Contacts of the helix formed by residues 360 - 372 (chain A) in PDB entry 5X61
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 360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A GLY* 4.9 6.1 - - - -
279A GLY* 5.3 0.7 - - - -
280A GLY* 4.9 4.9 + - - -
359A GLU* 1.3 80.9 - - - +
361A ALA* 1.3 64.7 + - - +
363A ALA* 3.0 5.9 + - - +
364A VAL* 2.9 28.6 + - - +
385A GLN 2.9 12.9 + - - -
386A SER 3.4 14.1 + - - -
387A GLY* 4.0 1.0 - - - -
393A TRP* 3.7 18.1 - - - -
490A PHE* 4.9 3.3 - - - -
560A PHE* 4.2 1.6 - - - -
600A HIS* 2.9 30.4 + - - -
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Residues in contact with ALA 361 (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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277A PHE 4.4 0.4 - - - -
278A GLY* 3.9 1.8 - - - -
279A GLY 3.8 7.0 - - - +
280A GLY* 3.4 29.6 - - - +
281A PHE* 3.4 32.9 - - + +
309A TYR* 4.6 2.0 - - - +
359A GLU 3.2 0.4 + - - -
360A SER* 1.3 80.3 + - - +
362A GLY* 1.3 57.1 + - - +
364A VAL* 3.7 3.8 - - - -
365A SER* 2.9 31.4 + - - -
393A TRP* 3.7 10.4 - - + -
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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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276A ILE* 3.3 27.1 - - - +
277A PHE 3.4 10.5 - - - -
278A GLY* 3.3 4.0 - - - -
358A GLY* 3.8 7.9 - - - -
359A GLU 2.9 10.5 + - - -
361A ALA* 1.3 77.5 - - - +
363A ALA* 1.3 56.1 + - - +
365A SER* 3.3 3.6 + - - -
366A VAL* 2.8 31.5 + - - +
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Residues in contact with ALA 363 (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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358A GLY 3.4 17.8 - - - +
359A GLU 3.5 0.4 - - - +
360A SER 3.0 7.5 + - - +
362A GLY* 1.3 73.1 - - - +
364A VAL* 1.3 60.7 + - - +
366A VAL* 3.3 7.7 + - - +
367A SER* 2.9 30.5 + - - -
384A LEU* 3.6 8.1 - - - +
385A GLN 3.3 33.7 - - - +
387A GLY* 3.8 18.4 - - - +
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Residues in contact with VAL 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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281A PHE* 3.6 23.6 - - + -
360A SER 2.9 18.0 + - - +
361A ALA 3.6 7.9 - - - +
363A ALA* 1.3 74.7 - - - +
365A SER* 1.3 57.0 + - - +
367A SER* 2.5 24.1 + - - +
368A LEU* 2.9 28.2 + - + +
388A SER 3.7 25.4 - - - +
389A PRO* 4.6 1.8 - - + -
393A TRP* 3.4 28.3 - - + -
394A ALA* 3.7 21.1 - - + +
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Residues in contact with SER 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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276A ILE* 3.9 8.1 - - - +
281A PHE* 3.4 14.2 - - - -
309A TYR* 4.7 0.9 + - - -
330A LEU* 4.1 3.4 - - - +
333A GLN* 3.0 39.2 + - - -
361A ALA 2.9 19.2 + - - -
362A GLY 3.3 8.7 - - - -
364A VAL* 1.3 73.4 - - - +
366A VAL* 1.3 64.8 + - - +
368A LEU* 2.9 21.2 + - - +
369A HIS* 3.0 19.7 + - - -
459A PHE* 5.6 0.2 - - - -
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Residues in contact with VAL 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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276A ILE* 4.1 11.2 - - + -
356A LEU* 3.7 22.2 - - + +
357A PHE 3.8 11.2 - - - +
358A GLY* 3.6 22.4 - - - +
362A GLY 2.8 23.5 + - - +
363A ALA* 3.3 7.4 + - - +
365A SER* 1.3 71.1 - - - +
367A SER* 1.3 62.1 + - - +
369A HIS* 3.4 13.1 + - - +
370A LEU* 3.4 20.3 + - - +
379A PHE* 4.7 1.2 - - - -
382A ALA* 3.5 28.5 - - + -
383A ILE 3.9 7.0 - - - +
384A LEU* 3.9 6.3 - - + -
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Residues in contact with SER 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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363A ALA 2.9 8.2 + - - -
364A VAL* 2.5 23.7 + - - -
366A VAL* 1.3 73.6 - - - +
368A LEU* 1.3 63.5 + - - +
370A LEU* 3.2 23.4 + - - +
371A LEU* 3.2 18.2 + - - +
384A LEU* 3.4 21.3 - - - +
388A SER* 4.5 0.9 - - - -
389A PRO* 3.2 38.4 - - - +
567A PHE* 4.0 4.5 - - - -
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Residues in contact with LEU 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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330A LEU* 3.8 28.7 - - + -
364A VAL* 2.9 30.0 + - + +
365A SER* 2.9 6.7 + - - +
367A SER* 1.3 76.0 + - - +
369A HIS* 1.3 52.4 + - - +
371A LEU* 3.3 6.0 + - + +
372A SER* 2.8 35.3 + - - -
389A PRO* 3.8 20.6 - - + -
395A LEU* 4.3 5.8 - - + -
453A PRO* 4.0 22.0 - - + -
459A PHE* 3.7 14.1 - - + -
460A LEU* 3.8 28.9 - - + +
464A PRO* 4.1 10.5 - - + -
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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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276A ILE* 3.8 18.1 - - + +
330A LEU* 4.1 1.8 - - + +
333A GLN* 2.8 40.8 + - + +
334A ASN 4.1 5.6 - - - -
337A LEU* 4.1 12.2 - - + +
356A LEU* 3.8 12.1 - - + -
365A SER 3.0 23.3 + - - -
366A VAL 3.6 6.7 - - - +
367A SER 3.2 0.2 - - - -
368A LEU* 1.3 75.4 - - - +
370A LEU* 1.3 62.7 + - - +
371A LEU 3.2 0.6 + - - -
372A SER 3.6 10.2 + - - +
375A SER* 2.7 35.4 + - - +
376A ARG* 4.4 2.6 - - - -
379A PHE* 3.4 27.8 - - + -
459A PHE* 3.5 23.2 - + - -
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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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366A VAL 3.4 16.1 + - - +
367A SER* 3.2 10.2 + - - +
369A HIS* 1.3 78.3 - - - +
371A LEU* 1.3 64.2 + - + +
376A ARG* 3.6 8.2 + - - -
379A PHE* 3.6 27.4 - - + -
382A ALA* 3.8 15.7 - - + +
384A LEU* 4.4 2.2 - - + -
473A PHE* 3.7 1.2 - - - -
474A LYS* 3.1 36.8 + - + +
476A THR* 4.6 9.2 - - - +
478A ILE* 3.7 25.6 - - + -
567A PHE* 3.8 21.5 - - + -
571A TYR* 3.3 20.9 - - + +
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Residues in contact with LEU 371 (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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367A SER 3.2 16.7 + - - +
368A LEU* 3.6 11.9 - - + +
369A HIS 3.2 0.4 - - - -
370A LEU* 1.3 81.2 - - + +
372A SER* 1.3 65.9 + - - +
373A ALA* 3.6 1.4 + - - -
376A ARG* 3.7 12.8 + - - -
389A PRO* 4.4 8.3 - - + -
460A LEU* 4.1 12.1 - - + -
464A PRO* 3.5 44.2 - - + +
467A SER* 3.7 23.5 + - - +
468A LEU* 4.8 6.3 - - + -
472A ARG 4.4 8.5 - - - +
473A PHE* 4.1 15.0 - - + -
567A PHE* 4.2 20.4 - - + -
210B ARG* 6.0 0.7 + - - -
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Residues in contact with SER 372 (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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368A LEU 2.8 21.5 + - - -
369A HIS 3.6 1.8 + - - +
370A LEU 3.6 1.0 - - - -
371A LEU* 1.3 75.5 - - - +
373A ALA* 1.3 65.0 + - - +
374A LEU 3.1 10.7 + - - -
375A SER* 3.6 17.9 + - - -
376A ARG* 3.4 24.1 + - - +
459A PHE* 2.8 49.3 + - - -
460A LEU* 4.4 2.2 - - - -
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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