Contacts of the helix formed by residues 403 - 421 (chain H) in PDB entry 4D1Q
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 403 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353H ASN* 5.6 4.9 - - - +
355H SER* 4.4 16.4 - - - +
356H ILE* 5.2 9.6 - - + -
359H THR* 5.9 1.8 - - - +
401H GLY 2.8 9.3 + - - +
402H ASP* 1.3 72.7 - - - +
404H ALA* 1.3 72.5 + - + +
405H ASP* 2.8 24.0 + - + +
406H ILE* 2.8 34.1 + - + +
407H ALA 3.3 2.8 + - - -
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Residues in contact with ALA 404 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402H ASP 3.4 4.1 + - - -
403H VAL* 1.3 75.4 - - + +
405H ASP* 1.3 63.4 + - - +
407H ALA* 3.6 6.4 + - - +
408H LYS* 3.3 32.3 + - - +
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Residues in contact with ASP 405 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281H THR* 4.3 7.3 - - - +
283H GLU* 2.8 45.8 - - + +
284H LEU* 4.8 6.5 - - + +
356H ILE* 4.2 24.4 - - + +
403H VAL* 2.8 19.1 + - + +
404H ALA* 1.3 77.2 - - - +
406H ILE* 1.3 62.3 + - - +
408H LYS* 3.3 18.3 + - - +
409H LEU* 3.4 9.5 + - - +
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Residues in contact with ILE 406 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284H LEU* 5.5 4.3 - - + -
356H ILE* 4.7 13.7 - - + +
359H THR* 3.6 35.2 - - + -
360H MET* 4.4 18.8 - - + -
363H ILE* 4.7 7.2 - - + -
402H ASP* 3.6 24.7 - - - +
403H VAL* 2.8 32.7 + - + +
405H ASP* 1.3 74.0 - - - +
407H ALA* 1.3 55.1 + - - +
409H LEU* 2.7 33.2 + - + +
410H LYS* 2.9 29.5 + - + +
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Residues in contact with ALA 407 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398H PRO* 6.1 5.8 - - + -
402H ASP* 4.2 21.1 - - + +
403H VAL 3.3 4.4 + - - +
404H ALA* 4.1 9.0 - - - +
405H ASP 3.5 0.2 - - - -
406H ILE* 1.3 78.9 - - - +
408H LYS* 1.3 61.2 + - - +
410H LYS* 3.9 9.8 - - + +
411H VAL* 2.8 34.4 + - + +
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Residues in contact with LYS 408 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280H GLU 5.3 1.6 - - - +
281H THR* 4.4 6.1 - - + -
283H GLU* 3.6 43.4 + - - +
404H ALA* 3.3 22.5 + - - +
405H ASP* 3.4 10.5 + - - +
406H ILE 3.1 0.6 - - - -
407H ALA* 1.3 74.9 - - - +
409H LEU* 1.3 63.9 + - - +
411H VAL* 3.8 5.3 - - - +
412H ASN* 2.5 39.8 + - - +
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Residues in contact with LEU 409 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H SER* 3.4 28.5 - - - +
278H PHE* 3.8 32.3 - - + -
281H THR* 3.7 17.7 - - + +
284H LEU* 3.9 20.0 - - + -
360H MET* 4.6 9.9 - - + -
363H ILE* 5.1 15.5 - - + -
364H LEU* 6.3 1.1 - - + -
405H ASP 3.4 2.5 + - - +
406H ILE* 2.7 16.7 + - + +
408H LYS* 1.3 77.7 - - - +
410H LYS* 1.3 58.1 + - - +
412H ASN* 2.5 27.2 + - - +
413H ILE* 2.8 32.4 + - + -
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Residues in contact with LYS 410 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359H THR* 5.8 1.3 - - - -
363H ILE* 3.8 30.2 - - + +
395H ILE 3.8 11.9 + - - -
396H CYS* 3.6 33.2 - - + +
397H SER 3.3 19.0 + - - +
398H PRO* 4.9 3.1 - - + -
399H ASP* 3.3 18.6 + - - +
402H ASP* 3.0 30.3 + - - +
406H ILE* 2.9 26.7 + - + +
407H ALA* 4.0 7.6 - - + +
409H LEU* 1.3 71.6 - - + +
411H VAL* 1.3 63.4 + - + +
413H ILE* 3.3 10.2 + - + +
414H ILE* 3.1 29.4 + - - +
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Residues in contact with VAL 411 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398H PRO* 6.2 4.0 - - + -
407H ALA* 2.8 27.1 + - + +
408H LYS* 3.8 7.0 - - - +
409H LEU 3.1 0.4 - - - -
410H LYS* 1.3 75.6 - - + +
412H ASN* 1.3 65.5 + - - +
414H ILE* 3.6 10.8 - - + +
415H LYS* 2.9 31.8 + - + +
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Residues in contact with ASN 412 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H SER* 3.7 9.6 - - - +
280H GLU* 3.6 28.1 + - - +
281H THR* 3.7 9.8 + - - +
408H LYS* 2.5 28.6 + - - +
409H LEU 2.5 15.3 + - - +
411H VAL* 1.3 77.5 - - - +
413H ILE* 1.3 61.5 + - - +
415H LYS* 2.8 39.0 - - - +
416H ASN* 2.7 35.8 + - - +
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Residues in contact with ILE 413 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273H VAL* 4.3 3.8 - - + +
274H LEU* 5.2 7.0 - - + -
277H SER* 3.1 27.1 + - - +
278H PHE* 6.1 0.4 - - + -
363H ILE* 4.8 8.1 - - + -
364H LEU* 5.9 1.6 - - + -
367H PHE* 3.9 24.9 - - + -
392H VAL* 3.5 30.3 - - + -
396H CYS* 3.6 17.7 - - - -
409H LEU* 2.8 38.3 + - + +
410H LYS* 3.5 9.9 - - + +
412H ASN* 1.3 75.7 - - - +
414H ILE* 1.3 50.9 - - - +
416H ASN* 3.0 4.9 + - - +
417H VAL* 2.7 38.0 + - + +
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Residues in contact with ILE 414 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393H LYS* 4.4 27.8 - - + +
396H CYS* 3.4 42.4 - - + +
397H SER* 5.5 0.4 - - - -
398H PRO* 5.8 1.8 - - + -
410H LYS 3.1 13.8 + - - +
411H VAL* 3.6 9.4 - - + +
413H ILE* 1.3 76.1 - - + +
415H LYS* 1.3 68.6 + - - +
417H VAL* 3.0 20.3 + - + +
418H ARG* 3.2 26.6 + - + +
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Residues in contact with LYS 415 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280H GLU* 2.9 19.8 + - - +
411H VAL* 2.9 21.7 + - + +
412H ASN* 2.8 33.3 - - - +
414H ILE* 1.3 80.7 - - - +
416H ASN* 1.3 62.2 + - - +
418H ARG* 3.3 22.3 + - - +
419H ILE* 2.9 56.3 + - + +
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Residues in contact with ASN 416 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273H VAL* 3.9 14.0 - - + +
276H ASN* 4.2 8.8 - - - +
277H SER* 3.2 29.1 + - - +
280H GLU* 3.3 29.6 + - - +
412H ASN 2.7 23.5 + - - +
413H ILE 3.4 3.6 - - - +
415H LYS* 1.3 76.2 - - - +
417H VAL* 1.3 66.6 + - - +
418H ARG 3.0 1.8 - - - -
419H ILE* 3.3 24.4 - - - +
420H ILE* 2.8 36.2 + - + +
421H TRP 3.4 0.7 + - - -
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Residues in contact with VAL 417 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273H VAL* 4.4 9.4 - - + +
389H ILE* 3.5 34.1 - - + +
392H VAL* 3.3 33.7 - - + -
393H LYS* 3.9 16.8 - - + -
413H ILE* 2.7 26.0 + - + +
414H ILE* 3.0 11.2 + - - +
416H ASN* 1.3 71.9 - - - +
418H ARG* 1.3 57.5 + - - +
421H TRP* 3.0 25.9 + - + +
422H GLU* 2.9 26.0 + - + +
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Residues in contact with ARG 418 (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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393H LYS* 4.3 10.3 - - - +
414H ILE* 3.2 21.2 + - + +
415H LYS* 3.5 26.7 - - - +
416H ASN 3.0 0.8 - - - -
417H VAL* 1.3 74.2 - - - +
419H ILE* 1.3 76.4 + - - +
420H ILE 3.2 2.3 + - - -
422H GLU* 3.2 26.5 - - + +
423H GLU* 3.0 30.8 + - - +
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Residues in contact with ILE 419 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415H LYS* 2.9 47.9 + - + +
416H ASN* 3.3 20.9 - - - +
418H ARG* 1.3 90.5 - - + +
420H ILE* 1.3 66.6 + - + +
423H GLU* 3.5 22.0 - - - +
424H ASN* 4.3 2.6 + - - -
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Residues in contact with ILE 420 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249H ARG* 4.1 25.1 - - - +
269H LEU* 4.0 6.7 - - - +
272H ASN* 3.9 26.5 - - + +
273H VAL* 3.5 22.4 - - + +
276H ASN* 4.8 15.0 - - - +
416H ASN* 2.8 30.9 + - + +
419H ILE* 1.3 85.7 - - + +
421H TRP* 1.3 62.8 + - - +
423H GLU 4.6 0.4 - - - -
424H ASN* 2.8 28.9 + - - +
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Residues in contact with TRP 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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266H SER* 3.7 14.7 - - - +
269H LEU* 3.3 26.5 - - + -
270H LEU* 4.3 31.6 - - + -
273H VAL* 4.1 12.3 - - + -
370H ILE* 4.6 0.4 - - + -
374H LEU* 4.1 17.0 - - + -
385H VAL* 3.7 20.3 - - + +
388H SER* 3.6 24.2 - - - -
389H ILE* 3.5 27.6 - - + -
392H VAL* 3.8 26.5 - - + -
416H ASN 3.4 0.2 + - - -
417H VAL* 3.0 25.2 + - + +
420H ILE* 1.3 76.2 - - + +
422H GLU* 1.3 56.2 + - - +
423H GLU 3.2 1.1 - - - -
424H ASN* 2.6 31.4 + - - +
425H LEU* 3.3 25.9 + - + +
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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
------------------------------------------------------------
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