Contacts of the helix formed by residues 441 - 452 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A HIS* 3.4 34.4 + + + +
271A TRP 2.7 14.3 + - - +
272A CYS* 4.0 7.9 - - - -
273A SER* 3.4 33.8 + - - -
288A HIS* 4.3 12.6 - + - -
439A HIS* 3.6 16.8 - - + +
440A LEU* 1.3 69.3 - - - +
442A GLY* 1.3 69.4 + - - +
444A LEU* 3.3 1.1 + - + -
445A GLN* 2.9 26.0 + - - +
302C PRO* 3.3 47.2 + - + +
303C SER* 5.9 0.8 - - - -
313C LEU* 6.2 0.2 - - - +
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Residues in contact with GLY 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A TRP* 4.1 6.3 + - - +
338A TYR* 6.0 1.8 - - - -
385A ASN* 5.5 0.4 - - - -
441A HIS* 1.3 81.1 - - - +
443A PRO* 1.3 68.5 - - - +
445A GLN* 3.0 13.7 + - - +
446A TRP* 3.1 35.5 + - - -
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Residues in contact with PRO 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A TRP 5.4 0.2 - - - +
338A TYR* 6.0 0.4 - - - +
383A PHE* 3.7 30.7 - - + -
385A ASN* 4.1 10.5 - - - +
388A PHE* 3.8 15.6 - - + -
410A CYS* 3.6 23.1 - - + -
440A LEU* 3.5 22.0 - - + +
442A GLY* 1.3 87.8 - - - +
444A LEU* 1.3 55.8 + - - +
446A TRP* 3.5 19.8 - - + +
447A LEU* 2.9 31.5 + - - +
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Residues in contact with LEU 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A THR* 4.4 13.5 - - + +
410A CYS* 3.7 21.8 - - + -
411A THR* 5.4 0.4 - - + -
439A HIS* 3.6 33.7 - - + -
440A LEU 3.1 31.3 + - - +
441A HIS 3.7 4.7 - - - +
443A PRO* 1.3 76.9 - - - +
445A GLN* 1.3 58.1 + - - +
447A LEU* 3.5 5.1 + - + +
448A ASP* 2.9 12.1 + - - +
300C THR* 2.7 44.8 + - - +
302C PRO* 4.0 15.9 - - + -
313C LEU* 3.9 23.8 - - + -
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Residues in contact with GLN 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A HIS* 2.9 18.9 + - - +
442A GLY* 3.3 6.0 - - - +
444A LEU* 1.3 74.9 - - - +
446A TRP* 1.3 69.3 + - + +
448A ASP* 2.8 28.2 + - - +
449A LYS* 3.0 30.0 + - - +
301C ASP* 3.2 27.0 + - - +
302C PRO* 4.0 9.3 - - + +
303C SER* 3.8 18.2 + - - -
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Residues in contact with TRP 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A TYR* 5.4 2.5 - - - -
385A ASN* 2.9 52.5 - - + -
388A PHE* 4.3 13.5 - + - -
389A ALA* 5.0 11.0 - - + -
392A LEU* 4.0 13.4 - - + +
442A GLY* 3.1 22.7 + - - -
443A PRO* 3.5 24.2 - - + +
445A GLN* 1.3 84.1 + - + +
447A LEU* 1.3 63.6 + - - +
448A ASP 3.0 0.7 + - - -
449A LYS* 3.1 25.4 + - - +
450A VAL* 3.3 14.4 + - - +
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Residues in contact with LEU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A PHE* 4.7 3.1 - - + -
392A LEU* 3.5 32.5 - - + +
403A VAL* 3.6 21.5 - - + +
406A LEU* 3.9 7.6 - - + +
407A THR* 3.6 44.4 - - + +
410A CYS* 4.6 6.7 - - - -
443A PRO 2.9 18.6 + - - +
444A LEU* 3.6 5.6 - - + +
446A TRP* 1.3 77.4 - - - +
448A ASP* 1.3 56.4 + - - +
450A VAL* 3.3 1.4 + - - +
451A LEU* 3.0 42.6 + - + +
300C THR* 4.0 10.3 - - + +
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Residues in contact with ASP 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A LEU 2.9 14.4 + - - +
445A GLN* 2.8 19.1 + - - +
447A LEU* 1.3 73.9 - - - +
449A LYS* 1.3 68.6 + - - +
450A VAL 2.8 3.5 + - - -
451A LEU* 3.0 4.4 + - - -
452A THR* 3.0 28.2 + - - -
299C PHE* 3.1 19.2 - - - +
300C THR* 3.3 9.1 + - - +
301C ASP* 3.8 17.1 - - - +
308C ARG* 2.6 45.9 + - - -
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Residues in contact with LYS 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A GLN* 3.0 52.9 + - + +
446A TRP* 3.1 16.6 + - + +
448A ASP* 1.3 81.2 + - + +
450A VAL* 1.3 62.5 + - + +
452A THR* 3.9 8.1 - - - -
453A GLN* 3.6 21.0 + - - -
301C ASP* 5.2 1.7 + - - -
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Residues in contact with VAL 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A LEU* 4.2 25.4 - - + +
396A VAL* 4.0 33.7 - - + +
403A VAL* 4.3 18.4 - - + -
446A TRP 3.3 11.8 + - - +
447A LEU 3.8 5.8 - - - +
448A ASP 2.8 2.0 + - - -
449A LYS* 1.3 80.3 - - + +
451A LEU* 1.3 60.2 + - - +
452A THR 3.0 2.0 - - - -
453A GLN* 2.9 33.1 + - + +
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Residues in contact with LEU 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A PHE* 4.3 12.6 - - + +
403A VAL* 3.3 42.0 - - + -
404A TYR* 4.0 26.7 - - + +
447A LEU* 3.0 39.2 + - + +
448A ASP* 3.0 3.8 + - - +
450A VAL* 1.3 71.2 - - - +
452A THR* 1.3 53.6 + - - +
453A GLN 2.7 18.6 + - - -
454A MET* 3.4 12.5 + - - +
298C GLY 5.7 0.9 - - - +
299C PHE* 3.4 31.4 - - + -
300C THR* 4.1 20.9 - - + +
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Residues in contact with THR 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A ASP* 3.0 28.6 + - - -
449A LYS* 3.9 9.1 + - - -
450A VAL 3.0 0.2 - - - -
451A LEU* 1.3 76.2 - - - +
453A GLN* 1.3 68.7 + - - +
454A MET* 3.2 16.7 + - - +
299C PHE* 4.2 15.6 - - + -
308C ARG* 4.5 7.1 + - - -
332C LYS* 4.8 6.7 - - - -
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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