Contacts of the helix formed by residues 413 - 426 (chain H) in PDB entry 2W3S
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 VAL 413 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379H PRO* 5.7 2.0 - - - -
380H PRO* 4.8 10.8 - - + -
411H ASP 3.3 16.1 + - - +
412H CYS* 1.3 73.1 - - - +
414H LEU* 1.3 65.4 + - - +
415H GLY 3.4 2.9 + - - -
416H GLU* 3.4 9.2 + - + +
417H LEU* 3.1 28.9 + - + +
624H TYR* 4.4 17.4 - - + -
650H ASP* 4.9 3.4 - - - +
713H TRP* 3.5 35.6 - - + +
715H GLN* 3.4 25.4 - - - +
726H LYS* 5.9 1.8 - - - +
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Residues in contact with LEU 414 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318H SER* 3.5 37.0 - - - +
376H PHE* 4.0 20.2 - - + -
412H CYS* 3.3 13.0 + - - -
413H VAL* 1.3 75.3 - - - +
415H GLY* 1.3 57.7 + - - +
417H LEU* 4.2 7.2 - - + -
418H VAL* 2.7 45.0 + - + +
452H PRO* 3.9 13.2 - - + -
453H VAL 3.9 4.7 - - - +
454H LYS* 5.7 0.2 - - + -
624H TYR* 3.5 29.6 - - + -
625H GLY 3.3 34.3 - - - +
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Residues in contact with GLY 415 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373H ALA* 5.9 1.6 - - - -
376H PHE* 3.9 19.0 - - - +
377H TYR 5.6 1.8 + - - -
379H PRO* 6.3 1.7 - - - +
412H CYS 5.1 1.0 + - - -
413H VAL 3.4 1.0 + - - -
414H LEU* 1.3 76.9 - - - +
416H GLU* 1.3 57.3 + - - +
418H VAL* 4.0 1.7 - - - +
419H THR* 2.9 33.3 + - - -
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Residues in contact with GLU 416 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413H VAL* 3.4 9.1 + - + +
414H LEU 3.3 0.4 - - - -
415H GLY* 1.3 71.5 - - - +
417H LEU* 1.3 60.5 + - - +
419H THR* 3.3 9.0 + - + -
420H ARG* 2.7 61.1 + - + +
713H TRP* 3.8 18.5 - - + -
715H GLN* 5.4 3.8 + - - -
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Residues in contact with LEU 417 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413H VAL* 3.1 23.9 + - + +
414H LEU* 3.6 9.2 - - + +
416H GLU* 1.3 75.0 - - - +
418H VAL* 1.3 57.1 + - - +
420H ARG 3.2 1.0 + - - -
421H LEU* 2.9 27.0 + - - +
624H TYR* 4.6 2.5 - - + -
625H GLY* 3.8 11.0 - - - +
626H ALA* 3.6 29.2 - - + +
648H LEU* 3.3 48.0 - - + +
650H ASP* 4.3 12.3 - - + -
713H TRP* 3.6 46.6 - - + -
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Residues in contact with VAL 418 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369H ALA* 6.0 1.1 - - + +
373H ALA* 5.2 8.3 - - + -
376H PHE* 3.7 31.2 - - + -
414H LEU* 2.7 30.9 + - + +
415H GLY 4.0 1.8 - - - +
417H LEU* 1.3 70.4 - - - +
419H THR* 1.3 66.5 + - - +
421H LEU* 3.9 4.9 - - - +
422H GLN* 3.0 44.6 + - - +
450H LEU* 4.1 19.5 - - + -
452H PRO* 4.8 0.9 - - + -
626H ALA* 3.8 24.7 - - + -
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Residues in contact with THR 419 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415H GLY 2.9 16.8 + - - -
416H GLU* 3.4 12.2 - - + -
418H VAL* 1.3 78.3 - - - +
420H ARG* 1.3 62.3 + - + +
422H GLN* 3.6 11.8 + - - +
423H LYS* 3.1 43.6 + - + +
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Residues in contact with ARG 420 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416H GLU* 2.7 50.0 + - - +
417H LEU* 3.5 4.7 - - - +
419H THR* 1.3 71.5 - - - +
421H LEU* 1.3 56.7 + - - +
423H LYS* 3.3 14.5 - - + +
424H SER* 2.8 37.5 + - - -
648H LEU* 4.1 14.4 - - + -
713H TRP* 3.1 33.1 - - - +
714H ASP 5.9 1.6 - - - +
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Residues in contact with LEU 421 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417H LEU* 2.9 17.3 + - + +
418H VAL 3.3 3.3 + - - +
420H ARG* 1.3 74.0 - - - +
422H GLN* 1.3 57.4 + - - +
424H SER* 3.3 12.3 - - - +
425H ALA* 2.7 38.6 + - - +
450H LEU* 4.4 2.7 - - + -
626H ALA* 3.4 43.5 - - + +
628H ILE* 3.7 24.0 - - + -
646H ASP* 3.6 32.3 - - + +
647H ILE 3.8 14.1 - - - +
648H LEU* 3.8 15.0 - - + +
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Residues in contact with GLN 422 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369H ALA* 4.0 15.0 + - - +
418H VAL* 3.0 34.6 + - - +
419H THR* 3.7 8.9 - - - +
421H LEU* 1.3 77.1 - - - +
423H LYS* 1.3 56.8 + - - +
425H ALA 3.3 0.5 + - - -
426H ASN 2.9 8.3 + - - -
427H PHE* 2.9 76.0 + - + +
431H ARG* 5.4 0.2 - - - +
450H LEU* 3.8 17.7 - - + +
628H ILE* 4.3 2.9 - - - -
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Residues in contact with LYS 423 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419H THR* 3.1 36.0 + - + +
420H ARG* 3.3 17.7 - - + +
422H GLN* 1.3 74.0 - - - +
424H SER* 1.3 68.1 + - - +
426H ASN* 3.3 14.6 + - - +
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Residues in contact with SER 424 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420H ARG* 2.8 22.1 + - - -
421H LEU* 3.3 18.9 + - - +
423H LYS* 1.3 80.0 - - - +
425H ALA* 1.3 59.6 + - - -
426H ASN* 3.4 3.6 + - - +
644H ARG* 4.9 3.6 + - - -
646H ASP* 4.7 4.5 + - - +
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Residues in contact with ALA 425 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421H LEU 2.7 20.3 + - - +
422H GLN 4.0 2.2 - - - +
423H LYS 3.3 0.2 - - - -
424H SER* 1.3 72.5 + - - +
426H ASN* 1.3 69.4 + - - +
427H PHE* 4.6 1.1 - - - +
430H ARG* 3.2 26.8 + - - +
628H ILE* 4.3 15.7 - - + -
644H ARG* 3.9 7.9 + - - +
646H ASP* 3.6 37.7 - - + -
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Residues in contact with ASN 426 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422H GLN 2.9 5.0 + - - -
423H LYS* 3.3 9.0 + - - +
424H SER 3.2 5.3 - - - +
425H ALA* 1.3 81.7 - - - +
427H PHE* 1.3 58.7 + - - +
428H THR 3.8 0.7 - - - -
429H THR* 3.2 39.1 + - - +
430H ARG* 2.9 36.6 + - + +
644H ARG* 5.7 1.3 - - - +
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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