Contacts of the helix formed by residues 309 - 318 (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 THR 309 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A GLY* 5.8 0.3 - - - -
276A SER* 4.4 3.1 - - - -
300A LEU 4.6 1.8 - - - -
301A ARG 4.2 1.8 - - - +
302A ARG 3.4 13.5 - - - +
303A GLN* 3.5 23.1 - - + -
307A GLY 4.4 0.2 - - - +
308A ASN* 1.3 75.0 - - - +
310A VAL* 1.3 64.9 + - - +
311A LEU* 3.3 19.4 + - - +
312A HIS* 3.1 23.4 + - + +
313A ALA* 3.1 20.8 + - - +
348A LEU* 4.3 16.2 + - + +
351A LEU* 4.1 30.5 - - + +
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Residues in contact with VAL 310 (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* 4.5 9.0 - - + +
276A SER* 3.6 29.2 + - - +
279A ALA* 3.4 33.4 - - + -
300A LEU* 4.1 19.6 + - + +
302A ARG 4.4 3.0 + - - -
309A THR* 1.3 74.0 - - - +
311A LEU* 1.3 66.9 + - + +
313A ALA* 3.3 4.3 + - + +
314A LEU* 2.9 26.8 + - + +
335A LEU* 3.6 34.1 - - + -
348A LEU* 4.2 6.1 - - + -
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Residues in contact with LEU 311 (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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309A THR* 3.2 3.9 - - - +
310A VAL* 1.3 76.9 - - + +
312A HIS* 1.3 65.7 + - - +
314A LEU* 3.4 4.6 + - + +
315A VAL* 3.2 26.0 + - - +
332A TYR* 3.6 65.8 - - + +
335A LEU* 4.0 15.0 - - + -
336A LEU* 4.4 5.8 - - + +
348A LEU* 3.2 38.1 - - + -
349A GLU* 3.8 25.4 - - + +
359A PRO* 3.7 11.7 - - + -
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Residues in contact with HIS 312 (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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307A GLY 4.0 0.2 - - - -
308A ASN* 3.2 31.5 + - - +
309A THR* 3.1 42.3 + - + +
311A LEU* 1.3 79.2 - - - +
313A ALA* 1.3 57.7 + - - +
315A VAL 3.2 0.9 + - - -
316A ALA* 2.9 25.3 + - - +
351A LEU 3.0 20.0 + - - -
352A LEU 4.0 0.6 - - - -
353A ASN* 3.5 16.8 + - - -
357A LEU 2.8 29.2 - - - -
358A SER 3.6 14.6 - - - -
359A PRO* 3.6 6.7 - - + +
362A MET* 3.0 35.8 - - + +
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A TYR* 4.6 4.0 - - + +
270A PHE 3.8 25.1 - - - +
271A GLY* 3.8 15.5 - - - +
276A SER* 4.4 5.4 - - - -
280A CYS* 4.0 7.0 - - - -
308A ASN* 4.6 0.8 - - + +
309A THR 3.1 13.1 + - - +
310A VAL 3.6 8.3 - - - +
311A LEU 3.3 0.4 - - - -
312A HIS* 1.3 77.9 - - - +
314A LEU* 1.3 61.1 + - - +
316A ALA* 3.2 10.0 + - - +
317A ILE* 3.1 27.4 + - - +
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Residues in contact with LEU 314 (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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279A ALA* 3.9 31.0 - - + +
280A CYS* 4.3 8.1 - - - +
310A VAL* 2.9 19.2 + - + +
311A LEU* 3.8 9.6 - - + +
312A HIS 3.3 0.4 - - - -
313A ALA* 1.3 76.2 - - - +
315A VAL* 1.3 56.3 + - - +
317A ILE* 3.5 11.0 - - + +
318A ALA* 3.0 26.5 + - - +
327A PHE* 4.4 1.1 - - + -
328A VAL* 3.5 30.0 - - + +
331A MET* 3.8 12.8 - - + -
332A TYR* 3.6 35.4 - - + +
335A LEU* 3.6 24.5 - - + -
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Residues in contact with VAL 315 (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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311A LEU 3.2 15.1 + - - +
312A HIS 3.2 7.8 + - - +
314A LEU* 1.3 74.4 - - - +
316A ALA* 1.3 60.7 + - - +
318A ALA* 3.3 13.0 - - - +
332A TYR* 4.6 2.5 - - + -
359A PRO* 3.7 24.0 - - + +
362A MET* 3.6 16.4 - - + -
363A ALA* 3.5 33.7 - - + +
366A THR* 4.3 1.8 - - - +
368A LYS* 2.8 30.9 + - + +
371A ILE* 4.1 24.7 - - + -
375A ILE* 5.2 0.2 - - + -
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Residues in contact with ALA 316 (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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269A TYR* 3.6 37.5 - - + +
306A ARG* 5.6 2.2 - - - +
308A ASN* 5.5 1.1 - - - +
312A HIS 2.9 13.9 + - - +
313A ALA 3.2 9.4 + - - +
315A VAL* 1.3 76.1 - - - +
317A ILE* 1.3 59.1 + - - +
318A ALA 3.7 0.3 - - - +
362A MET* 4.7 5.8 - - - +
368A LYS* 2.9 20.0 + - - +
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Residues in contact with ILE 317 (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* 3.9 23.6 - - + -
269A TYR 3.3 24.0 - - - +
280A CYS* 3.6 32.8 - - - +
313A ALA 3.1 13.6 + - - +
314A LEU* 3.5 16.2 - - + +
316A ALA* 1.3 72.2 - - - +
318A ALA* 1.3 70.3 + - - +
319A ASP* 2.9 7.1 + - - +
324A ASN* 3.3 12.4 + - - +
327A PHE* 3.3 36.1 - - + -
328A VAL* 3.8 8.7 - - + -
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Residues in contact with ALA 318 (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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314A LEU 3.0 15.8 + - - +
315A VAL 3.3 13.9 - - - +
316A ALA 3.7 0.5 - - - +
317A ILE* 1.3 75.8 - - - +
319A ASP* 1.3 64.9 + - - +
320A ASN* 5.7 0.4 - - - +
324A ASN* 3.2 10.5 - - - +
325A THR* 6.3 0.7 - - - -
328A VAL* 4.3 9.0 - - + -
368A LYS* 2.5 36.9 + - + +
371A ILE* 4.1 23.8 - - + +
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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