Contacts of the helix formed by residues 441 - 452 (chain D) in PDB entry 1KHU
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 HIS 441 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270D HIS* 3.4 44.6 + + + +
271D TRP 3.4 6.0 + - - +
272D CYS* 4.1 4.5 - - - -
273D SER* 3.3 33.7 + - - -
288D HIS* 4.5 9.2 - + - -
439D HIS* 3.5 18.1 - - + +
440D LEU* 1.3 70.7 - - - +
442D GLY* 1.3 56.2 + - - +
444D LEU* 3.5 10.8 - - + +
445D GLN* 2.7 38.9 + - - +
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Residues in contact with GLY 442 (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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270D HIS 5.2 0.4 + - - -
271D TRP* 4.5 5.7 + - - +
338D TYR* 5.9 2.9 - - - -
441D HIS* 1.3 76.1 - - - +
443D PRO* 1.3 69.6 - - - +
445D GLN* 2.9 17.4 + - - +
446D TRP* 3.0 36.4 + - - -
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Residues in contact with PRO 443 (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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271D TRP 5.6 0.2 - - - +
338D TYR* 6.0 1.6 - - + +
383D PHE* 3.9 27.4 - - + -
385D ASN* 4.2 5.8 - - + +
388D PHE* 3.7 23.5 - - + -
410D CYS* 3.9 13.5 - - - -
440D LEU* 3.5 24.2 - - + +
442D GLY* 1.3 88.5 - - - +
444D LEU* 1.3 61.1 + - - +
446D TRP* 3.4 25.6 + - + +
447D LEU* 3.0 24.9 + - - +
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Residues in contact with LEU 444 (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 THR* 4.3 20.9 - - + +
410D CYS* 3.5 23.8 - - + -
411D THR* 5.8 0.2 - - + -
439D HIS* 3.8 34.8 - - + -
440D LEU 3.0 32.9 + - - +
441D HIS* 3.5 12.8 - - + +
443D PRO* 1.3 77.8 - - - +
445D GLN* 1.3 56.6 + - - +
447D LEU* 3.3 9.1 - - + +
448D ASP* 3.1 24.8 + - - +
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Residues in contact with GLN 445 (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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441D HIS* 2.7 21.7 + - + +
442D GLY* 3.4 7.3 - - - +
444D LEU* 1.3 72.4 - - - +
446D TRP* 1.3 70.9 + - + +
448D ASP* 3.1 16.2 + - + +
449D LYS* 2.9 40.9 - - + +
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Residues in contact with TRP 446 (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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338D TYR* 5.4 4.7 - - - -
385D ASN* 3.5 54.3 - - + -
388D PHE* 4.1 12.3 - + - -
389D ALA* 5.2 7.6 - - + -
392D LEU* 4.1 15.3 - - + -
442D GLY* 3.0 23.5 + - - -
443D PRO* 3.4 24.2 - - + +
445D GLN* 1.3 81.8 + - + +
447D LEU* 1.3 67.7 + - - +
449D LYS* 2.9 30.8 + - + +
450D VAL* 3.3 10.9 + - - +
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Residues in contact with LEU 447 (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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388D PHE* 4.8 3.6 - - + -
392D LEU* 3.7 27.2 - - + +
403D VAL* 3.7 23.3 - - + +
406D LEU* 4.0 7.9 - - + -
407D THR* 3.5 44.6 - - + +
410D CYS* 4.0 13.9 - - - -
443D PRO 3.0 16.8 + - - +
444D LEU* 3.3 11.7 - - + +
446D TRP* 1.3 77.7 - - - +
448D ASP* 1.3 55.9 + - - +
450D VAL* 3.2 2.9 + - - +
451D LEU* 2.9 42.8 + - + +
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Residues in contact with ASP 448 (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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444D LEU 3.1 13.0 + - - +
445D GLN* 3.2 15.5 - - + +
446D TRP 3.1 0.2 - - - -
447D LEU* 1.3 76.6 - - - +
449D LYS* 1.3 71.8 + - - +
450D VAL 3.0 1.2 + - - -
451D LEU* 3.2 17.7 + - - +
452D THR* 3.4 26.4 + - - +
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Residues in contact with LYS 449 (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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445D GLN* 2.9 47.0 - - + +
446D TRP* 2.9 17.5 + - + +
448D ASP* 1.3 83.9 + - + +
450D VAL* 1.3 61.1 + - + +
452D THR* 3.3 15.7 + - - -
453D GLN 5.0 0.2 + - - -
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Residues in contact with VAL 450 (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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392D LEU* 3.9 30.7 - - + +
396D VAL* 5.0 15.0 - - + +
403D VAL* 4.0 15.7 - - + -
446D TRP 3.7 11.0 - - - +
447D LEU 3.2 6.9 + - - +
448D ASP 3.0 0.6 - - - -
449D LYS* 1.3 79.3 - - + +
451D LEU* 1.3 61.3 + - - +
452D THR 3.2 2.2 - - - -
453D GLN* 2.8 53.9 + - + +
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Residues in contact with LEU 451 (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 PHE* 4.1 28.2 - - + -
403D VAL* 3.6 38.4 - - + -
404D TYR* 4.0 22.0 - - + -
407D THR* 4.5 11.2 - - - +
447D LEU* 2.9 38.4 + - + +
448D ASP* 3.2 10.0 + - - +
450D VAL* 1.3 70.2 - - - +
452D THR* 1.3 59.4 + - + +
453D GLN* 2.7 20.6 + - - +
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Residues in contact with THR 452 (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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448D ASP* 3.4 24.1 + - - +
449D LYS* 3.3 19.0 + - - -
450D VAL 3.1 0.2 + - - -
451D LEU* 1.3 75.7 - - + +
453D GLN* 1.3 60.3 + - - +
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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