Contacts of the helix formed by residues 273 - 281 (chain C) in PDB entry 3JXI
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 LEU 273 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229C HIS* 4.2 1.1 - - - -
250C VAL 5.2 0.7 - - - +
251C HIS* 3.2 45.8 - - + +
252C ALA 3.9 0.2 - - - -
253C GLN* 3.4 21.3 - - + +
271C GLY 2.7 18.3 + - - +
272C GLU* 1.3 74.6 - - - +
274C PRO* 1.3 72.4 - - + +
275C LEU* 3.3 5.4 - - + +
276C SER* 3.1 15.7 + - - +
277C LEU* 2.9 22.0 + - - +
302C ARG* 3.8 41.5 - - + +
303C GLN 4.2 13.5 - - - +
304C ASP* 4.2 1.8 - - + +
308C ASN 5.0 1.1 - - - +
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Residues in contact with PRO 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C LEU* 3.7 24.5 - - + -
229C HIS* 3.7 20.0 - - + +
232C ILE* 3.4 31.3 - - + +
249C ASP 4.2 2.5 - - - +
250C VAL* 3.3 29.4 - - - +
251C HIS* 4.0 0.2 - - - -
252C ALA* 3.1 18.4 - - + +
273C LEU* 1.3 83.9 - - + +
275C LEU* 1.3 56.5 + - - +
277C LEU* 3.4 2.0 + - + +
278C ALA* 3.0 24.1 + - - +
290C LEU* 4.0 6.7 - - + -
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Residues in contact with LEU 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C VAL 4.7 1.8 + - - -
273C LEU* 3.3 4.2 - - + +
274C PRO* 1.3 79.5 - - - +
276C SER* 1.3 58.6 + - - +
278C ALA* 3.4 0.7 + - - +
279C ALA* 3.0 27.7 + - - +
287C VAL* 3.9 40.6 - - + +
290C LEU* 3.9 22.1 - - + +
291C THR* 3.9 12.1 - - + -
298C ALA* 3.9 20.6 - - + -
299C ASP 4.5 1.6 - - - +
300C LEU* 3.7 37.2 - - + +
310C VAL* 4.6 7.0 - - + -
335C LEU* 4.9 9.6 - - + -
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Residues in contact with SER 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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270C PHE 3.1 19.5 - - - -
271C GLY* 3.8 19.0 + - - -
273C LEU* 3.1 20.0 + - - +
275C LEU* 1.3 76.2 - - - +
277C LEU* 1.3 58.6 + - - +
279C ALA* 3.6 1.0 + - - +
280C CYS* 3.0 35.3 + - - -
302C ARG 5.5 0.2 + - - -
308C ASN 5.3 0.2 + - - -
309C THR 4.4 1.4 - - - -
310C VAL* 3.6 30.8 + - - +
313C ALA* 4.2 6.2 - - - +
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Residues in contact with LEU 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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229C HIS* 3.3 46.2 - - + +
232C ILE* 3.5 23.1 - - + -
233C GLU* 4.1 14.1 - - + +
268C PHE* 5.1 2.7 - - + -
270C PHE* 3.5 45.4 + - + -
273C LEU 2.9 9.8 + - - +
274C PRO* 3.6 6.3 - - + +
276C SER* 1.3 74.8 - - - +
278C ALA* 1.3 57.3 + - - +
281C THR* 2.6 53.9 + - + +
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Residues in contact with ALA 278 (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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232C ILE* 3.8 10.7 - - + +
274C PRO 3.0 17.5 + - - +
275C LEU 3.8 5.2 - - - +
277C LEU* 1.3 76.8 - - - +
279C ALA* 1.3 59.7 + - - +
281C THR* 3.6 2.4 + - - -
282C ASN 3.3 3.8 + - - -
283C GLN* 2.9 31.2 + - - +
286C ILE* 3.6 33.9 - - + -
287C VAL* 3.9 14.8 - - + +
290C LEU* 4.3 4.5 - - + -
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Residues in contact with ALA 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 LEU 3.0 11.2 + - - +
276C SER 3.9 1.1 - - - +
278C ALA* 1.3 76.7 - - - +
280C CYS* 1.3 63.2 + - - +
282C ASN 3.2 9.9 + - - -
287C VAL* 3.7 8.4 - - + +
310C VAL* 3.5 32.5 - - + -
314C LEU* 3.7 6.0 - - + +
327C PHE* 3.6 7.4 - - - -
331C MET* 3.5 38.5 - - + +
335C LEU* 4.2 3.1 - - + -
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Residues in contact with CYS 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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268C PHE* 4.8 7.0 - - + -
270C PHE* 3.8 19.5 - - + -
276C SER 3.0 23.9 + - - +
277C LEU 3.3 2.9 + - - +
279C ALA* 1.3 76.9 - - - +
281C THR* 1.3 59.5 + - + +
282C ASN 3.4 0.9 - - - -
310C VAL 5.2 0.2 - - - -
313C ALA* 3.4 44.2 - - - -
314C LEU* 4.0 10.8 - - - -
317C ILE* 3.8 24.1 - - + +
327C PHE* 3.4 18.4 - - - -
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Residues in contact with THR 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C ILE* 4.4 0.9 - - - +
233C GLU* 5.6 9.2 - - + +
235C ARG* 3.0 28.6 + - - -
268C PHE* 4.4 18.2 - - + -
277C LEU* 2.6 39.7 + - + +
278C ALA 3.6 1.0 + - - -
280C CYS* 1.3 78.7 - - + +
282C ASN* 1.3 67.0 + - - +
283C GLN* 2.7 27.5 + - - -
327C PHE* 4.6 0.9 - - - -
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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