Contacts of the helix formed by residues 273 - 281 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A HIS* 4.2 1.8 - - - -
250A VAL 5.3 0.4 - - - +
251A HIS* 3.2 39.5 - - + +
252A ALA 3.7 0.4 - - - -
253A GLN* 3.8 13.7 - - + -
270A PHE* 4.0 0.3 - - - -
271A GLY 2.8 19.2 + - - +
272A GLU* 1.3 74.3 - - - +
274A PRO* 1.4 65.6 - - + +
275A LEU* 3.5 4.7 - - + +
276A SER* 3.4 17.4 + - - +
277A LEU* 3.0 28.8 + - - +
302A ARG* 3.6 50.5 - - + +
303A GLN 4.1 11.2 - - - +
304A ASP* 4.1 5.8 - - + +
308A ASN 4.7 1.3 - - - +
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Residues in contact with PRO 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LEU* 4.1 20.4 - - + -
229A HIS* 3.9 15.5 - - + +
232A ILE* 3.4 30.6 - - + +
249A ASP 4.2 1.6 - - - +
250A VAL* 3.3 32.3 - - - +
251A HIS 4.0 0.2 - - - -
252A ALA* 3.1 22.9 - - + +
273A LEU* 1.4 85.0 - - + +
275A LEU* 1.3 61.4 + - - +
277A LEU* 3.4 5.0 + - + +
278A ALA* 3.2 18.5 + - - +
290A LEU* 3.9 7.2 - - + -
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A VAL 4.7 2.0 + - - +
273A LEU* 3.5 4.8 - - + +
274A PRO* 1.3 74.0 - - - +
276A SER* 1.3 67.3 + - - +
278A ALA* 3.2 3.5 + - - +
279A ALA* 3.0 22.9 + - - +
287A VAL* 3.9 31.2 - - + +
290A LEU* 3.8 15.5 - - + +
291A THR* 3.6 34.3 - - + -
298A ALA* 4.1 14.5 - - + +
299A ASP 4.0 8.1 - - - +
300A LEU* 3.8 36.1 - - + +
310A VAL* 4.8 8.3 - - + -
335A LEU* 4.9 4.7 - - + -
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Residues in contact with SER 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A PHE 3.2 19.3 - - - -
271A GLY* 3.9 17.8 + - - -
273A LEU* 3.4 20.6 + - - +
275A LEU* 1.3 79.0 - - - +
277A LEU* 1.3 57.1 + - - +
279A ALA* 3.4 1.0 + - - +
280A CYS* 2.9 35.0 + - - -
309A THR 4.4 1.7 + - - -
310A VAL* 3.6 33.0 + - - +
313A ALA* 4.4 6.2 - - - +
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A HIS* 3.6 46.4 - - + +
232A ILE* 3.8 19.3 - - + -
233A GLU* 4.2 14.1 - - + +
268A PHE* 5.2 2.2 - - + -
270A PHE* 3.7 41.3 + - + -
273A LEU 3.0 12.3 + - - +
274A PRO 3.5 7.6 - - - +
275A LEU 3.3 0.2 - - - -
276A SER* 1.3 76.5 - - - +
278A ALA* 1.3 52.2 + - - +
280A CYS 3.8 0.2 - - - -
281A THR* 2.6 59.1 + - + +
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ILE* 3.9 7.8 - - + +
274A PRO 3.2 10.0 + - - +
275A LEU 3.2 8.0 + - - +
277A LEU* 1.3 79.4 - - - +
279A ALA* 1.3 58.6 + - - +
281A THR* 3.6 5.5 + - - -
282A ASN 3.4 3.1 + - - -
283A GLN* 2.9 31.3 + - + +
286A ILE* 3.7 33.0 - - + -
287A VAL* 3.6 16.8 - - + +
290A LEU* 4.2 4.9 - - + -
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Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A LEU 3.0 9.8 + - - +
276A SER 3.7 1.8 - - - +
278A ALA* 1.3 75.3 - - - +
280A CYS* 1.3 57.5 + - - +
282A ASN 3.1 14.6 + - - -
287A VAL* 3.6 11.1 - - + +
310A VAL* 3.4 33.4 - - + -
314A LEU* 3.9 6.7 - - + +
327A PHE* 3.5 12.8 - - - -
331A MET* 3.6 31.7 - - + +
335A LEU* 4.1 4.0 - - + -
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Residues in contact with CYS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A PHE* 4.6 8.4 - - + -
270A PHE* 3.8 25.6 - - + -
276A SER 2.9 24.6 + - - +
277A LEU 4.1 1.1 - - - +
279A ALA* 1.3 73.9 - - - +
281A THR* 1.3 60.3 + - - +
282A ASN 3.3 1.3 - - - -
310A VAL 5.3 0.2 - - - -
313A ALA* 3.8 22.0 - - - -
314A LEU* 4.3 6.5 - - - -
317A ILE* 3.6 53.7 - - + +
327A PHE* 3.6 7.2 - - - -
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Residues in contact with THR 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ILE* 4.5 0.9 - - - +
233A GLU* 5.5 9.2 - - - +
235A ARG* 2.9 26.3 + - - +
268A PHE* 4.7 13.0 - - + -
277A LEU* 2.6 42.8 + - + +
278A ALA 3.6 1.7 + - - -
280A CYS* 1.3 79.9 - - + +
282A ASN* 1.3 71.1 + - - +
283A GLN* 2.8 28.9 + - - +
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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