Contacts of the helix formed by residues 367 - 379 (chain H) in PDB entry 3WTU
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 367 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352H SER 4.6 2.0 - - - +
353H PHE* 3.1 19.4 + - + +
365H LEU* 3.3 10.7 - - - +
366H SER* 1.3 80.0 - - - +
368H PRO* 1.3 71.0 - - - +
369H ASP* 3.4 15.1 + - - +
370H GLU* 3.2 44.8 + - + +
371H VAL* 3.7 7.8 + - - +
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Residues in contact with PRO 368 (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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365H LEU* 3.0 19.7 - - + -
366H SER 3.7 5.8 - - - +
367H ASP* 1.3 86.9 - - - +
369H ASP* 1.3 73.1 + - - +
370H GLU 2.7 14.7 + - - -
371H VAL* 3.3 4.3 + - - +
372H ALA* 3.1 21.0 + - - +
386H TYR* 3.9 21.3 - - + +
410H TYR* 3.4 40.2 - - + +
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Residues in contact with ASP 369 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367H ASP* 3.4 10.0 + - - +
368H PRO* 1.3 87.2 - - - +
370H GLU* 1.3 60.2 + - - +
372H ALA* 3.5 5.6 - - - +
373H ARG* 2.7 50.4 + - - +
386H TYR* 5.3 3.6 - - - +
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Residues in contact with GLU 370 (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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353H PHE* 3.3 42.3 - - + -
367H ASP* 3.2 35.1 + - + +
368H PRO 2.7 1.4 + - - -
369H ASP* 1.3 74.9 - - - +
371H VAL* 1.3 57.1 + - + +
372H ALA 2.9 3.4 - - - -
373H ARG* 2.7 29.7 + - - +
374H ARG* 2.7 54.9 + - + +
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Residues in contact with VAL 371 (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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340H PHE* 3.8 18.8 - - + -
341H LEU* 3.8 28.5 - - + -
344H LEU* 4.2 14.1 - - + -
353H PHE* 4.3 11.7 - - + +
354H ILE* 4.9 7.6 - - + -
365H LEU* 4.0 16.4 - - + -
367H ASP 3.7 14.6 - - - +
368H PRO 3.3 4.1 + - - +
370H GLU* 1.3 79.3 - - + +
372H ALA* 1.3 55.7 + - - +
374H ARG* 3.4 8.7 - - - -
375H TRP* 2.8 31.5 + - - +
389H LEU* 4.1 13.2 - - + +
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Residues in contact with ALA 372 (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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368H PRO 3.1 16.1 + - - +
369H ASP* 3.5 13.0 - - - +
370H GLU 2.9 0.8 + - - -
371H VAL* 1.3 78.5 - - - +
373H ARG* 1.3 62.6 + - - +
376H GLY 3.3 4.3 + - - -
384H MET* 2.9 32.2 - - - +
385H ASN* 3.4 11.8 + - - -
386H TYR* 3.3 30.3 - - - +
389H LEU* 4.2 11.6 - - - +
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Residues in contact with ARG 373 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369H ASP* 2.7 52.1 + - - +
370H GLU* 2.7 9.8 + - - +
372H ALA* 1.3 86.6 - - - +
374H ARG* 1.3 63.6 + - - +
375H TRP 3.3 0.7 - - - -
376H GLY* 3.7 1.6 - - - +
377H LYS* 2.9 37.8 + - + +
382H PRO* 4.7 9.6 + - + +
384H MET 3.5 21.9 + - - -
385H ASN* 4.3 9.1 - - - +
386H TYR 5.7 0.2 - - - +
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Residues in contact with ARG 374 (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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340H PHE* 3.2 26.9 - - + -
344H LEU* 3.9 16.1 - - + +
349H SER 5.4 0.2 + - - -
350H CYS* 3.4 22.6 - - - -
353H PHE* 3.3 20.8 - - - -
370H GLU* 2.7 49.2 + - + +
371H VAL* 3.4 16.8 - - - +
373H ARG* 1.3 81.4 - - - +
375H TRP* 1.3 57.3 + - - +
377H LYS* 4.5 1.3 - - - +
378H ARG* 3.3 19.9 + - - +
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Residues in contact with TRP 375 (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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335H ILE* 3.6 15.0 - - + -
336H GLN 3.4 11.0 - - - -
337H LEU* 3.1 49.0 - - + +
340H PHE* 3.4 42.2 - + + -
371H VAL 2.8 11.2 + - - +
374H ARG* 1.3 77.4 - - - +
376H GLY* 1.3 64.4 + - - +
377H LYS 3.2 0.4 - - - -
378H ARG* 3.1 4.4 + - + +
379H LYS* 3.0 61.5 + - + +
384H MET* 3.2 29.4 - - + +
389H LEU* 4.5 7.2 - - + -
8I C 3.7 14.6 - - - -
9I A 2.9 28.7 + - - -
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Residues in contact with GLY 376 (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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372H ALA 3.3 12.2 + - - -
373H ARG* 3.5 1.1 + - - -
375H TRP* 1.3 82.9 - - - +
377H LYS* 1.3 56.0 + - - +
379H LYS* 3.6 0.7 + - - -
380H ASN 3.4 1.9 + - - -
381H LYS* 2.6 54.4 + - - +
382H PRO* 4.9 1.3 - - - -
384H MET* 3.3 20.4 - - - -
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Residues in contact with LYS 377 (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 ARG* 2.9 22.2 + - + +
374H ARG* 4.5 2.0 - - - +
376H GLY* 1.3 73.9 - - - +
378H ARG* 1.3 64.2 + - - +
379H LYS 3.2 0.7 - - - -
380H ASN* 3.3 17.8 + - - +
381H LYS 4.7 1.1 - - - +
382H PRO* 5.3 17.1 - - + +
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Residues in contact with ARG 378 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335H ILE* 4.1 36.4 - - + +
340H PHE* 3.5 27.8 - - + -
343H GLU* 2.9 29.5 + - - -
344H LEU* 5.1 1.8 - - - +
374H ARG 3.3 18.9 + - - +
375H TRP* 3.1 11.6 + - + +
377H LYS* 1.3 80.3 - - - +
379H LYS* 1.3 60.2 + - + +
380H ASN* 3.4 6.3 + - - +
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Residues in contact with LYS 379 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334H PRO* 5.3 9.2 - - + -
335H ILE* 3.6 21.3 - - + +
375H TRP* 3.0 48.0 + - + +
376H GLY* 4.3 2.0 - - - +
377H LYS 3.2 0.2 - - - -
378H ARG* 1.3 78.8 - - + +
380H ASN* 1.3 72.8 + - - +
381H LYS* 3.1 17.9 + - + +
8I C 3.1 32.4 + - - -
9I A 3.1 20.9 + - - +
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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