Contacts of the helix formed by residues 371 - 385 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B THR 3.4 13.8 + - - +
368B ASN 4.0 4.0 + - - +
369B ALA 3.5 2.6 - - - -
370B ALA* 1.3 76.8 - - + +
372B PRO* 1.3 70.4 - - - +
373B GLY 3.3 2.0 - - - -
374B LEU* 3.2 20.3 + - + +
375B HIS* 3.2 12.3 + - - +
438B LEU 3.3 14.4 - - - +
439B TYR* 3.4 30.5 - - + +
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Residues in contact with PRO 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ILE* 5.2 6.1 - - + -
180B LYS* 3.8 15.5 - - - +
336B GLN* 5.8 8.5 - - + +
370B ALA 2.9 17.2 - - - +
371B ALA* 1.3 78.8 - - - +
373B GLY* 1.3 59.9 + - - +
375B HIS* 3.0 20.8 + - + +
376B ALA* 3.2 12.1 + - - +
438B LEU 4.0 0.4 - - - +
439B TYR 4.2 4.5 - - - +
530B THR* 4.3 2.5 - - - +
531B PRO* 3.2 31.9 - - + +
532B PHE* 3.3 32.8 - - + -
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Residues in contact with GLY 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B PRO* 1.3 76.1 - - - +
374B LEU* 1.3 65.2 + - - +
376B ALA* 3.5 8.7 + - - +
377B ILE* 3.1 22.1 + - - +
436B SER* 5.0 0.8 + - - -
437B ASP 3.4 21.8 - - - -
438B LEU* 3.1 10.7 + - - -
530B THR* 3.5 19.0 + - - -
532B PHE* 3.7 2.8 - - - -
535B VAL* 5.7 0.9 - - - +
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ASN* 4.4 27.4 - - + +
371B ALA* 3.2 15.8 + - + +
373B GLY* 1.3 74.5 - - - +
375B HIS* 1.3 72.0 + - - +
377B ILE* 3.0 15.9 + - - +
378B TYR* 3.0 51.9 + - + +
410B TYR* 4.0 28.0 - - + -
433B PHE* 4.5 7.4 - - + -
438B LEU* 3.4 26.5 + - + +
439B TYR* 4.8 14.6 - - + +
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Residues in contact with HIS 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B PRO 4.3 7.7 + - - -
336B GLN* 5.2 7.6 - - + -
338B SER* 3.6 18.2 + - - -
339B ALA* 3.2 46.9 + - + +
342B TYR* 5.0 0.4 - + - -
368B ASN 5.4 4.2 + - - +
369B ALA 5.7 1.1 - - - +
371B ALA 3.2 8.0 + - - +
372B PRO* 3.0 14.5 + - + +
374B LEU* 1.3 88.7 - - - +
376B ALA* 1.3 65.5 + - - +
378B TYR* 3.1 5.4 + - - +
379B GLY* 3.0 21.2 + - - -
382B ARG* 4.8 15.5 + - - -
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Residues in contact with ALA 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B PRO 3.2 6.7 + - - +
373B GLY 3.8 6.7 - - - +
374B LEU 3.1 0.4 - - - -
375B HIS* 1.3 84.2 - - - +
377B ILE* 1.3 61.9 + - + +
379B GLY* 3.1 3.1 + - - -
380B GLU* 3.0 22.7 + - - +
528B VAL* 3.5 32.1 - - + +
529B GLN 4.4 3.6 - - - +
530B THR* 3.7 18.6 - - + +
531B PRO* 6.1 0.4 - - + -
535B VAL* 6.2 0.9 - - + -
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Residues in contact with ILE 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B GLY 3.1 24.2 + - - +
374B LEU 3.0 2.7 + - - +
376B ALA* 1.3 80.0 - - + +
378B TYR* 1.3 67.2 + - - +
380B GLU* 3.1 6.7 + - - +
381B CYS* 3.0 21.1 + - - -
431B ILE* 3.9 20.6 - - + -
432B SER 4.6 0.4 - - - +
433B PHE* 3.0 37.7 - - + -
436B SER* 3.8 14.8 - - - +
438B LEU* 3.8 22.7 - - + -
459B GLU* 4.2 9.6 - - + +
528B VAL* 5.5 0.7 - - + -
535B VAL* 4.7 8.3 - - + -
537B PHE* 4.2 23.8 - - + -
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Residues in contact with TYR 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B TYR* 6.0 4.0 - - + -
345B ARG* 5.9 5.2 - - - -
368B ASN* 5.8 8.6 + - + -
374B LEU* 3.0 34.7 + - + +
375B HIS* 3.1 11.9 + - - +
377B ILE* 1.3 77.3 - - - +
379B GLY* 1.3 62.9 + - - +
381B CYS* 3.1 8.4 + - - +
382B ARG* 3.0 42.7 + - - +
393B GLN* 3.2 26.6 + - - -
410B TYR* 4.6 13.9 - + - -
412B SER* 4.7 1.6 - - - -
414B TYR* 4.8 3.0 + - - -
433B PHE* 3.3 39.9 - + - -
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Residues in contact with GLY 379 (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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375B HIS* 3.0 16.2 + - - -
376B ALA 3.1 4.2 + - - -
377B ILE 3.0 0.6 - - - -
378B TYR* 1.3 76.6 - - - +
380B GLU* 1.3 64.3 + - - +
382B ARG* 3.1 20.0 + - - +
383B ARG* 3.0 22.0 + - - +
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Residues in contact with GLU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ALA 3.0 11.1 + - - +
377B ILE* 3.1 9.1 + - - +
379B GLY* 1.3 76.2 - - - +
381B CYS* 1.3 62.9 + - - +
383B ARG* 3.2 45.6 + - - +
384B LEU* 3.6 11.3 + - - +
525B MET* 4.4 16.5 - - + +
526B GLN* 3.4 35.2 + - - +
527B PRO 5.1 0.3 - - - +
528B VAL* 3.2 29.3 - - + +
537B PHE* 4.4 3.4 - - + -
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Residues in contact with CYS 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ILE* 3.0 33.9 + - - -
378B TYR* 3.4 8.7 - - - +
379B GLY 3.1 0.2 - - - -
380B GLU* 1.3 78.3 - - - +
382B ARG* 1.3 64.6 + - - +
384B LEU* 3.0 3.7 + - - +
385B TYR* 3.0 28.8 + - - +
414B TYR* 3.1 40.4 - - + +
431B ILE* 4.0 23.6 - - - -
433B PHE* 4.5 8.5 - - - -
525B MET* 4.5 9.2 - - - -
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Residues in contact with ARG 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU* 3.5 36.9 - - + +
50B GLN* 3.8 2.9 + - - -
67B ARG* 5.8 0.8 - - - +
342B TYR* 3.1 51.7 + - - +
345B ARG* 5.8 2.0 - - - +
375B HIS* 4.8 8.3 + - - -
378B TYR* 3.0 37.0 + - - +
379B GLY* 3.1 18.0 + - - +
381B CYS* 1.3 79.7 - - - +
383B ARG* 1.3 62.6 + - - +
384B LEU 2.8 1.7 + - - -
385B TYR* 2.9 22.2 + - - +
386B PRO* 3.1 17.1 - - + +
388B GLN 5.3 5.2 - - - +
389B PRO* 5.4 11.7 + - + +
414B TYR* 5.1 5.2 - - + +
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Residues in contact with ARG 383 (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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49B PRO* 4.1 7.4 - - + -
50B GLN* 2.6 71.1 + - + +
379B GLY 3.0 12.7 + - - +
380B GLU* 3.2 33.6 + - - +
381B CYS 3.2 0.4 - - - -
382B ARG* 1.3 76.1 - - - +
384B LEU* 1.3 79.6 + - - +
524B GLN 3.4 23.4 + - - -
526B GLN* 3.7 16.7 - - - +
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Residues in contact with LEU 384 (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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380B GLU* 3.9 10.3 - - - +
381B CYS* 3.0 7.0 + - - +
382B ARG 2.9 0.8 - - - -
383B ARG* 1.3 107.9 - - - +
385B TYR* 1.3 88.4 + - + +
386B PRO* 3.3 12.7 - - - +
429B HIS* 4.5 2.0 - - + -
524B GLN* 3.9 43.1 - - + +
525B MET* 3.6 34.1 - - + +
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Residues in contact with TYR 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B CYS* 3.0 13.9 + - - +
382B ARG* 2.9 13.5 + - - +
384B LEU* 1.3 103.9 - - + +
386B PRO* 1.3 66.0 - - - +
387B ASP 3.1 3.7 + - - -
388B GLN* 3.2 37.1 + - + +
414B TYR* 3.2 53.1 - + + -
415B ARG 4.0 12.6 - - - -
416B ASN* 3.1 30.5 + - + -
429B HIS* 2.8 34.0 + - + +
431B ILE* 4.8 2.5 - - + -
524B GLN* 3.9 3.1 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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