Contacts of the helix formed by residues 372 - 391 (chain A) in PDB entry 6HBU
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 372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A THR* 1.3 82.4 - - - +
373A PHE* 1.3 66.1 + - - +
374A CYS* 3.9 5.6 + - - +
375A HIS* 3.5 16.8 + - - +
376A GLN* 3.2 21.0 + - - +
465A ARG* 4.7 7.4 - - - +
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Residues in contact with PHE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A SER* 1.3 75.8 - - - +
374A CYS* 1.3 71.6 + - - +
376A GLN* 3.2 4.1 + - - +
377A LEU* 2.9 48.3 + - + +
465A ARG* 3.6 29.3 - - - +
467A SER* 3.3 29.8 - - - -
468A SER* 3.5 25.4 - - - -
471A LEU* 3.7 27.1 - - + -
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Residues in contact with CYS 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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372A SER* 3.4 5.2 + - - +
373A PHE* 1.3 94.5 - - - +
375A HIS* 1.3 60.1 + - - +
377A LEU* 3.9 10.9 - - + +
378A ARG* 2.9 42.9 + - - +
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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
----------------------------------------------------------
145A ALA* 2.8 30.4 + - - +
146A LEU* 3.8 5.6 - - + -
150A THR* 3.8 22.2 - - + +
157A LYS* 4.4 4.4 + - - -
371A THR* 3.4 28.4 - - + +
372A SER* 3.5 12.8 + - - +
373A PHE 3.2 0.6 - - - -
374A CYS* 1.3 78.2 - - - +
376A GLN* 1.3 62.4 + - - +
378A ARG* 3.3 24.9 + - - +
379A TRP* 3.0 55.9 + + - -
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Residues in contact with GLN 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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146A LEU* 3.7 24.4 + - + -
369A TYR* 4.0 15.0 - - - +
371A THR* 2.8 35.0 + - - +
372A SER 3.2 10.5 + - - +
373A PHE 3.2 1.4 + - - +
375A HIS* 1.3 74.9 - - - +
377A LEU* 1.3 64.4 + - - +
379A TRP* 4.4 0.2 - - - +
380A VAL* 3.2 30.3 + - - +
463A TYR 3.1 23.2 + - - +
464A TYR* 3.6 6.3 - - + +
465A ARG* 3.1 32.9 + - - -
468A SER* 3.2 18.6 + - - +
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Residues in contact with LEU 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 PHE* 2.9 37.7 + - + +
374A CYS* 4.0 11.9 - - + +
375A HIS 3.2 0.2 - - - -
376A GLN* 1.3 78.1 - - - +
378A ARG* 1.3 60.0 - - + +
379A TRP 3.3 0.7 - - - -
381A SER* 2.9 27.7 + - - -
468A SER* 4.0 13.2 - - - +
471A LEU* 3.7 21.1 - - + +
472A GLY* 3.5 29.5 - - - +
475A LEU* 4.7 12.6 - - + -
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Residues in contact with ARG 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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374A CYS* 2.9 30.1 + - - +
375A HIS* 3.3 26.3 + - - +
376A GLN 3.3 1.0 - - - -
377A LEU* 1.3 82.5 - - + +
379A TRP* 1.3 66.5 + - + +
381A SER* 3.9 5.6 - - - -
382A LYS* 3.2 23.3 - - - +
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Residues in contact with TRP 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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141A GLN* 4.2 17.3 - - + -
142A PHE* 3.2 33.9 - + + -
145A ALA* 3.5 27.8 - - + -
146A LEU* 4.0 16.4 - - + -
154A ASN* 4.6 22.4 - - - -
375A HIS* 3.0 58.6 + + - +
377A LEU 3.3 0.4 - - - -
378A ARG* 1.3 86.6 + - + +
380A VAL* 1.3 61.0 + - - +
381A SER 3.3 1.3 - - - -
382A LYS* 3.7 39.2 - - + +
383A ARG* 3.0 21.2 + - + +
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Residues in contact with VAL 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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142A PHE* 4.4 11.4 - - + -
146A LEU* 4.6 2.9 - - + -
376A GLN 3.2 20.3 + - - +
379A TRP* 1.3 76.4 - - - +
381A SER* 1.3 53.9 + - - +
383A ARG* 4.0 6.9 + - - +
384A SER* 2.6 38.8 + - - +
464A TYR* 3.9 33.4 - - + -
468A SER 4.0 11.9 - - - +
469A TYR* 3.7 39.0 - - + +
472A GLY* 4.3 8.1 - - - -
473A LYS* 4.4 2.0 - - - +
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Residues in contact with SER 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU 2.9 22.8 + - - -
378A ARG* 3.9 6.4 - - - -
380A VAL* 1.3 77.9 - - - +
382A LYS* 1.3 61.1 + - - +
384A SER* 3.0 2.0 + - - -
385A PHE* 2.8 52.2 + - - -
472A GLY* 3.3 27.3 + - - -
475A LEU* 4.8 12.3 - - - +
476A SER* 4.3 0.2 - - - -
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Residues in contact with LYS 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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154A ASN* 5.6 1.8 + - - -
378A ARG 3.2 23.3 - - - +
379A TRP* 3.6 46.2 + - + -
380A VAL 3.4 0.8 - - - -
381A SER* 1.3 82.0 + - - +
383A ARG* 1.3 61.2 + - - +
385A PHE* 3.7 7.2 + - - +
386A LYS* 3.3 50.1 + - - +
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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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131A MET* 3.7 34.0 - - - +
134A LEU* 3.9 32.7 - - + +
139A ASN* 5.7 1.0 + - - -
142A PHE* 3.3 36.1 - - + -
379A TRP* 3.0 18.3 + - + +
380A VAL* 4.1 8.1 + - - +
382A LYS* 1.3 77.4 - - - +
384A SER* 1.3 63.2 + - - +
386A LYS* 3.3 9.9 + - - +
387A ASN* 2.9 26.5 + - - +
454A LEU* 4.1 11.3 - - - +
458A GLU* 2.8 40.2 + - - -
464A TYR* 4.8 1.6 - - - -
469A TYR* 4.6 17.2 - - - -
473A LYS* 5.7 2.8 - - - +
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Residues in contact with SER 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A VAL* 2.6 22.6 + - - +
381A SER* 3.0 4.1 + - - -
383A ARG* 1.3 77.8 + - - +
385A PHE* 1.3 62.6 + - - +
387A ASN* 3.5 10.1 + - - +
388A LEU* 3.3 29.1 + - - +
472A GLY 4.5 1.0 + - - -
473A LYS* 3.6 29.3 - - - +
476A SER* 3.2 26.0 - - - -
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Residues in contact with PHE 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 SER* 2.8 40.3 + - - +
382A LYS* 4.2 7.0 - - - +
384A SER* 1.3 75.9 - - - +
386A LYS* 1.3 61.0 + - + +
388A LEU* 3.2 7.9 + - + +
389A LEU* 2.8 41.8 + - + +
475A LEU* 3.4 31.2 - - + -
476A SER* 3.8 17.0 - - - -
479A LEU* 4.4 14.8 - - + -
480A PRO* 4.0 18.6 - - + -
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Residues in contact with LYS 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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133A THR 5.6 1.6 - - - +
134A LEU* 5.0 11.9 - - + -
138A GLU* 5.1 16.0 + - - +
382A LYS* 3.3 43.3 + - - +
383A ARG* 3.3 12.5 + - + +
384A SER 3.3 0.6 - - - -
385A PHE* 1.3 79.2 - - + +
387A ASN* 1.3 58.2 + - - +
389A LEU* 4.0 8.9 - - + +
390A GLY* 3.1 22.2 + - - -
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Residues in contact with ASN 387 (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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131A MET* 3.7 26.0 - - - +
133A THR* 2.4 37.9 + - + +
134A LEU* 3.9 7.9 - - - +
383A ARG* 2.9 21.4 + - - +
384A SER* 3.8 10.4 - - - +
385A PHE 3.2 0.8 - - - -
386A LYS* 1.3 77.4 + - - +
388A LEU* 1.3 64.9 + - + +
390A GLY* 5.0 0.4 - - - -
391A ASN* 3.1 33.5 + - - +
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Residues in contact with LEU 388 (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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384A SER* 3.3 21.1 + - - +
385A PHE* 3.2 12.4 + - + +
387A ASN* 1.3 84.1 - - + +
389A LEU* 1.3 64.5 + - + +
390A GLY 3.2 0.4 - - - -
391A ASN 4.4 4.7 - - - +
392A PRO* 3.3 30.4 - - + +
395A SER* 5.0 13.8 - - - -
476A SER* 3.5 30.3 - - - +
480A PRO* 3.7 27.8 - - + -
481A MET* 5.0 6.7 - - + -
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Residues in contact with LEU 389 (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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385A PHE* 2.8 28.1 + - + +
386A LYS* 4.5 8.1 - - + +
388A LEU* 1.3 79.7 - - + +
390A GLY* 1.3 60.2 + - - +
392A PRO* 4.3 10.4 - - + +
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Residues in contact with GLY 390 (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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386A LYS 3.1 18.1 + - - -
387A ASN 4.2 0.4 - - - -
389A LEU* 1.3 80.7 - - - +
391A ASN* 1.3 72.0 + - - +
392A PRO* 3.6 6.5 - - - +
393A GLN* 5.3 0.7 + - - -
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Residues in contact with ASN 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A THR* 3.7 30.5 - - - +
387A ASN* 3.1 20.6 + - - +
388A LEU* 3.7 6.5 - - - +
390A GLY* 1.3 86.5 - - - +
392A PRO* 1.4 58.5 - - - +
393A GLN* 3.1 33.1 + - - +
394A ALA 4.7 1.4 + - - -
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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
------------------------------------------------------------
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