Contacts of the helix formed by residues 404 - 419 (chain D) in PDB entry 4P0S
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 SER 404 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D ILE* 5.1 0.3 - - - +
368D LYS* 6.0 2.0 - - - -
403D VAL* 1.3 87.9 + - - +
405D ARG* 1.3 61.2 + - - +
406D VAL* 4.6 4.1 + - - +
407D ASP* 3.6 22.9 + - - +
408D ALA* 3.1 24.6 + - - +
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Residues in contact with ARG 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407C GLU* 2.7 48.8 + - - +
368D LYS 5.6 4.9 + - - +
369D CYS* 5.3 1.3 - - - +
370D PHE* 3.9 39.1 - - - +
404D SER* 1.3 72.3 - - - +
406D VAL* 1.3 68.6 + - + +
408D ALA* 4.0 9.0 - - - -
409D GLU* 3.1 58.6 + - + +
425D ILE* 5.9 0.9 - - - -
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Residues in contact with VAL 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C LEU* 4.0 20.8 - - + +
404D SER* 3.6 5.5 + - - +
405D ARG* 1.3 78.8 - - + +
407D ASP* 1.3 65.3 + - - +
409D GLU* 5.3 0.2 - - - -
410D GLU* 3.3 31.1 + - - +
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Residues in contact with ASP 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D ILE* 3.6 19.9 - - + +
329D LYS* 4.7 29.7 - - + +
403D VAL* 4.6 7.6 + - - +
404D SER* 3.6 22.5 + - - +
405D ARG 3.2 0.4 - - - -
406D VAL* 1.3 82.3 - - - +
408D ALA* 1.3 60.4 + - - +
410D GLU* 3.8 11.1 + - - +
411D ALA* 3.3 21.5 + - - +
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Residues in contact with ALA 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D PHE* 3.9 19.4 - - + -
322D VAL* 6.5 0.2 - - + -
325D ILE* 4.0 11.2 - - + +
369D CYS* 4.6 20.4 - - + -
404D SER 3.1 18.7 + - - +
405D ARG* 3.3 14.5 + - - +
407D ASP* 1.3 74.4 - - - +
409D GLU* 1.3 63.2 + - + +
411D ALA* 3.3 16.6 + - - +
412D LEU* 3.4 9.7 + - - +
425D ILE* 5.8 4.7 - - + -
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Residues in contact with GLU 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400C LYS* 3.1 34.4 + - - -
411C TYR* 4.5 9.9 - - + +
414C LEU* 4.2 15.7 - - + -
370D PHE* 4.4 1.6 - - - +
405D ARG* 3.1 55.2 + - + +
406D VAL* 5.3 0.2 - - - -
408D ALA* 1.3 76.0 - - + +
410D GLU* 1.3 65.9 + - - +
411D ALA 3.1 0.2 - - - -
412D LEU* 3.1 11.0 + - - +
413D VAL* 3.0 25.4 + - + +
425D ILE* 3.4 24.4 - - + +
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Residues in contact with GLU 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C LEU* 3.9 19.9 - - + +
417C ARG* 6.1 3.3 - - - +
418C GLY* 6.4 1.1 - - - -
421C ARG* 3.8 18.0 + - - -
329D LYS* 2.9 30.4 + - + +
406D VAL* 3.3 26.3 + - - +
407D ASP* 4.1 13.1 - - - +
408D ALA 3.4 0.2 - - - -
409D GLU* 1.3 76.7 - - - +
411D ALA* 1.3 57.1 - - - +
413D VAL* 3.2 7.4 + - + +
414D ASP* 2.9 35.0 + - - +
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Residues in contact with ALA 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D PHE* 3.9 4.5 - - + -
325D ILE* 3.5 28.9 - - + -
329D LYS* 5.2 6.2 - - + +
343D LEU* 3.8 13.5 - - + +
407D ASP 3.3 12.3 + - - +
408D ALA 3.3 11.8 + - - +
409D GLU 3.1 0.6 - - - -
410D GLU* 1.3 79.9 - - - +
412D LEU* 1.3 62.2 + - - +
414D ASP* 4.3 6.0 - - - +
415D LEU* 3.1 25.8 + - - +
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Residues in contact with LEU 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398C PHE* 4.7 6.9 - - + -
400C LYS* 4.4 15.0 - - - +
411C TYR* 6.2 2.7 - - + -
321D PHE* 3.3 31.4 - - + -
361D LEU* 6.1 1.6 - - + -
363D ILE* 4.6 7.4 - - + -
408D ALA 3.4 14.0 + - - +
409D GLU* 3.1 13.3 + - - +
411D ALA* 1.3 80.9 - - - +
413D VAL* 1.3 58.8 + - + +
415D LEU* 3.6 11.3 + - + +
416D GLN* 3.1 27.8 + - - +
423D ALA* 3.9 29.1 - - + +
424D GLN 5.3 0.9 - - - +
425D ILE* 3.9 34.8 - - + -
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Residues in contact with VAL 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C TYR* 4.6 14.8 - - + -
414C LEU* 3.5 35.2 - - + +
415C LEU* 4.0 30.1 - - + +
418C GLY* 4.3 7.4 - - - -
409D GLU* 3.0 14.4 + - + +
410D GLU* 3.2 10.5 + - + +
412D LEU* 1.3 73.4 - - + +
414D ASP* 1.3 68.6 + - - +
415D LEU 3.1 1.6 - - - -
416D GLN* 3.0 17.9 + - - +
417D LEU* 3.2 28.7 + - + +
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Residues in contact with ASP 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418C GLY* 4.6 8.1 - - - +
421C ARG* 2.6 26.3 + - - -
329D LYS* 2.3 38.6 + - - -
344D GLN* 4.1 16.0 + - - +
410D GLU* 2.9 23.0 + - - +
411D ALA* 4.3 4.9 - - - +
413D VAL* 1.3 78.1 - - - +
415D LEU* 1.3 61.5 + - - +
417D LEU* 3.4 4.9 + - - +
418D HIS* 3.2 38.7 + - - +
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Residues in contact with LEU 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D PHE* 5.0 1.8 - - + -
343D LEU* 3.7 34.5 - - + -
344D GLN* 3.9 27.1 - - + +
347D VAL* 4.2 13.7 - - + -
361D LEU* 5.4 10.1 - - + -
411D ALA 3.1 18.6 + - - +
412D LEU* 3.6 20.9 - - + +
413D VAL 3.1 0.2 - - - -
414D ASP* 1.3 77.8 - - - +
416D GLN* 1.3 58.8 + - - +
419D THR* 2.3 52.9 + - + +
421D ALA* 5.0 7.9 - - + -
422D GLN 6.0 0.4 - - - +
423D ALA* 5.3 6.7 - - + -
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Residues in contact with GLN 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C HIS* 4.0 16.2 - - - +
363C ARG* 3.2 12.8 + - - +
365C VAL* 3.3 32.3 - - - +
398C PHE* 3.6 42.7 - - + +
411C TYR* 3.4 12.7 + - - -
415C LEU* 3.3 27.2 - - - +
412D LEU 3.1 14.7 + - - +
413D VAL* 3.0 11.9 + - - +
415D LEU* 1.3 76.4 - - - +
417D LEU* 1.3 58.3 + - + +
419D THR* 3.0 17.0 - - - +
421D ALA 4.9 2.9 - - - -
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Residues in contact with LEU 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C HIS* 3.0 43.1 - - + +
363C ARG* 3.2 3.8 + - - +
415C LEU* 4.9 5.6 - - + +
418C GLY* 4.3 12.8 - - - +
419C LEU* 3.9 22.2 - - + -
422C LEU* 3.6 24.4 - - + +
448C ASN* 3.1 32.8 + - - +
413D VAL* 3.2 32.0 + - + +
414D ASP* 3.4 7.2 + - - +
415D LEU 3.2 0.6 - - - -
416D GLN* 1.3 81.2 - - + +
418D HIS* 1.3 64.0 + - + +
419D THR 3.3 0.9 - - - -
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Residues in contact with HIS 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363C ARG* 5.4 0.2 - - - -
421C ARG* 5.4 5.4 - - - -
422C LEU* 3.9 33.1 - - + +
448C ASN* 5.2 5.4 - - - +
449C PRO* 6.0 4.3 - - + -
344D GLN* 4.0 24.7 + - - +
414D ASP* 3.2 35.0 + - + +
417D LEU* 1.3 81.2 - - + +
419D THR* 1.3 66.2 + - + +
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Residues in contact with THR 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363C ARG* 3.7 9.0 + - - -
344D GLN* 5.1 11.0 - - + +
347D VAL* 4.3 15.5 - - + -
348D THR* 6.0 0.7 - - - +
415D LEU* 2.3 47.4 + - + +
416D GLN* 3.0 21.5 - - - +
418D HIS* 1.3 89.8 - - + +
420D GLU* 1.3 63.3 + - - +
421D ALA* 3.3 22.7 + - - +
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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
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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