Contacts of the helix formed by residues 386 - 405 (chain A) in PDB entry 3H44
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 HIS 386 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A TRP* 3.4 40.7 + + + +
382A GLU* 3.0 43.1 + - - +
383A GLY 2.9 8.2 + - - +
385A LEU* 1.3 89.6 + - + +
387A VAL* 1.3 56.5 + - - +
388A GLU* 3.1 4.3 - - - +
389A ASP* 2.8 28.2 + - - +
390A ILE* 2.7 34.3 + - - +
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Residues in contact with VAL 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LEU* 3.8 27.8 - - + -
379A LEU* 4.7 4.7 - - + -
383A GLY 3.4 7.3 + - - +
384A LEU* 3.4 22.0 - - + +
385A LEU 3.7 0.8 - - - -
386A HIS* 1.3 77.2 - - - +
388A GLU* 1.3 65.0 + - - +
390A ILE* 3.6 7.6 - - - +
391A ILE* 3.1 34.5 + - + +
478A VAL* 4.6 3.1 - - + -
480A ILE* 4.0 39.5 - - + -
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Residues in contact with GLU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A HIS* 3.1 1.5 - - - -
387A VAL* 1.3 78.8 - - - +
389A ASP* 1.3 63.6 + - - +
392A LEU* 3.1 12.7 + - - +
509A VAL* 3.1 46.4 - - + +
512A LYS* 3.8 25.9 + - - +
513A TRP* 3.0 34.1 + - + -
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Residues in contact with ASP 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A TRP* 3.7 23.1 - - + -
386A HIS* 2.8 38.0 + - + +
388A GLU* 1.3 81.7 - - - +
390A ILE* 1.3 67.9 + - - +
392A LEU* 3.1 17.9 + - + +
393A HIS* 2.9 30.5 + - + +
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Residues in contact with ILE 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LEU* 3.9 15.5 - - + -
350A LEU* 3.8 32.3 - - + +
355A TRP* 4.0 20.6 - - + -
356A VAL* 4.0 9.9 - - + -
377A VAL* 4.6 4.3 - - + -
379A LEU* 3.5 32.3 - - + -
383A GLY 3.6 15.0 - - - +
386A HIS 2.7 16.7 + - - +
387A VAL* 3.3 9.4 + - - +
389A ASP* 1.3 72.9 - - - +
391A ILE* 1.3 65.0 + - - +
393A HIS* 3.0 13.7 + - - +
394A MET* 3.0 28.7 + - + +
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Residues in contact with ILE 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LEU* 4.3 12.6 - - + -
315A VAL* 4.2 17.3 - - + -
387A VAL* 3.1 20.9 + - + +
390A ILE* 1.3 74.9 - - - +
392A LEU* 1.3 63.4 + - - +
394A MET* 2.9 25.2 + - - +
395A PHE* 3.0 39.7 + - + -
476A VAL* 5.7 0.7 - - + -
478A VAL* 3.6 38.6 - - + -
513A TRP* 3.5 34.1 - - + -
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Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A GLU 3.1 14.2 + - - +
389A ASP* 3.1 22.6 + - - +
391A ILE* 1.3 72.9 - - - +
393A HIS* 1.3 56.2 + - + +
395A PHE* 3.0 6.7 + - - +
396A GLN* 2.7 54.5 + - - +
512A LYS* 3.8 24.0 - - + +
513A TRP* 3.6 17.9 - - + +
516A ALA* 3.9 21.5 - - + -
517A ASP 5.5 0.2 - - - +
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Residues in contact with HIS 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 4.2 2.7 - - + -
349A GLU* 4.4 11.8 - - + +
350A LEU* 4.3 13.2 - - + -
353A LYS* 4.0 20.8 + - + -
355A TRP* 3.5 31.3 - + - -
389A ASP* 2.9 30.3 + - + +
390A ILE* 3.0 9.7 + - - +
392A LEU* 1.3 77.7 - - + +
394A MET* 1.3 58.3 + - - +
396A GLN* 3.1 17.9 + - - +
397A TYR* 2.8 27.4 + - - +
519A ASN* 3.5 26.7 + - - -
522A PHE* 3.5 21.2 - - + -
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Residues in contact with MET 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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313A LEU* 5.0 0.7 - - + -
315A VAL* 3.9 26.2 - - + -
346A LEU* 3.8 27.9 - - + +
350A LEU* 5.0 2.0 - - + -
375A ILE* 3.3 49.6 - - + +
377A VAL* 4.1 23.3 - - + -
390A ILE* 3.0 23.8 + - + +
391A ILE* 2.9 26.8 + - + +
393A HIS* 1.3 75.6 - - - +
395A PHE* 1.3 56.9 + - + +
397A TYR* 3.1 5.5 + - - +
398A ILE* 3.0 33.4 + - + +
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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
----------------------------------------------------------
315A VAL* 5.6 0.7 - - + -
317A PHE* 3.7 29.2 - + - -
391A ILE* 3.0 42.8 + - + -
392A LEU 3.0 5.4 + - - +
394A MET* 1.3 73.8 - - + +
396A GLN* 1.3 56.2 + - - +
398A ILE* 3.6 14.9 - - + +
399A GLN* 2.7 37.2 + - - +
402A ARG* 5.5 2.9 + - - -
471A LEU 3.8 5.4 - - - -
472A ARG 3.7 5.6 - - - -
473A PRO* 3.5 47.6 - - + -
476A VAL* 4.5 7.0 - - + -
513A TRP* 3.8 36.8 - + + +
516A ALA* 4.0 5.6 - - + -
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Residues in contact with GLN 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A LEU* 2.7 47.0 + - + +
393A HIS* 3.2 24.8 + - - +
395A PHE* 1.3 73.5 - - - +
397A TYR* 1.3 60.7 + - - +
399A GLN* 3.3 5.0 - - - +
400A LYS* 3.1 19.8 + - - +
516A ALA* 3.8 13.1 - - + +
517A ASP* 3.3 27.5 - - - +
518A LEU* 4.8 2.8 - - - +
519A ASN* 2.7 43.7 + - + +
522A PHE* 4.0 8.2 - - + -
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Residues in contact with TYR 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 3.0 39.0 + - - +
338A ILE* 3.8 25.4 - - + -
340A HIS* 4.8 2.4 - - - +
344A GLY 4.2 9.4 - - - -
345A SER* 4.4 2.7 - - - -
346A LEU* 3.7 37.6 + - + -
393A HIS 2.8 15.8 + - - +
394A MET 3.6 7.0 - - - +
396A GLN* 1.3 70.5 - - - +
398A ILE* 1.3 66.6 + - + +
400A LYS* 2.9 20.1 + - + +
401A LEU* 3.1 28.6 + - + +
522A PHE* 3.6 37.9 - + + -
523A LYS 4.4 13.7 + - - -
524A LEU* 5.0 2.2 - - + -
525A PRO* 4.8 7.1 - - - +
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Residues in contact with ILE 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A PHE* 4.5 7.0 - - + -
338A ILE* 4.9 15.0 - - + -
375A ILE* 4.6 13.5 - - + -
394A MET* 3.0 14.9 + - + +
395A PHE* 3.3 25.8 + - + +
397A TYR* 1.3 75.1 - - + +
399A GLN* 1.3 63.2 + - - +
401A LEU* 2.9 21.8 + - + +
402A ARG* 3.0 36.1 + - - +
468A LEU* 3.6 23.6 - - + -
471A LEU* 3.6 32.5 - - + +
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Residues in contact with GLN 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A PHE 2.7 17.7 + - - +
396A GLN* 3.3 11.4 - - - +
397A TYR 3.2 0.2 - - - -
398A ILE* 1.3 72.1 - - - +
400A LYS* 1.3 64.1 + - - +
402A ARG* 2.9 35.8 + - - +
403A ALA* 2.8 27.3 + - - +
472A ARG* 5.1 2.9 + - - -
514A GLN 6.2 0.2 - - - +
516A ALA* 3.3 26.7 - - + +
517A ASP 4.4 0.9 - - - +
518A LEU* 4.1 17.5 - - + +
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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
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396A GLN 3.1 7.6 + - - +
397A TYR* 2.9 16.8 + - + +
399A GLN* 1.3 77.0 - - - +
401A LEU* 1.3 58.0 + - + +
403A ALA* 3.3 1.8 + - + +
404A GLU* 2.8 70.0 + - + +
518A LEU* 3.8 30.2 - - + +
519A ASN 5.7 2.9 - - - +
522A PHE* 3.9 35.0 + - + +
523A LYS* 4.9 10.5 - - - +
524A LEU* 4.7 14.8 - - + +
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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
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333A TYR* 5.8 0.7 - - + -
334A LEU* 4.0 24.5 - - + -
337A LEU* 4.2 27.6 - - + -
338A ILE* 4.2 19.7 - - + -
397A TYR* 3.1 32.6 + - + +
398A ILE* 2.9 11.0 + - - +
400A LYS* 1.3 76.0 - - + +
402A ARG* 1.3 60.8 + - - +
404A GLU* 3.3 3.3 + - - +
405A GLY* 2.8 31.4 + - - -
468A LEU* 4.2 16.5 - - + +
524A LEU* 3.6 29.2 - - + -
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Residues in contact with ARG 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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395A PHE* 5.5 3.0 + - - -
398A ILE* 3.0 33.6 + - - +
399A GLN* 2.9 34.8 + - - +
401A LEU* 1.3 75.9 - - - +
403A ALA* 1.3 61.8 + - - +
405A GLY* 3.1 14.0 + - - -
465A GLU* 6.5 0.9 - - + -
468A LEU* 2.8 48.9 + - + +
469A ASP* 3.7 1.2 - - - +
471A LEU 3.6 12.5 + - - -
472A ARG* 3.4 46.7 - - - +
473A PRO* 5.8 1.0 - - - +
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Residues in contact with ALA 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 GLN* 2.8 24.3 + - - +
400A LYS* 3.7 4.5 - - - +
402A ARG* 1.3 74.5 - - - +
404A GLU* 1.3 64.2 + - - +
518A LEU* 4.2 25.6 - - + -
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Residues in contact with GLU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LYS* 2.8 60.0 + - - +
401A LEU* 3.9 2.5 - - - +
403A ALA* 1.3 76.6 - - - +
405A GLY* 1.3 68.9 + - - +
406A PRO 4.7 0.3 - - - +
407A GLN* 3.2 17.5 - - - +
518A LEU* 5.5 1.6 - - - +
524A LEU* 4.1 26.1 - - + +
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Residues in contact with GLY 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A TYR* 4.4 1.7 + - - -
401A LEU 2.8 16.4 + - - +
402A ARG* 3.1 11.0 + - - -
404A GLU* 1.3 84.6 - - - +
406A PRO* 1.3 80.4 - - - +
407A GLN* 3.0 11.8 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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