Contacts of the helix formed by residues 393 - 411 (chain A) in PDB entry 6B0Z
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 393 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324A GLU* 2.9 34.0 + - + +
325A THR 3.1 17.7 - - - +
326A SER* 3.8 5.6 - - - -
373A THR* 5.0 0.2 - - - -
388A ARG* 3.6 10.4 - - - +
391A TYR* 5.0 1.6 - - + -
392A LEU* 1.3 74.6 - - - +
394A THR* 1.3 66.5 + - - +
395A PHE* 3.0 17.1 + - - +
396A GLU* 2.9 54.7 + - - +
397A PHE* 3.0 21.3 + - - +
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Residues in contact with THR 394 (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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18A MET* 5.0 4.9 - - + +
22A ILE* 3.9 27.4 - - + -
25A LEU* 5.1 4.5 - - + -
325A THR* 2.8 28.3 + - - -
326A SER* 3.7 2.0 - - - +
327A THR* 2.7 46.7 + - - +
329A PRO* 5.4 2.4 - - + +
373A THR* 4.9 0.9 - - - -
393A ASN* 1.3 71.4 - - - +
395A PHE* 1.3 67.6 + - + +
397A PHE* 3.5 5.8 + - - +
398A MET* 3.1 39.0 + - + +
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Residues in contact with PHE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET* 4.9 4.3 - - + -
21A ILE* 4.4 13.7 - - + -
25A LEU* 3.6 31.2 - - + -
29A LYS* 5.5 0.5 - - - -
319A TYR* 3.8 29.6 - + - -
325A THR* 4.0 20.4 - - - -
393A ASN* 3.1 13.4 + - - +
394A THR* 1.3 80.5 - - + +
396A GLU* 1.3 67.0 + - - +
398A MET* 3.3 6.8 + - - +
399A ASP* 2.9 33.9 + - - +
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Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ARG* 3.0 14.3 + - - -
392A LEU* 3.6 23.4 - - + +
393A ASN* 2.9 50.5 + - - +
395A PHE* 1.3 77.2 - - - +
397A PHE* 1.3 57.3 + - - +
399A ASP* 3.2 10.2 + - - +
400A LYS* 2.9 28.9 + - - +
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Residues in contact with PHE 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ASN* 4.6 0.9 - - - -
329A PRO* 3.6 31.2 - - + -
330A ILE* 3.7 21.1 - - + -
366A THR* 4.0 12.1 - - + -
367A ILE* 3.9 19.7 - - + -
371A PHE 3.1 28.9 - - - -
372A MET* 3.6 19.3 - - - -
373A THR* 4.0 16.4 - - + -
376A LEU* 5.1 1.3 - - + -
392A LEU* 3.9 15.1 - - + +
393A ASN 3.0 15.9 + - - +
394A THR 3.7 4.3 - - - +
396A GLU* 1.3 75.7 - - - +
398A MET* 1.3 57.2 + - - +
400A LYS* 3.3 2.9 + - + +
401A LEU* 2.9 52.0 + - + +
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Residues in contact with MET 398 (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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22A ILE* 5.1 2.2 - - + -
25A LEU* 4.1 41.7 - - + +
26A ILE* 4.2 13.5 - - + +
29A LYS* 4.4 17.2 - - + +
30A LEU* 3.7 31.6 - - + +
329A PRO* 3.6 34.8 - - + -
333A ILE* 4.5 5.2 - - - -
394A THR* 3.1 22.8 + - + +
395A PHE* 3.7 5.8 - - - +
396A GLU 3.2 0.2 - - - -
397A PHE* 1.3 73.2 - - - +
399A ASP* 1.3 60.3 + - - +
401A LEU* 3.2 6.9 + - - +
402A GLY* 2.8 26.3 + - - -
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Residues in contact with ASP 399 (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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29A LYS* 3.1 30.5 + - - -
395A PHE* 2.9 26.5 + - - +
396A GLU* 3.4 10.9 - - - +
398A MET* 1.3 74.3 - - - +
400A LYS* 1.3 58.5 + - - +
402A GLY* 3.0 3.4 + - - +
403A GLU* 2.8 28.8 + - - +
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Residues in contact with LYS 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A THR* 4.1 13.5 - - + -
371A PHE* 3.5 49.2 - - + -
392A LEU* 4.4 7.6 - - + -
396A GLU 2.9 13.6 + - - +
397A PHE* 3.5 11.7 - - - +
399A ASP* 1.3 76.7 - - - +
401A LEU* 1.3 62.3 + - - +
403A GLU* 3.3 10.5 + - + +
404A ASN* 3.0 46.2 + - - +
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Residues in contact with LEU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 4.3 10.8 - - + -
329A PRO* 4.5 2.2 - - + -
330A ILE* 4.2 2.0 - - + -
333A ILE* 3.7 28.3 - - + -
359A LEU* 6.0 1.6 - - + -
362A VAL* 3.8 7.7 - - + +
363A SER* 3.6 28.5 - - - +
366A THR* 3.5 30.1 - - + +
397A PHE* 2.9 47.1 + - + +
398A MET* 3.6 11.9 - - - +
400A LYS* 1.3 75.7 - - - +
402A GLY* 1.3 53.4 + - - +
404A ASN* 3.7 0.4 - - - -
405A LEU* 2.7 37.8 + - - +
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Residues in contact with GLY 402 (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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29A LYS* 5.1 8.5 - - - -
30A LEU* 3.9 15.8 - - - +
34A TYR* 4.5 2.3 + - - -
398A MET 2.8 14.4 + - - -
399A ASP* 3.4 3.8 - - - -
401A LEU* 1.3 73.5 - - - +
403A GLU* 1.3 59.2 + - - +
405A LEU* 3.7 2.7 - - - +
406A LYS* 2.9 32.1 + - - +
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Residues in contact with GLU 403 (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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399A ASP 2.8 16.0 + - - +
400A LYS* 3.3 15.7 + - + +
402A GLY* 1.3 71.2 - - - +
404A ASN* 1.3 65.4 + - - +
406A LYS* 3.3 18.0 + - - +
407A ILE* 3.1 48.1 + - + +
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Residues in contact with ASN 404 (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 VAL* 3.9 18.4 - - + +
366A THR* 3.0 32.3 + - - +
371A PHE* 5.1 2.4 - - - -
400A LYS* 3.0 38.5 + - - +
403A GLU* 1.3 76.5 - - - +
405A LEU* 1.3 60.7 + - - +
407A ILE* 3.4 15.7 + - - +
408A LYS* 2.9 30.3 + - - +
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Residues in contact with LEU 405 (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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29A LYS 5.0 0.2 - - - +
30A LEU* 3.7 32.5 - - + +
34A TYR* 3.6 26.0 - - + -
355A PHE* 4.3 6.1 - - + -
358A ALA* 4.7 0.4 - - + -
359A LEU* 4.1 29.8 - - + +
362A VAL* 3.7 25.0 - - + +
401A LEU 2.7 22.5 + - - +
402A GLY* 3.7 4.0 - - - +
404A ASN* 1.3 71.2 - - - +
406A LYS* 1.3 64.8 + - - +
408A LYS* 3.4 0.4 + - + -
409A LEU* 3.0 49.1 + - + +
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Residues in contact with LYS 406 (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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34A TYR* 3.5 22.3 + - + +
402A GLY 2.9 18.3 + - - +
403A GLU* 3.6 20.9 - - - +
405A LEU* 1.3 75.5 - - - +
407A ILE* 1.3 59.3 + - + +
409A LEU* 3.9 2.3 - - - +
410A ALA* 2.9 33.0 + - + +
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Residues in contact with ILE 407 (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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403A GLU* 3.1 38.9 + - + +
404A ASN* 3.7 15.7 - - - +
405A LEU 3.2 0.2 - - - -
406A LYS* 1.3 73.8 - - + +
408A LYS* 1.3 57.4 + - - +
410A ALA* 2.9 8.3 + - + +
411A GLN* 2.8 63.3 + - + +
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Residues in contact with LYS 408 (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 PHE* 5.7 4.4 - - + -
358A ALA* 4.1 19.5 - - + -
361A GLU* 2.8 29.3 + - - +
362A VAL* 3.6 24.7 - - + -
365A GLU* 2.6 41.6 + - - -
404A ASN 2.9 17.1 + - - +
405A LEU 3.8 1.6 - - - +
407A ILE* 1.3 79.4 - - - +
409A LEU* 1.3 64.8 + - + +
411A GLN* 3.4 22.4 + - - +
412A ALA* 4.2 5.0 - - - +
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Residues in contact with LEU 409 (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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34A TYR* 3.5 43.5 - - + -
354A PHE* 4.6 15.5 - - + -
355A PHE* 3.8 20.9 - - + -
358A ALA* 4.0 26.0 - - + -
405A LEU* 3.0 37.4 + - + +
406A LYS 4.1 2.7 - - - +
408A LYS* 1.3 76.6 - - - +
410A ALA* 1.3 62.6 + - - +
412A ALA* 3.8 13.8 + - - +
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Residues in contact with ALA 410 (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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406A LYS* 2.9 21.2 + - + +
407A ILE* 2.9 8.1 + - - +
409A LEU* 1.3 75.4 - - - +
411A GLN* 1.3 53.2 + - + +
412A ALA 2.6 25.3 + - - +
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Residues in contact with GLN 411 (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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407A ILE* 2.8 43.8 + - + +
408A LYS* 3.4 11.7 + - - +
410A ALA* 1.3 68.6 - - + +
412A ALA* 1.3 60.9 + - - +
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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