Contacts of the helix formed by residues 309 - 318 (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 THR 309 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271C GLY* 5.6 0.2 - - - -
276C SER* 4.4 2.9 - - - -
300C LEU 4.7 1.1 - - - -
301C ARG 4.1 1.8 - - - +
302C ARG 3.5 13.2 - - - +
303C GLN* 3.5 22.2 - - + -
307C GLY 3.5 0.2 + - - -
308C ASN* 1.3 75.7 - - - +
310C VAL* 1.3 65.3 + - - +
311C LEU* 3.2 18.2 + - - +
312C HIS* 3.0 23.6 + - + -
313C ALA* 3.0 21.1 + - - +
348C LEU* 4.2 15.0 + - + +
351C LEU* 3.8 31.0 - - + +
359C PRO* 4.7 1.0 - - - +
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Residues in contact with VAL 310 (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* 4.2 8.5 - - + +
276C SER* 3.6 29.5 + - - +
279C ALA* 3.5 32.5 - - + -
300C LEU* 4.0 21.9 + - + +
302C ARG 4.4 3.6 + - - -
309C THR* 1.3 74.6 - - - +
311C LEU* 1.3 69.7 + - + +
313C ALA* 3.3 3.2 + - + +
314C LEU* 3.0 23.3 + - + +
335C LEU* 3.5 34.3 - - + -
348C LEU* 4.5 5.8 - - + -
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Residues in contact with LEU 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C THR* 3.1 6.3 + - - +
310C VAL* 1.3 78.8 - - - +
312C HIS* 1.3 62.0 + - - +
314C LEU* 3.4 6.7 + - + +
315C VAL* 3.2 24.8 + - - +
332C TYR* 3.9 44.7 - - + +
335C LEU* 4.3 16.8 - - + -
336C LEU* 3.7 8.7 - - + -
348C LEU* 3.5 40.4 - - + -
349C GLU* 3.6 31.2 - - + -
359C PRO* 3.5 17.0 - - + -
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Residues in contact with HIS 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C GLY 3.8 2.5 - - - -
308C ASN* 3.1 34.9 + - + +
309C THR* 3.0 37.0 + - - +
311C LEU* 1.3 76.9 - - - +
313C ALA* 1.3 58.0 + - - +
315C VAL* 3.2 8.3 + - - +
316C ALA* 2.8 27.8 + - - +
351C LEU 3.1 20.7 + - - -
353C ASN* 3.7 15.8 + - - -
357C LEU 2.8 27.9 + - - -
358C SER 3.3 18.8 - - - -
359C PRO* 3.4 12.9 - - + +
362C MET* 3.7 13.9 - - - +
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Residues in contact with ALA 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C TYR* 4.7 5.1 - - - +
270C PHE 3.8 2.5 - - - +
271C GLY* 3.8 27.1 - - - -
276C SER* 4.2 2.9 - - - -
280C CYS* 3.4 26.5 - - - -
308C ASN* 4.5 1.1 - - + +
309C THR 3.0 12.4 + - - +
310C VAL* 3.5 13.0 - - - +
312C HIS* 1.3 75.1 - - - +
314C LEU* 1.3 59.7 + - - +
316C ALA* 3.2 9.2 + - - +
317C ILE* 3.0 24.4 + - - +
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Residues in contact with LEU 314 (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 ALA* 3.7 32.3 - - + +
280C CYS* 4.2 8.5 - - - -
310C VAL* 3.0 18.7 + - + +
311C LEU* 3.7 8.3 - - - +
312C HIS 3.3 0.2 - - - -
313C ALA* 1.3 73.0 - - - +
315C VAL* 1.3 66.8 + - - +
317C ILE* 3.5 15.2 + - + +
318C ALA* 3.0 22.5 + - - +
327C PHE* 4.6 0.4 - - + -
328C VAL* 3.8 24.4 - - + +
331C MET* 4.1 10.5 - - + -
332C TYR* 4.0 26.2 - - + +
335C LEU* 3.5 33.0 - - + -
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Residues in contact with VAL 315 (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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311C LEU 3.2 16.0 + - - +
312C HIS 3.2 7.4 + - - +
314C LEU* 1.3 75.2 - - - +
316C ALA* 1.3 60.1 + - - +
318C ALA* 3.0 15.4 + - - +
332C TYR* 4.6 2.7 - - + -
359C PRO* 3.6 28.3 - - + +
362C MET* 3.8 15.7 - - + +
363C ALA* 3.4 42.0 - - + +
366C THR* 4.3 1.1 - - - +
368C LYS* 2.9 27.7 + - + -
371C ILE* 4.3 16.2 - - + -
375C ILE* 5.0 0.4 - - + -
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Residues in contact with ALA 316 (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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269C TYR* 3.7 34.5 - - + +
306C ARG* 5.7 1.1 - - - +
308C ASN* 5.3 0.7 - - - +
312C HIS 2.8 13.8 + - - +
313C ALA 3.4 9.2 - - - +
315C VAL* 1.3 77.4 - - - +
317C ILE* 1.3 58.2 + - - +
318C ALA 3.9 0.2 - - - +
362C MET* 4.8 7.8 - - + -
368C LYS* 2.8 20.1 + - - +
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Residues in contact with ILE 317 (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* 3.5 22.4 - - + -
269C TYR 3.2 26.5 - - - +
280C CYS* 3.8 26.2 - - + +
313C ALA 3.0 20.9 + - - +
314C LEU* 3.5 8.3 - - + +
316C ALA* 1.3 72.7 - - - +
318C ALA* 1.3 65.0 + - - +
319C ASP* 3.2 2.9 + - - +
324C ASN* 3.1 20.0 + - - +
327C PHE* 3.7 20.6 - - + -
328C VAL* 3.2 36.1 - - + -
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Residues in contact with ALA 318 (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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314C LEU 3.0 13.4 + - - +
315C VAL 3.0 15.9 + - - +
316C ALA 3.9 0.2 - - - +
317C ILE* 1.3 77.2 - - - +
319C ASP* 1.3 61.7 + - - +
320C ASN* 5.6 0.2 - - - +
324C ASN* 3.4 10.8 - - - +
325C THR* 5.1 4.0 - - + -
328C VAL* 4.4 7.6 - - + -
368C LYS* 2.6 49.7 + - + -
371C ILE* 4.0 12.6 - - + +
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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