Contacts of the helix formed by residues 363 - 376 (chain A) in PDB entry 1BHG
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 TRP 363 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A TYR* 5.2 6.5 - - - -
39A LYS* 6.2 1.3 - - - -
41A LEU* 5.1 20.6 - - + -
361A PHE* 3.4 27.7 - + - -
362A ASP* 1.3 69.6 + - - +
364A PRO* 1.3 76.2 - - + +
366A LEU* 3.1 23.6 + - + +
367A VAL* 3.0 35.3 + - + +
390A GLU* 3.6 22.2 + - - -
394A GLN* 5.5 1.9 + - - -
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Residues in contact with PRO 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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362A ASP* 3.2 21.5 - - - +
363A TRP* 1.3 94.1 - - + +
365A LEU* 1.3 59.4 + - - +
367A VAL* 3.1 8.6 + - + +
368A LYS* 3.0 25.2 + - - +
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Residues in contact with LEU 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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354A ALA* 3.9 24.7 - - + -
357A ARG* 4.4 10.8 - - - +
362A ASP* 3.0 27.8 + - + +
363A TRP 3.4 0.2 - - - -
364A PRO* 1.3 75.8 - - - +
366A LEU* 1.3 61.1 + - - +
368A LYS* 4.5 9.0 - - + -
369A ASP* 3.2 31.7 + - - +
613A ARG* 3.4 47.8 - - + +
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Residues in contact with LEU 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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361A PHE* 3.0 40.6 - - + -
362A ASP 3.2 11.8 + - - +
363A TRP* 3.1 23.5 + - + +
364A PRO 3.1 0.4 - - - -
365A LEU* 1.3 78.9 - - - +
367A VAL* 1.3 63.6 + - + +
369A ASP* 3.5 3.2 + - - +
370A PHE* 3.1 49.5 + - + -
390A GLU* 4.8 1.6 - - - +
391A GLU* 4.2 18.8 - - + +
394A GLN* 2.9 34.3 - - + +
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Residues in contact with VAL 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 TRP* 3.0 28.4 + - + +
364A PRO* 3.8 6.7 - - + +
366A LEU* 1.3 76.1 - - + +
368A LYS* 1.3 66.2 + - - +
370A PHE* 3.0 7.8 + - - +
371A ASN* 2.9 39.8 + - - +
394A GLN* 5.2 6.1 - - - +
399A TYR* 4.7 13.5 - - - +
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Residues in contact with LYS 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 PRO 3.0 16.7 + - - +
365A LEU* 4.1 11.7 - - + +
367A VAL* 1.3 72.7 - - - +
369A ASP* 1.3 55.8 + - - +
371A ASN* 2.8 34.7 + - + +
372A LEU* 2.9 24.7 + - + +
613A ARG* 4.3 31.9 - - + -
614A GLN* 5.4 8.4 - - - +
551B GLN* 6.0 1.6 - - - +
552B ASP* 5.7 7.1 - - - +
553B PRO* 6.1 2.2 - - - +
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Residues in contact with ASP 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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350A LYS* 3.3 24.0 + - - +
351A HIS 5.3 0.3 - - - +
365A LEU* 3.2 20.4 + - - +
366A LEU* 3.6 6.1 - - - +
368A LYS* 1.3 77.4 - - - +
370A PHE* 1.3 62.7 + - + +
372A LEU* 3.5 2.0 + - - -
373A LEU* 3.1 32.6 + - - +
589A PHE* 3.5 20.8 - - + -
613A ARG* 2.8 53.1 + - - +
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Residues in contact with PHE 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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350A LYS* 5.5 2.9 - - - -
366A LEU* 3.1 46.1 + - + +
367A VAL* 3.0 8.2 + - - +
369A ASP* 1.3 78.3 - - + +
371A ASN* 1.3 64.5 + - - +
373A LEU* 4.0 25.5 - - + +
374A ARG* 3.6 19.6 + - - +
381A PHE* 4.3 3.6 - + - -
391A GLU* 3.9 12.6 - - - -
394A GLN* 3.3 29.8 - - + -
395A MET* 3.3 37.2 - - + -
399A TYR* 3.5 40.2 - + + +
401A ILE* 4.4 11.0 - - + -
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Residues in contact with ASN 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 VAL* 2.9 40.7 + - - +
368A LYS* 2.8 15.1 + - + +
370A PHE* 1.3 78.6 - - - +
372A LEU* 1.3 53.9 + - + +
374A ARG* 2.7 53.9 + - - +
375A TRP* 2.8 18.4 + - - +
399A TYR* 5.7 3.5 + - - -
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Residues in contact with LEU 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 LYS* 2.9 27.8 + - + +
369A ASP* 3.7 7.2 - - - +
371A ASN* 1.3 75.8 - - - +
373A LEU* 1.3 56.1 + - - +
375A TRP* 3.2 17.2 - - + +
376A LEU* 2.8 37.3 + - - +
589A PHE* 3.8 20.0 - - + -
609A PHE* 3.2 35.9 - - + -
613A ARG* 3.6 45.3 - - + +
615A PRO* 5.8 2.5 - - + -
552B ASP* 5.3 5.8 - - + +
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Residues in contact with LEU 373 (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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348A VAL* 3.9 13.0 - - + -
350A LYS* 3.7 28.5 - - + -
369A ASP 3.1 25.9 + - - +
370A PHE* 4.1 36.6 - - + +
371A ASN 3.4 0.4 - - - -
372A LEU* 1.3 74.1 - - - +
374A ARG* 1.3 58.5 + - - +
376A LEU* 3.3 5.1 + - + +
377A GLY 2.9 24.4 + - - -
378A ALA* 3.2 30.7 + - + +
380A ALA 5.6 0.4 - - - +
381A PHE* 4.5 12.8 - - + -
401A ILE* 4.6 12.6 - - + -
589A PHE* 3.6 21.5 - - + -
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Residues in contact with ARG 374 (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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291A TYR* 2.9 46.6 + - + +
370A PHE 3.6 9.6 + - - +
371A ASN* 2.7 60.8 + - - +
373A LEU* 1.3 75.2 - - - +
375A TRP* 1.3 84.1 + - - +
376A LEU 3.4 0.3 + - - -
377A GLY 3.4 3.3 + - - -
399A TYR* 6.1 2.5 - - + -
401A ILE* 5.6 0.6 - - - +
627A TRP* 3.3 11.8 - - - -
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Residues in contact with TRP 375 (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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371A ASN 2.8 16.3 + - - +
372A LEU* 3.2 19.5 - - + +
374A ARG* 1.3 95.9 - - - +
376A LEU* 1.3 75.3 + - + +
609A PHE* 3.4 40.4 - + - -
615A PRO* 4.1 17.5 - - + -
619A ALA* 4.3 7.4 - - + -
620A PHE* 3.9 27.6 - + - -
623A ARG* 2.8 58.8 + - - +
627A TRP* 3.0 18.2 + - - -
552B ASP* 3.3 27.7 + - - -
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Residues in contact with LEU 376 (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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348A VAL* 5.5 3.1 - - + -
372A LEU 2.8 15.1 + - - +
373A LEU* 3.6 4.9 - - + +
375A TRP* 1.3 84.5 - - + +
377A GLY* 1.3 58.3 + - - +
378A ALA* 4.2 13.7 - - + +
589A PHE* 4.5 10.3 - - + -
608A ILE* 3.8 15.5 - - + -
609A PHE* 3.4 36.8 - - + -
619A ALA 3.6 25.6 - - - +
622A LEU* 4.4 13.2 - - + -
623A ARG* 3.4 29.8 - - + +
626A TYR* 3.6 8.7 - - + +
627A TRP* 3.0 18.0 - - - -
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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