Contacts of the helix formed by residues 361 - 371 (chain A) in PDB entry 5IXC
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 SER 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A GLY* 4.0 4.0 - - - -
360A ILE* 1.3 84.6 - - - +
362A GLY* 1.3 62.0 + - - -
364A THR* 2.6 33.1 + - - +
365A TRP* 3.7 8.6 - - - -
463A LEU 4.6 1.8 + - - -
527A TRP 3.4 22.8 + - - -
528A SER* 3.5 6.1 - - - -
650A TYR 5.5 0.4 - - - -
901A 7FA 1.6 55.5 + - - +
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Residues in contact with GLY 362 (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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329A GLY* 4.2 1.4 - - - -
331A GLY* 3.4 31.0 - - - -
334A ALA* 4.2 4.0 - - - -
335A MET* 3.8 7.8 - - - +
360A ILE 3.2 1.0 + - - -
361A SER* 1.3 81.5 + - - +
363A SER* 1.3 61.4 + - - +
365A TRP* 3.1 33.8 + - - +
366A THR 3.8 2.4 + - - -
901A 7FA 3.4 4.4 + - - +
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Residues in contact with SER 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ALA* 3.3 21.5 - - - +
328A THR 2.7 20.9 + - - -
334A ALA* 4.0 7.2 - - - +
338A LEU* 3.6 12.8 - - - +
359A GLY* 4.0 3.6 - - - -
360A ILE 3.1 22.4 + - - -
362A GLY* 1.3 76.0 - - - +
364A THR* 1.3 62.0 + - - +
365A TRP 3.4 0.2 + - - -
366A THR* 3.4 8.2 + - - -
367A MET* 3.1 24.2 + - - +
674A TYR* 3.6 11.4 - - - -
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Residues in contact with THR 364 (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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359A GLY 3.8 23.8 - - - +
360A ILE* 3.9 0.4 - - - -
361A SER 2.6 33.9 + - - +
363A SER* 1.3 74.4 - - - +
365A TRP* 1.3 64.2 + - - +
366A THR 3.4 0.2 - - - -
367A MET* 3.5 9.8 - - - +
368A ALA* 2.7 38.0 + - - +
462A TYR* 3.8 20.3 - - + -
463A LEU 4.9 1.1 - - - +
524A GLU* 5.0 0.4 - - - -
527A TRP* 3.5 36.1 - - + +
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Residues in contact with TRP 365 (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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331A GLY* 3.7 37.2 - - - -
332A ALA* 3.7 4.3 - - - -
335A MET* 3.9 28.3 - - - -
339A TYR* 4.7 0.2 + - - -
361A SER 3.7 2.8 + - - -
362A GLY* 3.1 13.2 + - - +
364A THR* 1.3 85.0 - - - +
366A THR* 1.3 64.2 + - - +
368A ALA* 3.5 1.7 + - - +
369A HIS* 3.3 23.7 + - - +
428A TRP* 4.6 0.7 - + - -
432A LEU* 3.7 26.8 - - + +
436A LEU* 4.1 19.6 - - + +
524A GLU* 4.0 20.4 - - + +
528A SER* 2.8 37.8 + - - -
771A MET* 3.8 33.0 - - + -
901A 7FA 4.1 17.0 - - + -
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Residues in contact with THR 366 (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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335A MET* 2.7 38.4 + - - +
338A LEU* 3.7 24.9 - - + +
339A TYR* 3.8 31.6 + - + -
342A LEU* 4.0 2.9 - - + -
357A PHE* 5.3 0.2 - - + -
362A GLY 3.8 0.4 + - - -
363A SER 3.4 9.3 + - - -
365A TRP* 1.3 79.2 - - - +
367A MET* 1.3 61.7 + - - +
370A LEU* 3.2 43.8 + - + +
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Residues in contact with MET 367 (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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357A PHE* 3.3 57.2 - - + +
358A SER 4.1 2.0 - - - -
359A GLY* 3.5 27.1 - - - +
363A SER* 3.1 15.1 + - - +
364A THR* 3.2 10.3 + - - +
366A THR* 1.3 80.7 - - - +
368A ALA* 1.3 64.5 + - - +
369A HIS 3.3 0.3 + - - -
370A LEU* 3.8 1.7 - - - +
371A TYR* 3.0 35.5 + - + -
460A PRO* 4.1 7.2 - - + -
461A LEU 3.5 22.4 - - - +
462A TYR* 3.5 27.6 - - + +
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Residues in contact with ALA 368 (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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364A THR 2.7 21.7 + - - +
365A TRP 3.9 1.3 - - - +
367A MET* 1.3 74.5 - - - +
369A HIS* 1.3 61.5 + - - +
371A TYR* 3.8 1.7 + - - -
372A GLY* 3.4 14.0 + - - -
443A GLN* 4.6 4.7 - - - +
448A GLN* 4.2 7.3 + - - +
462A TYR* 3.9 12.8 - - + -
520A ILE* 4.1 20.4 - - + +
524A GLU* 3.7 31.6 - - + +
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Residues in contact with HIS 369 (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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339A TYR* 3.4 24.4 + - - +
365A TRP 3.3 11.3 + - - +
367A MET 3.3 0.4 - - - -
368A ALA* 1.3 76.5 - - - +
370A LEU* 1.3 68.4 + - - +
372A GLY* 2.8 17.0 + - - -
373A ASP* 3.9 2.1 + - - +
384A PRO* 4.2 20.1 - - + +
387A TYR* 3.4 49.8 - + + -
437A HIS* 3.8 29.4 - + + -
441A MET* 5.3 7.7 - - + +
443A GLN* 4.9 4.6 - - - +
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Residues in contact with LEU 370 (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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339A TYR* 3.9 10.1 - - + -
342A LEU* 3.4 33.2 - - + -
357A PHE* 5.0 3.4 - - + -
366A THR* 3.2 26.5 + - + +
367A MET 3.8 3.1 - - - +
369A HIS* 1.3 79.1 - - - +
371A TYR* 1.3 58.8 + - + +
373A ASP* 3.1 17.9 + - - +
376A TRP* 3.0 50.4 - - + +
381A LEU* 3.4 27.8 - - + -
384A PRO* 3.9 25.4 - - + -
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Residues in contact with TYR 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A PHE* 3.9 18.8 - + - +
367A MET* 3.0 32.8 + - + +
368A ALA 4.0 0.9 - - - +
370A LEU* 1.3 73.7 - - + +
372A GLY* 1.3 62.3 + - - +
373A ASP 3.1 7.0 + - - +
374A PRO* 4.7 0.7 - - - +
376A TRP* 3.5 44.5 - + - -
448A GLN* 3.5 45.9 - - + +
451A ALA* 3.9 20.3 - - + +
452A LEU* 4.5 2.2 - - + -
457A ASN* 4.0 6.7 - - + -
458A PRO* 2.4 42.0 + - - +
460A PRO* 3.5 36.3 - - + +
462A TYR* 4.1 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