Contacts of the helix formed by residues 371 - 385 (chain A) in PDB entry 4BL8
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 ALA 371 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LYS* 5.0 0.7 - - - +
367A THR 3.0 19.5 + - - +
368A ASN* 3.7 15.9 - - - +
369A ALA 3.3 3.3 - - - -
370A ALA* 1.4 72.4 - - - +
372A PRO* 1.3 69.4 - - - +
373A GLY 3.5 1.5 + - - -
374A LEU* 3.6 7.9 + - + +
375A HIS* 3.6 15.6 + - - +
438A LEU 3.7 6.1 - - - +
439A TYR* 3.5 32.1 - - + +
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Residues in contact with PRO 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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180A LYS* 4.0 10.3 - - - +
370A ALA 3.2 13.2 - - - +
371A ALA* 1.3 81.8 - - - +
373A GLY* 1.3 64.0 + - - +
375A HIS* 3.1 20.0 + - + +
376A ALA* 3.3 12.8 + - - +
438A LEU 4.0 0.7 - - - +
439A TYR 4.2 2.0 - - - +
530A THR* 4.6 2.3 - - - +
531A PRO* 3.5 29.3 - - + +
532A PHE* 3.5 27.1 - - + -
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Residues in contact with GLY 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PRO* 1.3 75.8 - - - +
374A LEU* 1.3 61.2 + - - +
375A HIS 3.5 0.2 + - - -
376A ALA* 3.8 8.0 + - - +
377A ILE* 3.6 19.6 + - - +
436A SER* 5.1 1.1 + - - -
437A ASP 3.5 16.6 - - - -
438A LEU* 2.9 22.5 + - - -
530A THR* 3.6 19.2 + - - +
532A PHE* 3.8 3.2 - - - -
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Residues in contact with LEU 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ASN* 3.6 44.2 - - + +
371A ALA* 3.8 12.6 - - + +
372A PRO 3.2 0.4 - - - -
373A GLY* 1.3 73.9 - - - +
375A HIS* 1.3 68.7 + - - +
376A ALA 3.3 0.2 + - - -
377A ILE* 3.4 6.1 + - - +
378A TYR* 3.1 60.1 + - + +
410A TYR* 3.9 23.3 - - + -
433A PHE* 4.3 9.0 - - + -
438A LEU* 3.4 29.7 + - + +
439A TYR* 5.1 3.1 - - - +
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Residues in contact with HIS 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A PRO 5.6 0.8 + - - -
338A SER* 3.8 23.0 + - - -
339A ALA* 3.8 33.3 + - + +
342A TYR* 3.9 22.6 - + - +
368A ASN 5.4 1.6 - - - +
371A ALA 3.6 9.9 + - - +
372A PRO* 3.1 13.9 + - + +
374A LEU* 1.3 87.1 - - + +
376A ALA* 1.3 61.0 + - - +
378A TYR* 3.2 6.0 + - - +
379A GLY* 3.0 24.6 + - - -
382A ARG* 4.4 5.5 + - - -
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Residues in contact with ALA 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PRO 3.3 8.3 + - - +
373A GLY 4.1 5.6 - - - +
374A LEU 3.2 0.4 - - - -
375A HIS* 1.3 82.1 - - + +
377A ILE* 1.3 65.3 + - + +
379A GLY* 3.1 10.4 + - - -
380A GLU* 3.1 11.6 + - - +
528A VAL* 3.6 33.1 - - + +
529A GLN 4.2 5.6 - - - +
530A THR* 3.9 16.2 - - + +
531A PRO* 5.8 1.1 - - + -
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Residues in contact with ILE 377 (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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373A GLY 3.6 16.1 + - - +
374A LEU 3.4 2.0 + - - +
375A HIS 3.3 0.6 - - - -
376A ALA* 1.3 73.5 - - + +
378A TYR* 1.3 66.8 + - - +
379A GLY 2.9 1.6 - - - -
380A GLU* 3.1 6.9 + - - +
381A CYS* 3.1 20.8 + - - -
431A ILE* 4.1 18.2 - - + -
432A SER 4.8 0.2 - - - +
433A PHE* 3.2 43.1 - - + -
436A SER* 3.8 21.5 - - - +
438A LEU* 4.1 4.3 - - + -
459A GLU* 3.9 19.1 - - + +
528A VAL* 5.2 2.7 - - + -
530A THR* 6.0 0.4 - - - +
535A VAL* 4.6 9.9 - - + -
537A PHE* 4.1 22.4 - - + -
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Residues in contact with TYR 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A TYR* 5.8 7.0 - - + -
346A THR* 5.9 2.7 - - - -
368A ASN* 5.4 6.4 + - + -
374A LEU* 3.1 45.9 + - + +
375A HIS* 3.6 9.6 - - - +
377A ILE* 1.3 77.2 - - - +
379A GLY* 1.3 64.1 + - - +
381A CYS* 3.1 4.7 + - - +
382A ARG* 2.9 42.4 + - - +
393A GLN* 2.9 24.8 + - - -
410A TYR* 4.6 10.0 - - - -
412A SER* 4.0 10.5 - - - -
414A TYR* 4.8 11.6 + - - -
433A PHE* 3.4 29.4 - + - -
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Residues in contact with GLY 379 (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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50A GLN* 5.0 3.5 + - - -
375A HIS* 3.0 14.2 + - - -
376A ALA* 3.1 6.0 + - - -
377A ILE 2.9 1.0 - - - -
378A TYR* 1.3 79.4 - - - +
380A GLU* 1.3 61.5 + - - +
382A ARG* 3.4 20.3 + - - +
383A ARG* 3.1 18.9 + - - +
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Residues in contact with GLU 380 (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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376A ALA 3.1 9.3 + - - +
377A ILE* 3.1 7.4 + - - +
379A GLY* 1.3 75.5 - - - +
381A CYS* 1.3 65.8 + - - +
383A ARG* 2.8 57.2 + - - +
384A LEU* 3.2 12.3 + - - +
525A MET* 3.8 20.7 - - + +
526A GLN* 3.2 35.8 + - - +
528A VAL* 3.4 29.6 - - + -
537A PHE* 4.7 0.7 - - + -
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Residues in contact with CYS 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ILE* 3.1 27.8 + - - -
378A TYR* 3.5 10.8 - - + +
380A GLU* 1.3 77.4 - - - +
382A ARG* 1.3 57.2 + - - +
384A LEU* 3.0 5.8 + - - -
385A TYR* 2.9 34.7 + - - +
414A TYR* 3.3 38.4 - - + +
431A ILE* 4.0 26.5 - - - -
433A PHE* 4.6 6.7 - - - -
525A MET* 4.3 8.3 - - - -
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Residues in contact with ARG 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLU* 3.7 27.7 - - - +
50A GLN* 4.7 5.0 + - - +
342A TYR* 3.1 53.6 + - - +
345A ARG* 3.6 23.7 - - - +
375A HIS* 4.4 8.5 + - - -
378A TYR* 2.9 37.5 + - - +
379A GLY* 3.8 17.6 + - - +
381A CYS* 1.3 77.7 - - - +
383A ARG* 1.3 61.5 + - - +
385A TYR 3.9 11.2 - - - +
386A PRO* 3.5 24.9 - - + +
388A GLN 5.6 4.0 - - - +
389A PRO* 5.6 4.3 - - + -
414A TYR* 5.3 5.8 - - + +
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Residues in contact with ARG 383 (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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50A GLN* 3.8 41.1 - - + +
379A GLY 3.1 11.6 + - - +
380A GLU* 2.8 48.3 + - - +
382A ARG* 1.3 79.4 - - - +
384A LEU* 1.3 81.0 + - - +
386A PRO* 4.2 5.7 - - - +
524A GLN 3.5 18.8 + - - -
526A GLN* 3.9 11.0 - - - +
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Residues in contact with LEU 384 (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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380A GLU* 3.8 9.2 - - - +
381A CYS* 3.0 7.4 + - - +
383A ARG* 1.3 109.6 - - - +
385A TYR* 1.3 88.4 + - + +
386A PRO* 3.3 11.6 - - - +
429A HIS* 4.5 2.9 - - + -
524A GLN* 4.0 41.3 - - + +
525A MET* 3.5 33.4 - - + +
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Residues in contact with TYR 385 (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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381A CYS* 2.9 16.1 + - - +
382A ARG* 3.9 11.4 - - - +
384A LEU* 1.3 103.0 - - + +
386A PRO* 1.3 65.0 - - - +
387A ASP 3.1 4.0 + - - +
388A GLN* 3.2 37.1 + - + +
414A TYR* 3.2 52.6 - + + -
415A ARG 3.9 13.7 - - - -
416A ASN* 2.9 32.9 + - + -
429A HIS* 2.8 35.8 + - + +
431A ILE* 4.8 1.8 - - + -
524A GLN* 4.0 2.3 + - - -
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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