Contacts of the helix formed by residues 309 - 318 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276B SER* 4.4 2.9 - - - -
300B LEU 4.6 1.6 - - - -
301B ARG 4.1 7.9 - - - +
302B ARG 3.4 12.3 - - - +
303B GLN* 3.6 22.2 - - + -
308B ASN* 1.3 75.7 - - - +
310B VAL* 1.3 64.1 + - - +
311B LEU* 3.1 20.0 + - - +
312B HIS* 3.1 22.9 + - + -
313B ALA* 3.0 21.5 + - - +
348B LEU* 4.4 16.6 + - + +
351B LEU* 4.2 23.6 - - + -
359B PRO* 4.8 0.3 - - - +
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Residues in contact with VAL 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LEU* 4.1 14.8 - - + +
276B SER* 3.6 27.9 + - - +
279B ALA* 3.4 33.9 - - + -
300B LEU* 4.0 19.2 + - + +
302B ARG 4.3 3.6 + - - -
309B THR* 1.3 73.7 - - - +
311B LEU* 1.3 71.2 + - + +
313B ALA* 3.2 5.3 + - + +
314B LEU* 3.0 23.4 + - + +
335B LEU* 3.6 33.7 - - + -
348B LEU* 4.4 4.5 - - + -
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Residues in contact with LEU 311 (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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309B THR* 3.0 7.4 + - - +
310B VAL* 1.3 76.1 - - + +
312B HIS* 1.3 64.4 + - - +
314B LEU* 3.5 6.7 + - + +
315B VAL* 3.3 25.1 + - - +
332B TYR* 3.6 62.5 - - + +
335B LEU* 4.2 10.1 - - + -
336B LEU* 4.6 3.8 - - + +
348B LEU* 3.7 41.7 - - + +
349B GLU* 3.8 23.8 - - + +
359B PRO* 3.7 13.2 - - + -
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Residues in contact with HIS 312 (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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307B GLY 4.0 0.6 + - - -
308B ASN* 3.2 35.5 + - + +
309B THR* 3.1 39.3 + - + +
311B LEU* 1.3 77.3 - - - +
313B ALA* 1.3 57.6 + - - +
315B VAL* 3.2 5.2 + - - +
316B ALA* 2.9 24.1 + - - +
351B LEU 3.0 19.8 + - - -
352B LEU 4.0 0.6 - - - -
353B ASN* 3.7 18.8 + - + -
357B LEU 2.8 29.6 - - - -
358B SER 3.5 15.2 - - - -
359B PRO* 3.5 9.8 - - + +
362B MET* 3.4 24.1 - - - +
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B TYR* 4.8 4.9 - - - +
270B PHE 3.7 23.7 - - - +
271B GLY* 4.0 13.2 - - - -
276B SER* 4.2 2.9 - - - -
280B CYS* 3.6 16.6 - - - -
308B ASN* 4.6 1.5 - - + +
309B THR 3.0 12.4 + - - +
310B VAL* 3.2 13.7 + - - +
312B HIS* 1.3 76.5 - - - +
314B LEU* 1.3 55.7 + - - +
316B ALA* 3.2 11.6 - - - +
317B ILE* 3.0 24.4 + - - +
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Residues in contact with LEU 314 (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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279B ALA* 3.8 31.4 - - + +
280B CYS* 4.3 2.7 - - - -
310B VAL* 3.0 18.4 + - + +
311B LEU* 3.8 11.7 - - + +
313B ALA* 1.3 72.7 - - - +
315B VAL* 1.3 61.1 + - - +
317B ILE* 3.3 18.0 - - + +
318B ALA* 2.9 28.6 + - - +
327B PHE* 4.5 0.7 - - + -
328B VAL* 3.5 32.0 - - + +
331B MET* 4.0 15.5 - - + -
332B TYR* 3.6 39.3 - - + +
335B LEU* 4.2 10.8 - - + -
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Residues in contact with VAL 315 (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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311B LEU 3.3 13.6 + - - +
312B HIS 3.2 9.0 + - - +
314B LEU* 1.3 74.2 - - - +
316B ALA* 1.3 56.1 + - - +
318B ALA* 3.1 15.6 + - - +
332B TYR* 4.6 3.1 - - + -
359B PRO* 3.7 25.8 - - + +
362B MET* 4.0 15.9 - - + -
363B ALA* 3.5 41.3 - - + +
366B THR* 4.2 1.6 - - - +
368B LYS* 2.7 35.9 + - + +
371B ILE* 4.2 17.0 - - + -
375B ILE* 4.9 0.4 - - + -
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Residues in contact with ALA 316 (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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269B TYR* 3.8 33.2 - - + +
306B ARG* 5.9 0.9 - - - +
312B HIS 2.9 12.4 + - - +
313B ALA 3.2 11.6 + - - +
315B VAL* 1.3 76.2 - - - +
317B ILE* 1.3 58.2 + - + +
318B ALA 4.0 0.5 - - - +
362B MET* 3.8 13.6 - - + +
368B LYS* 3.0 17.5 + - - +
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Residues in contact with ILE 317 (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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268B PHE* 3.7 20.6 - - + -
269B TYR 3.5 24.9 - - - +
280B CYS* 3.3 48.0 - - + +
313B ALA 3.0 15.4 + - - +
314B LEU* 3.3 17.7 - - + +
316B ALA* 1.3 73.2 - - - +
318B ALA* 1.3 65.4 + - - +
319B ASP* 3.1 6.2 + - - +
324B ASN* 3.3 14.2 + - - +
327B PHE* 3.4 22.4 - - + -
328B VAL* 3.7 11.9 - - + -
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Residues in contact with ALA 318 (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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314B LEU 2.9 14.3 + - - +
315B VAL 3.1 12.7 + - - +
316B ALA 4.0 0.3 - - - +
317B ILE* 1.3 77.2 - - - +
319B ASP* 1.3 63.7 + - - +
320B ASN* 5.5 0.4 - - - +
324B ASN* 3.1 11.2 - - - +
325B THR* 6.4 0.4 - - - -
328B VAL* 4.4 7.2 - - + -
368B LYS* 2.8 38.5 + - + -
371B ILE* 4.0 26.0 - - + +
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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