B LYS* 2.9 33.3 + - - +
75F ASN* 4.2 23.2 + - - -
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Residues in contact with PRO 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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272B SER* 1.3 91.9 - - - +
274B GLY* 1.3 65.2 + - - +
276B LYS* 3.7 9.4 - - + +
277B THR* 2.9 27.1 + - - -
71F GLY* 5.5 0.9 - - - +
74F ILE* 4.3 22.4 - - + -
75F ASN* 4.8 2.2 - - - +
96F GLN* 6.0 1.8 - - - +
128F TYR* 4.1 28.5 - - + +
129F ALA* 4.2 16.6 - - + +
131F ARG* 4.6 18.9 + - + +
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Residues in contact with GLY 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ASN* 4.1 6.2 + - - -
272B SER 3.2 2.0 - - - +
273B PRO* 1.3 84.7 - - - +
275B MET* 1.3 55.2 + - - +
277B THR* 3.1 9.9 + - - -
278B ARG* 3.0 49.6 + - - +
129F ALA* 5.2 3.2 - - - +
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Residues in contact with MET 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A VAL* 6.3 1.1 - - + -
2B PDY 4.4 11.0 - - + -
263B PHE* 4.3 9.9 - - + +
264B TYR* 3.3 44.0 - - - +
265B SER* 3.7 8.7 - - - -
272B SER* 3.3 22.9 + - - +
273B PRO 3.2 0.2 - - - -
274B GLY* 1.3 75.2 - - - +
276B LYS* 1.3 74.1 + - - +
278B ARG* 3.3 16.8 + - - +
279B ILE* 3.1 45.0 + - + +
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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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230A VAL* 5.2 5.9 - - - +
235A LEU* 3.3 50.6 - - + +
272B SER* 2.9 23.0 + - - +
273B PRO* 3.7 9.6 - - + +
274B GLY 3.3 0.2 - - - -
275B MET* 1.3 82.6 - - - +
277B THR* 1.3 62.2 + - - +
279B ILE* 3.5 14.0 + - - +
280B ARG* 3.2 41.3 + - - +
131F ARG* 5.4 7.4 - - - +
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Residues in contact with THR 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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179A SER* 3.6 31.3 + - - +
273B PRO 2.9 14.2 + - - -
274B GLY* 3.1 12.2 + - - -
276B LYS* 1.3 75.1 - - - +
278B ARG* 1.3 63.0 + - + +
280B ARG* 3.2 15.7 + - - +
281B MET* 2.8 42.0 + - + +
283B GLN* 4.4 5.4 - - - +
129F ALA* 5.5 4.9 + - - +
131F ARG* 5.8 3.1 + - - -
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Residues in contact with ARG 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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263B PHE* 3.3 11.0 - - + +
264B TYR* 2.6 43.8 + - - +
266B ASN* 2.7 51.3 + - - +
274B GLY* 3.0 26.6 + - - +
275B MET* 3.3 14.3 + - - +
277B THR* 1.3 77.2 - - + +
279B ILE* 1.3 55.5 - - - +
282B GLY* 2.7 23.4 + - - -
283B GLN* 2.9 53.3 + - + +
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Residues in contact with ILE 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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230A VAL* 3.8 25.4 - - + +
232A PRO* 3.6 31.6 - - + +
235A LEU* 4.3 15.5 - - + -
247B TRP* 3.9 11.2 - - + -
263B PHE* 3.6 28.3 - - + -
275B MET* 3.1 44.9 + - + +
276B LYS* 3.7 12.6 - - - +
277B THR 3.2 0.2 - - - -
278B ARG* 1.3 73.2 - - - +
280B ARG* 1.3 68.0 + - - +
282B GLY* 3.1 10.9 + - - -
308B THR* 3.7 3.5 + - - -
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Residues in contact with ARG 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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179A SER 5.9 0.2 + - - -
181A ASN* 3.5 36.1 + - - +
215A THR* 5.6 5.5 + - - -
232A PRO* 3.8 18.1 - - + +
235A LEU* 3.0 53.4 - - + +
242A LYS* 5.0 8.3 - - - +
276B LYS* 3.2 25.6 + - - +
277B THR* 3.2 15.9 + - - +
279B ILE* 1.3 78.1 - - - +
281B MET* 1.3 66.7 + - + +
308B THR* 3.0 24.4 + - - +
131F ARG* 4.3 24.7 - - - +
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Residues in contact with MET 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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175A GLN* 3.6 31.0 - - + +
178A HIS* 3.8 10.8 - - - +
179A SER* 3.4 24.0 - - - +
242A LYS* 5.1 3.8 - - - -
315A THR* 4.6 6.8 + - - -
316A ILE* 3.7 25.8 - - + -
317A THR* 3.0 32.2 + - - +
277B THR* 2.8 33.5 + - + +
280B ARG* 1.3 76.8 - - + +
282B GLY* 1.3 60.9 + - - +
283B GLN* 3.4 30.5 - - + +
308B THR* 4.1 3.0 + - - -
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Residues in contact with GLY 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A THR* 4.0 9.0 - - - +
247B TRP* 6.0 0.4 - - - -
263B PHE* 4.1 9.0 - - - -
278B ARG 2.7 12.6 + - - -
279B ILE 3.1 11.8 + - - -
280B ARG 3.1 0.2 - - - -
281B MET* 1.3 79.8 - - - +
283B GLN* 1.3 58.3 + - - -
284B TYR* 3.4 22.8 - - - +
306B LEU 5.5 3.8 - - - -
308B THR* 3.9 9.2 - - - -
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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