Contacts of the helix formed by residues 414 - 428 (chain A) in PDB entry 3W6R
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 ASP 414 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A ILE* 6.0 0.2 - - - +
387A SER 4.8 1.4 - - - +
388A GLY* 4.1 12.3 - - - -
389A CYS* 4.6 4.2 + - - +
412A VAL* 3.5 13.0 - - - +
413A ASP* 1.3 76.7 - - + +
415A ILE* 1.3 64.5 + - - +
416A HIS* 3.2 38.3 + - - +
417A ALA* 3.2 24.6 + - + +
418A ILE 3.9 0.3 + - - -
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Residues in contact with ILE 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLU* 3.8 25.4 - - + +
373A ILE* 4.0 17.5 - - + -
376A ARG* 4.0 32.3 - - + +
377A GLY* 3.8 22.7 - - - +
380A GLU* 3.7 33.2 - - + +
383A LEU* 4.4 9.9 - - + -
413A ASP 3.4 5.2 + - - +
414A ASP* 1.3 73.5 + - - +
416A HIS* 1.3 65.1 + - + +
418A ILE* 3.0 29.0 + - + +
419A CYS* 3.1 12.1 + - - -
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Residues in contact with HIS 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A GLU* 4.1 27.2 + - + +
381A THR 3.9 17.9 + - - -
383A LEU* 4.1 25.5 - - + +
384A TYR 4.7 1.0 + - - -
386A ILE* 3.6 51.1 + - + +
387A SER 4.2 2.5 - - - +
388A GLY* 3.9 8.1 - - - +
414A ASP* 3.1 25.7 - - - +
415A ILE* 1.3 78.4 - - + +
417A ALA* 1.3 58.8 + - - +
419A CYS* 3.4 7.3 + - - +
420A SER* 2.8 32.4 + - - -
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Residues in contact with ALA 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A GLY* 3.8 16.3 - - - -
389A CYS 4.8 1.1 - - - +
392A THR* 4.4 23.8 - - + -
393A VAL* 3.8 17.8 - - + +
396A LEU* 5.0 5.9 - - + +
412A VAL* 5.0 4.3 - - + -
414A ASP* 3.2 20.5 + - + +
415A ILE 3.2 0.6 - - - -
416A HIS* 1.3 78.2 - - - +
418A ILE* 1.3 58.8 + - - +
420A SER* 3.4 1.9 + - - -
421A LEU* 2.8 29.6 + - - +
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Residues in contact with ILE 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A CYS* 3.8 24.8 - - - +
372A GLU* 4.3 5.2 - - + -
373A ILE* 3.8 21.8 - - + -
376A ARG* 4.7 0.7 - - - +
396A LEU* 4.5 10.3 - - + -
409A LEU* 3.7 38.4 - - + +
412A VAL* 3.5 31.6 - - + -
414A ASP 4.4 0.9 - - - +
415A ILE* 3.0 23.6 + - + +
417A ALA* 1.3 75.7 - - - +
419A CYS* 1.3 64.3 + - - +
421A LEU* 3.3 6.1 + - + +
422A LEU* 3.0 23.6 + - - +
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Residues in contact with CYS 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ILE* 3.8 20.6 - - - -
383A LEU* 3.4 39.3 - - - -
384A TYR* 3.6 35.4 - - + +
386A ILE 5.3 1.8 - - - +
415A ILE* 3.1 15.4 + - - -
416A HIS* 3.5 12.3 - - + +
418A ILE* 1.3 77.6 - - - +
420A SER* 1.3 61.0 + - - +
422A LEU* 3.4 2.8 + - - +
423A LYS* 3.1 29.2 + - - +
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Residues in contact with SER 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ILE 4.4 1.0 + - - -
387A SER* 3.6 12.1 - - - -
388A GLY 3.0 23.0 + - - -
393A VAL* 3.7 23.2 - - - +
416A HIS 2.8 13.5 + - - -
417A ALA 3.7 4.7 - - - -
419A CYS* 1.3 73.8 - - - +
421A LEU* 1.3 59.8 + - - +
423A LYS* 3.5 14.5 + - - +
424A ASP* 2.9 31.0 + - - +
427A ARG* 5.2 0.5 + - - -
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Residues in contact with LEU 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ILE* 4.3 24.5 - - + -
369A CYS* 4.0 18.2 - - - -
393A VAL* 3.9 14.3 - - + +
396A LEU* 4.2 20.0 - - + +
397A LYS* 4.0 40.4 - - + +
406A VAL* 6.1 0.2 - - + -
407A PRO* 6.0 2.7 - - + -
409A LEU* 4.2 21.1 - - + -
417A ALA 2.8 17.9 + - - +
418A ILE* 3.3 7.1 + - + +
420A SER* 1.3 73.9 - - - +
422A LEU* 1.3 59.5 + - - +
424A ASP* 3.4 1.6 + - + +
425A PHE* 2.8 30.7 + - + +
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Residues in contact with LEU 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ILE* 5.0 1.3 - - + +
366A VAL* 3.8 42.0 - - + -
369A CYS* 4.1 18.8 - - + -
370A VAL* 4.2 21.3 - - + -
373A ILE* 4.4 1.6 - - + -
384A TYR* 3.4 26.7 - - + +
418A ILE 3.0 16.7 + - - +
419A CYS* 3.7 4.9 - - - +
421A LEU* 1.3 75.0 - - - +
423A LYS* 1.3 66.2 + - + +
425A PHE* 3.5 5.9 + - + +
426A LEU* 3.1 42.9 + - + +
476A LEU* 4.2 13.0 - - + -
500A PHE* 5.6 1.3 - - + -
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Residues in contact with LYS 423 (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 TYR* 2.9 42.7 + - + +
385A ARG 4.9 4.8 + - - -
386A ILE 5.5 1.8 + - - -
387A SER* 5.8 3.6 - - - +
419A CYS* 3.1 20.2 + - - +
420A SER* 3.9 16.8 + - - +
422A LEU* 1.3 74.5 - - - +
424A ASP* 1.3 54.1 + - - +
426A LEU* 3.3 1.0 + - - -
427A ARG* 2.8 52.4 + - - +
499A VAL* 3.7 24.8 - - + +
500A PHE* 4.1 15.5 - - + -
503A THR* 3.5 21.4 - - - +
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Residues in contact with ASP 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A VAL* 4.1 14.4 - - + +
394A LYS* 5.8 1.6 + - - -
397A LYS* 3.1 24.7 + - + +
420A SER 2.9 19.1 + - - +
421A LEU* 3.6 7.4 - - + +
423A LYS* 1.3 75.6 - - - +
425A PHE* 1.3 63.1 + - - +
427A ARG* 3.9 21.9 + - - +
428A ASN* 2.4 56.7 + - - +
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Residues in contact with PHE 425 (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 GLU* 2.5 44.2 - - - +
351A LEU* 4.7 1.8 - - + -
354A PHE* 3.8 42.2 - + + -
363A PRO* 4.0 7.9 - - + -
365A ILE* 3.7 33.7 - - + -
366A VAL* 3.8 23.3 - - + -
397A LYS* 5.1 3.7 - - + +
400A PHE* 3.8 31.6 - + - -
421A LEU* 2.8 23.2 + - + +
422A LEU* 3.7 5.6 - - + +
424A ASP* 1.3 73.6 - - - +
426A LEU* 1.3 76.6 + - + +
429A LEU* 3.4 12.5 + - + +
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Residues in contact with LEU 426 (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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351A LEU* 5.2 0.4 - - + -
366A VAL* 4.2 13.5 - - + -
422A LEU* 3.1 37.8 + - + +
425A PHE* 1.3 91.7 - - + +
427A ARG* 1.3 63.9 + - - +
428A ASN 3.3 0.9 + - - -
429A LEU* 3.3 33.5 + - + +
432A PRO* 4.9 2.3 - - - +
433A LEU* 4.8 15.3 + - + -
472A THR* 4.4 15.7 - - + -
476A LEU* 3.8 31.4 - - + -
500A PHE* 4.8 2.5 - - + -
503A THR* 3.8 21.8 - - + +
504A ILE* 4.2 10.5 - - + -
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Residues in contact with ARG 427 (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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420A SER 5.2 0.4 + - - -
423A LYS* 2.8 47.8 + - - +
424A ASP* 3.9 27.8 + - - +
426A LEU* 1.3 74.0 - - - +
428A ASN* 1.3 72.2 + - - +
429A LEU 3.4 5.1 + - - +
432A PRO* 5.7 3.7 - - - +
502A PRO* 3.8 28.0 - - - +
503A THR* 3.5 23.7 + - - -
506A ALA* 5.8 3.7 - - + +
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Residues in contact with ASN 428 (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 GLU* 3.2 25.1 + - + +
349A GLY 4.9 0.2 + - - -
397A LYS* 3.0 20.6 - - - +
424A ASP* 2.4 46.1 + - - +
427A ARG* 1.3 97.0 + - - +
429A LEU* 1.3 65.7 + - - +
430A LYS* 3.7 0.7 + - - -
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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