Contacts of the helix formed by residues 273 - 285 (chain C) in PDB entry 3J82
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 GLY 273 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178C LEU* 5.7 0.7 - - - -
261C LEU 3.7 4.5 - - - -
262C PHE 3.1 26.9 + - - -
264C PRO* 4.2 0.8 - - - +
272C CYS* 1.3 77.2 - - - +
274C ILE* 1.3 58.6 + - - -
275C HIS* 3.1 16.8 - - - -
276C GLU* 4.2 1.6 - - - +
277C THR* 2.7 34.4 + - - -
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Residues in contact with ILE 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C MET* 4.1 35.2 - - + -
155C SER* 4.2 15.0 - - - +
160C THR* 4.8 15.0 - - + +
162C THR* 4.7 7.0 - - + -
178C LEU* 6.0 2.9 - - + +
180C LEU* 6.3 0.4 - - + -
261C LEU* 3.5 50.1 + - + +
262C PHE* 4.7 11.4 - - + +
273C GLY* 1.3 71.9 - - - -
275C HIS* 1.3 59.3 + - - +
277C THR* 3.1 8.0 + - - -
278C THR* 2.8 33.1 + - + +
313C MET* 4.5 10.3 - - + -
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Residues in contact with HIS 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C PHE* 3.5 37.8 - + + -
273C GLY* 3.5 14.7 - - - -
274C ILE* 1.3 81.1 + - - +
276C GLU* 1.3 76.6 + - + +
278C THR* 2.6 22.6 + - - -
279C PHE* 3.1 6.8 + - - +
313C MET* 3.8 18.3 - - + +
316C GLU* 3.3 45.7 + - + +
317C ILE* 5.0 5.4 - - + +
320C LEU* 4.9 16.6 - - + +
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Residues in contact with GLU 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C CYS* 2.9 45.0 - - + -
273C GLY 3.3 5.2 + - - +
275C HIS* 1.3 96.2 - - + +
277C THR* 1.3 51.3 + - - +
279C PHE* 3.0 14.4 + - - +
280C ASN* 2.7 71.8 + - - +
320C LEU* 4.9 7.6 - - + +
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Residues in contact with THR 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C THR* 6.3 1.8 - - + -
161C HIS 5.5 0.2 - - - -
162C THR* 3.4 15.7 - - + +
176C LEU* 2.9 50.7 - - + +
178C LEU* 4.7 5.6 - - + +
272C CYS* 3.8 12.1 + - - +
273C GLY 2.7 25.2 + - - -
274C ILE* 3.2 8.7 - - - -
276C GLU* 1.3 74.6 - - - +
278C THR* 1.3 65.4 + - - +
280C ASN* 3.5 9.9 + - - +
281C SER* 3.1 21.3 + - - -
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Residues in contact with THR 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ILE* 3.6 25.5 - - + +
152C VAL 5.7 0.4 - - - +
153C MET* 5.3 6.1 - - + +
162C THR* 3.7 19.7 - - + -
274C ILE* 2.8 22.7 + - + +
275C HIS* 2.6 21.3 + - - -
277C THR* 1.3 75.1 - - - +
279C PHE* 1.3 57.7 + - - +
281C SER* 3.1 4.5 + - - -
282C ILE* 2.8 28.5 + - - +
313C MET* 4.6 16.4 - - + -
317C ILE* 4.1 14.7 - - - +
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Residues in contact with PHE 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C HIS 3.1 3.3 + - - +
276C GLU* 3.0 12.7 + - - +
278C THR* 1.3 79.5 + - - +
280C ASN* 1.3 76.4 + - - +
282C ILE* 2.8 28.9 - - + +
283C MET* 3.1 50.2 + - + -
290C ARG* 6.0 0.4 - - - -
294C TYR* 3.5 23.6 - - - -
320C LEU* 3.5 52.0 - - + -
321C ALA* 5.6 0.7 - - - -
322C PRO* 6.4 0.4 - - + -
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Residues in contact with ASN 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C LEU* 5.3 2.9 - - + +
272C CYS* 4.6 3.6 - - - +
276C GLU* 2.7 65.1 + - - +
277C THR* 3.5 11.3 + - - +
279C PHE* 1.3 80.5 - - - +
281C SER* 1.3 65.2 + - - +
283C MET* 3.3 6.0 + - - +
284C LYS* 3.0 40.6 + - - +
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Residues in contact with SER 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ILE* 3.7 6.3 - - - +
162C THR* 3.6 15.5 - - - -
164C PRO* 2.9 36.4 - - - +
174C ALA* 3.6 11.8 + - - +
176C LEU* 4.3 0.9 - - - -
277C THR 3.1 10.7 + - - -
278C THR 3.4 8.7 - - - -
280C ASN* 1.3 79.2 - - - +
282C ILE* 1.3 64.8 + - - +
284C LYS* 3.0 29.2 + - - +
285C CYS* 3.4 6.6 + - - -
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Residues in contact with ILE 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ILE* 4.8 7.0 - - + -
278C THR 2.8 13.6 + - - +
279C PHE* 2.8 28.9 + - + +
281C SER* 1.3 78.3 - - - +
283C MET* 1.3 68.8 + - + +
285C CYS* 3.2 13.3 + - - +
290C ARG* 3.4 40.0 + - + +
293C LEU* 3.6 28.9 - - + -
294C TYR* 3.0 47.1 - - + +
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Residues in contact with MET 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279C PHE* 3.1 47.2 + - + +
280C ASN* 3.8 8.7 - - - +
282C ILE* 1.3 78.4 - - + +
284C LYS* 1.3 59.5 + - - +
285C CYS 2.7 21.6 - - - +
290C ARG* 3.1 37.9 + - - +
246D GLN* 5.6 9.2 - - + +
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Residues in contact with LYS 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C LEU* 5.0 4.9 - - + +
173C HIS* 4.1 10.4 - - + +
174C ALA* 2.8 45.0 + - - +
175C ILE 4.5 1.6 - - - -
176C LEU* 4.1 19.8 - - - +
280C ASN* 3.0 39.6 + - - +
281C SER* 3.0 14.2 + - - +
283C MET* 1.3 78.1 - - - +
285C CYS* 1.3 59.0 + - - +
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Residues in contact with CYS 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C PRO* 3.7 38.6 - - - -
171C LEU* 4.4 14.4 - - - -
174C ALA* 4.2 6.7 - - - -
281C SER 3.4 1.3 + - - -
282C ILE 3.2 12.8 + - - +
283C MET 2.7 16.9 - - - +
284C LYS* 1.3 81.1 - - - +
286C ASP* 1.4 66.8 + - - +
287C VAL 3.7 0.7 + - - -
289C ILE* 2.9 28.0 - - + -
290C ARG* 3.9 3.5 + - - -
293C LEU* 4.0 7.9 - - + -
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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