Contacts of the helix formed by residues 372 - 386 (chain A) in PDB entry 6BQG
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 ASN 372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A LEU* 4.8 5.7 - - - +
89A ASN* 5.2 2.4 - - - +
368A TYR* 3.6 9.6 + - - +
369A THR 3.5 7.7 + - - +
371A PHE* 1.3 77.9 - - + +
373A LYS* 1.3 67.3 + - - +
374A ILE* 2.9 35.5 + - - +
375A TYR* 3.4 38.1 + - + -
376A ARG* 3.0 20.3 + - - +
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Residues in contact with LYS 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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371A PHE 3.8 3.6 + - - -
372A ASN* 1.3 74.3 + - - +
374A ILE* 1.3 80.8 + - + +
376A ARG* 3.2 19.6 + - - +
377A ARG* 3.0 55.3 + - - +
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Residues in contact with ILE 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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81A GLU* 4.7 15.4 - - + +
83A LYS* 3.6 40.6 - - + +
84A LEU* 3.7 35.9 - - + -
372A ASN* 2.9 15.8 + - - +
373A LYS* 1.3 96.0 - - + +
375A TYR* 1.3 57.1 + - - +
377A ARG* 3.9 9.1 - - - +
378A ALA* 2.9 31.4 + - - +
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Residues in contact with TYR 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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74A VAL* 4.1 18.4 - - + -
77A ALA* 3.6 31.2 - - + -
78A VAL* 3.6 16.9 - - + +
84A LEU* 3.8 19.4 - - + +
89A ASN* 2.9 23.6 + - - +
92A LEU* 3.7 19.8 - - + +
368A TYR* 3.5 28.7 - - + +
369A THR* 3.9 10.8 - - - +
372A ASN* 3.4 36.5 + - - +
373A LYS 3.3 0.4 - - - -
374A ILE* 1.3 74.9 - - - +
376A ARG* 1.3 60.5 - - - +
378A ALA* 4.0 4.0 - - - -
379A PHE* 2.7 47.4 + + + +
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Residues in contact with ARG 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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369A THR* 3.2 25.2 + - - +
370A LEU* 3.6 18.1 + - - +
371A PHE* 3.4 24.5 + - - +
372A ASN 3.0 11.3 + - - +
373A LYS* 3.5 23.6 - - - +
375A TYR* 1.3 77.0 - - - +
377A ARG* 1.3 60.8 + - + +
379A PHE* 3.4 2.2 + - - +
380A SER* 2.9 35.6 + - - +
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Residues in contact with ARG 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LYS* 3.0 56.8 + - - +
374A ILE* 4.3 7.8 - - - +
376A ARG* 1.3 75.9 - - + +
378A ALA* 1.3 62.9 + - - +
380A SER* 4.2 6.3 - - - -
381A ASN* 2.8 38.9 + - - +
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Residues in contact with ALA 378 (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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77A ALA* 4.1 13.5 - - + -
81A GLU* 3.9 26.9 - - + +
374A ILE 2.9 21.5 + - - +
375A TYR* 3.7 7.4 - - - +
376A ARG 3.3 0.2 - - - -
377A ARG* 1.3 76.6 - - - +
379A PHE* 1.3 56.7 + - - +
381A ASN* 3.4 3.5 + - - +
382A TYR* 3.0 50.2 + - + -
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Residues in contact with PHE 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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70A GLY* 4.1 7.2 - - - -
73A LEU* 3.4 57.9 - - + -
74A VAL* 3.5 23.6 - - + -
77A ALA* 4.3 0.9 - - + -
365A PRO* 4.9 4.9 - - + -
366A LEU* 6.1 0.2 - - - -
369A THR* 3.8 29.6 - - + +
375A TYR* 2.7 47.4 + + + +
376A ARG* 3.8 2.7 - - - +
378A ALA* 1.3 73.7 - - + +
380A SER* 1.3 64.9 + - - +
381A ASN 3.0 2.0 - - - -
382A TYR* 3.2 5.2 + + - -
383A LEU* 3.0 36.9 + - + +
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Residues in contact with SER 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ARG* 2.9 27.5 + - - +
377A ARG* 4.0 8.5 - - - -
379A PHE* 1.3 75.4 - - - +
381A ASN* 1.3 64.1 + - - +
383A LEU* 4.3 7.0 - - - +
384A ARG* 3.1 43.4 + - - +
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Residues in contact with ASN 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLU* 5.7 3.0 + - - +
377A ARG* 2.8 30.7 + - - +
378A ALA* 3.8 4.9 - - - +
379A PHE 3.0 1.0 - - - -
380A SER* 1.3 83.1 - - - +
382A TYR* 1.3 66.7 + - + +
383A LEU 3.3 1.8 - - - -
384A ARG* 4.3 10.6 + - - +
385A CYS* 2.8 45.5 + - - +
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Residues in contact with TYR 382 (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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73A LEU* 3.7 28.5 - - + +
76A MET* 3.5 28.9 - - + +
77A ALA* 3.4 36.7 - - + -
80A MET* 3.3 37.7 - - + +
81A GLU* 3.5 17.1 + - - +
378A ALA* 3.0 30.2 + - + +
379A PHE* 3.9 3.1 - - - +
381A ASN* 1.3 83.5 - - + +
383A LEU* 1.3 63.0 + - - +
385A CYS* 4.5 5.7 - - + +
386A ASN* 3.7 18.7 + - - +
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Residues in contact with LEU 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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73A LEU* 3.9 32.5 - - + -
379A PHE* 3.0 27.8 + - + +
380A SER* 4.6 6.1 - - - +
382A TYR* 1.3 78.8 - - - +
384A ARG* 1.3 60.2 + - + +
386A ASN 3.1 20.6 - - - +
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Residues in contact with ARG 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A SER* 3.1 33.6 + - - +
381A ASN* 3.6 13.8 + - - +
382A TYR 3.5 0.2 - - - -
383A LEU* 1.3 77.5 - - + +
385A CYS* 1.3 65.9 + - - +
386A ASN* 3.2 3.4 + - - +
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Residues in contact with CYS 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 ASN* 2.8 34.9 + - - +
382A TYR* 4.5 7.6 - - + +
383A LEU 3.6 0.4 - - - -
384A ARG* 1.3 78.1 - - - +
386A ASN* 1.3 65.3 + - + +
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Residues in contact with ASN 386 (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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382A TYR 3.7 11.8 + - - +
383A LEU* 3.1 19.7 - - - +
384A ARG 3.2 2.3 - - - +
385A CYS* 1.3 84.2 + - + +
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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