Contacts of the helix formed by residues 424 - 432 (chain D) in PDB entry 3KHU
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 424 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402D TYR* 2.9 21.0 + - + +
422D GLU 3.8 1.0 + - - -
423D LEU* 1.3 67.3 - - - +
425D TYR* 1.3 61.8 + - - +
426D GLU* 3.4 11.8 + - - +
427D ARG* 3.2 36.5 + - + +
428D ILE* 3.1 24.6 + - - +
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Residues in contact with TYR 425 (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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334D LEU* 5.1 0.9 - - - +
411D VAL* 5.4 9.0 - - + -
413D ILE* 4.0 11.8 - - - +
420D PHE 2.6 30.1 + - - -
421D LYS 4.4 5.4 - - - -
423D LEU* 3.1 43.1 + - + +
424D ASP* 1.3 70.9 + - - +
426D GLU* 1.3 60.4 + - - +
428D ILE* 3.7 21.1 - - + -
429D HIS* 2.9 29.5 + - - +
438D ILE* 4.0 28.5 - - + -
445D LEU* 3.7 24.3 - - + +
448D LEU* 5.2 4.9 - - + -
452D LEU* 3.6 25.1 - - + -
455D ILE* 4.3 5.4 - - + -
457D PHE* 3.4 12.9 - + + -
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Residues in contact with GLU 426 (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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424D ASP* 3.2 9.8 + - - +
425D TYR* 1.3 77.7 - - - +
427D ARG* 1.3 63.5 + - - +
429D HIS* 3.3 3.3 + - - +
430D LYS* 3.2 42.2 + - - +
451D GLU* 5.5 2.4 - - - +
455D ILE* 4.1 36.5 - - + +
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Residues in contact with ARG 427 (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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400D ASP* 5.3 0.4 + - - -
402D TYR* 3.6 59.5 - - + +
424D ASP* 3.2 30.2 + - - +
426D GLU* 1.3 80.7 - - - +
428D ILE* 1.3 63.6 + - - +
430D LYS* 3.3 25.2 + - - +
431D LYS* 3.7 9.8 + - + +
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Residues in contact with ILE 428 (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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334D LEU* 6.0 0.2 - - + -
401D PRO 5.5 0.9 - - - +
402D TYR* 3.8 27.1 - - + -
405D CYS* 3.7 37.4 - - + +
411D VAL* 4.4 3.4 - - + -
423D LEU* 4.2 15.7 - - + -
424D ASP 3.1 15.2 + - - +
425D TYR* 3.7 31.9 - - + +
427D ARG* 1.3 78.8 - - - +
429D HIS* 1.3 64.9 + - - +
431D LYS* 3.3 5.9 + - - +
432D MET* 3.2 41.0 + - - +
457D PHE* 4.2 6.3 - - + -
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Residues in contact with HIS 429 (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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425D TYR 2.9 17.9 + - - +
426D GLU 3.5 5.6 - - - +
428D ILE* 1.3 76.6 - - - +
430D LYS* 1.3 64.4 + - - +
432D MET* 3.1 14.6 + - - +
434D LYS* 2.9 39.9 + - + -
436D ALA* 4.8 3.9 - - + +
455D ILE* 2.9 48.7 + - + -
456D GLY* 3.3 23.8 - - - -
457D PHE* 3.6 19.9 - + + -
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Residues in contact with LYS 430 (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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426D GLU* 3.2 34.0 + - - +
427D ARG* 3.3 14.6 + - - +
429D HIS* 1.3 81.1 + - - +
431D LYS* 1.3 65.4 + - + +
432D MET 4.3 0.3 - - - +
434D LYS* 3.5 13.7 + - - +
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Residues in contact with LYS 431 (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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405D CYS 4.6 0.7 - - - -
406D ASP* 3.7 31.6 + - + +
407D GLY* 2.7 30.7 + - - +
427D ARG* 3.7 6.7 + - + +
428D ILE* 3.3 7.3 + - - +
429D HIS 3.2 0.6 - - - -
430D LYS* 1.3 82.5 - - + +
432D MET* 1.3 62.0 + - - +
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Residues in contact with MET 432 (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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405D CYS 3.5 15.7 - - - +
408D ALA* 3.3 26.0 - - + +
409D HIS 3.3 26.5 - - - +
410D ALA* 3.4 15.9 - - - +
411D VAL* 3.8 7.9 - - + -
428D ILE* 3.2 33.6 + - + +
429D HIS 3.1 8.2 + - - +
430D LYS 4.3 0.3 - - - +
431D LYS* 1.3 79.8 - - - +
433D LEU* 1.3 64.5 + - - +
434D LYS* 2.7 29.5 + - - -
436D ALA* 4.0 11.0 - - + -
437D PHE 3.7 9.0 - - - +
457D PHE* 3.7 19.5 - - - -
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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