Contacts of the helix formed by residues 404 - 419 (chain D) in PDB entry 4PKY
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 404 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400D CYS* 3.7 15.8 - - - -
401D HIS* 2.7 16.2 + - + +
403D GLU* 1.3 76.1 - - - +
405D GLN* 1.3 62.4 + - - +
406D GLN 3.3 2.2 - - - -
407D LEU* 3.2 17.7 + - + +
408D LEU* 3.1 16.8 + - - +
426D MET 5.0 2.2 - - - -
427D PHE* 3.9 14.8 - - + +
428D ARG* 2.9 56.2 + - - +
438D TRP* 4.1 7.3 - - - -
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Residues in contact with GLN 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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397D VAL* 3.7 33.2 + - + +
398D GLU* 5.6 1.0 - - - +
400D CYS* 3.4 28.7 + - + +
401D HIS 3.1 14.9 + - - +
402D PRO* 3.5 24.9 + - + +
403D GLU 3.5 0.2 - - - -
404D ASP* 1.3 77.4 - - - +
406D GLN* 1.3 64.1 + - - +
408D LEU* 3.0 5.0 + - - +
409D ARG* 2.9 45.1 + - - +
430D ARG* 5.4 3.6 - - - +
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Residues in contact with GLN 406 (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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402D PRO 4.9 1.2 + - - -
403D GLU 5.0 3.7 + - - +
404D ASP 3.3 0.6 - - - -
405D GLN* 1.3 78.8 - - - +
407D LEU* 1.3 63.8 + - - +
409D ARG* 3.3 21.5 + - - +
410D ASP* 3.0 57.7 + - - +
413D GLN* 5.3 0.2 + - - -
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Residues in contact with LEU 407 (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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403D GLU 5.4 0.6 + - - +
404D ASP* 3.2 22.4 + - - +
406D GLN* 1.3 79.8 - - - +
408D LEU* 1.3 60.3 + - - +
410D ASP* 3.3 8.8 + - + +
411D SER* 2.9 28.9 + - - +
425D VAL* 3.7 18.4 - - + -
426D MET* 3.3 28.3 - - + +
427D PHE* 5.2 1.3 - - + -
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Residues in contact with LEU 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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396D ILE* 3.6 22.4 - - + +
397D VAL* 3.9 13.5 - - + -
400D CYS* 3.4 31.6 - - + -
404D ASP 3.1 7.7 + - - +
405D GLN* 3.0 9.5 + - - +
407D LEU* 1.3 80.8 - - - +
409D ARG* 1.3 61.8 + - - +
411D SER* 3.3 7.8 + - - -
412D PHE* 3.2 48.0 + - + -
425D VAL* 5.1 7.0 - - + -
427D PHE* 3.6 36.8 - - + -
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Residues in contact with ARG 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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397D VAL* 4.1 35.9 - - + +
405D GLN* 2.9 31.6 + - - +
406D GLN* 3.3 26.4 + - - +
408D LEU* 1.3 73.1 - - - +
410D ASP* 1.3 65.1 + - - +
411D SER 3.0 2.2 + - - -
412D PHE* 3.3 7.2 + - - +
413D GLN* 3.0 31.3 + - + +
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Residues in contact with ASP 410 (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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406D GLN* 3.0 46.7 + - - +
407D LEU* 3.3 9.3 + - + +
409D ARG* 1.3 76.0 - - - +
411D SER* 1.3 60.3 + - - +
413D GLN* 3.4 21.3 - - - +
414D GLN* 3.2 23.9 + - - +
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Residues in contact with SER 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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407D LEU* 2.9 21.7 + - - +
408D LEU* 3.4 10.5 + - - -
409D ARG 3.0 0.2 - - - -
410D ASP* 1.3 75.9 - - - +
412D PHE* 1.3 64.6 + - - +
414D GLN* 2.9 17.7 + - - +
415D VAL* 3.0 20.3 + - - +
423D LEU* 3.8 16.4 - - - +
425D VAL* 3.7 29.8 - - - +
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Residues in contact with PHE 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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367D HIS* 3.9 25.1 - + + -
369D ILE 4.1 11.6 - - - +
370D GLU 4.8 4.9 - - - +
371D GLY* 3.7 24.0 - - - -
396D ILE* 3.8 21.5 - - + -
397D VAL* 5.9 0.7 - - + -
408D LEU* 3.2 43.4 + - + +
409D ARG* 3.3 8.0 + - - +
411D SER* 1.3 82.8 - - - +
413D GLN* 1.3 62.1 + - + +
415D VAL* 3.3 8.6 - - + +
416D VAL* 3.2 24.6 - - - +
443D SER* 5.5 3.4 - - - -
457D ILE* 3.5 33.4 - - + -
459D CYS* 4.4 10.5 - - - -
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Residues in contact with GLN 413 (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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406D GLN* 5.3 0.2 + - - -
409D ARG* 3.0 21.3 + - + +
410D ASP* 3.4 27.7 - - - +
412D PHE* 1.3 77.3 - - + +
414D GLN* 1.3 60.8 + - - +
416D VAL* 3.7 6.9 - - - +
417D LYS* 3.4 35.4 + - - +
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Residues in contact with GLN 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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410D ASP 3.2 18.3 + - - +
411D SER 2.9 7.2 + - - +
413D GLN* 1.3 75.8 - - - +
415D VAL* 1.3 56.5 + - - +
416D VAL 3.0 1.8 - - - -
417D LYS* 2.6 43.4 + - - +
418D LEU* 2.8 41.0 + - + +
423D LEU* 3.6 19.7 - - + +
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Residues in contact with VAL 415 (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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411D SER* 3.0 12.7 + - - +
412D PHE* 3.3 20.0 - - + +
414D GLN* 1.3 75.5 - - - +
416D VAL* 1.3 59.5 + - + +
418D LEU* 3.8 7.9 - - - +
419D LYS 3.0 23.0 + - - -
420D GLY 4.5 0.7 + - - -
421D GLN 4.9 2.0 - - - +
423D LEU* 3.7 32.1 - - + +
443D SER* 4.1 26.9 - - - +
444D PHE* 4.5 6.5 - - - -
445D THR* 3.3 18.1 + - + +
457D ILE* 3.8 26.9 - - + -
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Residues in contact with VAL 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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369D ILE* 4.3 24.5 - - + +
412D PHE 3.2 18.2 - - - +
413D GLN* 3.7 10.5 - - - +
414D GLN 3.0 0.4 - - - -
415D VAL* 1.3 84.6 - - + +
417D LYS* 1.3 58.1 + - + +
419D LYS* 3.0 29.8 - - - +
445D THR* 4.0 9.4 - - + -
454D ILE* 3.7 16.8 - - + +
457D ILE* 4.2 13.7 - - + -
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Residues in contact with LYS 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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413D GLN* 3.4 25.7 - - - +
414D GLN* 2.6 36.8 + - - +
416D VAL* 1.3 74.8 - - + +
418D LEU* 1.3 62.0 + - + +
419D LYS* 4.1 7.6 - - - +
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Residues in contact with LEU 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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414D GLN* 2.8 47.2 + - + +
415D VAL* 3.8 6.7 - - - +
417D LYS* 1.3 79.0 - - + +
419D LYS* 1.3 75.1 + - - +
421D GLN* 3.6 56.4 + - + +
422D VAL 4.1 2.2 - - - +
423D LEU* 3.6 28.3 - - + -
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Residues in contact with LYS 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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415D VAL 3.0 10.1 + - - -
416D VAL* 3.0 25.6 - - - +
417D LYS* 4.1 6.5 - - - +
418D LEU* 1.3 86.9 - - - +
420D GLY* 1.3 56.9 + - - +
421D GLN* 3.4 3.9 + - - +
445D THR* 3.2 11.0 - - - -
447D GLN* 3.1 35.7 - - + +
453D GLU* 5.1 8.1 + - - -
454D ILE* 4.3 17.9 - - + -
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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