Contacts of the helix formed by residues 397 - 406 (chain D) in PDB entry 1KU7
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 THR 397 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387D ARG* 3.6 5.4 - - - +
395D GLU 5.6 0.7 - - - +
396D HIS* 1.3 75.8 - - - +
398D LEU* 1.3 62.1 + - - +
399D GLU* 2.9 24.6 + - - +
400D GLU* 2.9 38.9 + - - +
401D VAL* 3.1 25.2 + - - +
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Residues in contact with LEU 398 (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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387D ARG* 3.4 36.8 - - - +
397D THR* 1.3 73.4 - - - +
399D GLU* 1.3 67.2 + - - +
401D VAL* 3.4 0.4 + - - -
402D GLY* 2.8 28.6 + - - -
409D ARG* 3.5 32.2 - - + +
410D GLU* 5.7 0.2 - - - -
412D ILE* 3.7 14.5 - - + +
413D ARG* 3.7 33.2 - - + +
416D GLU* 3.5 10.5 - - - +
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Residues in contact with GLU 399 (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 THR* 2.9 26.5 - - - +
398D LEU* 1.3 85.9 + - - +
400D GLU* 1.3 58.2 + - + +
402D GLY* 3.2 2.3 + - - -
403D ALA* 2.9 28.5 + - - +
409D ARG* 3.1 50.4 + - + +
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Residues in contact with GLU 400 (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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437A LEU* 3.5 40.9 - - + +
386D MET* 5.6 1.1 - - - -
395D GLU 4.5 1.2 - - - +
396D HIS* 3.2 24.2 + - + -
397D THR* 2.9 44.3 + - - +
399D GLU* 1.3 76.9 - - + +
401D VAL* 1.3 63.5 + - - +
403D ALA* 3.2 9.6 + - - +
404D TYR* 3.0 21.3 + - - +
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Residues in contact with VAL 401 (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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383D VAL* 4.6 12.8 - - + -
386D MET* 4.2 18.4 - - + -
387D ARG* 3.9 21.5 - - + -
396D HIS* 4.0 15.9 - - + -
397D THR 3.1 17.4 + - - +
398D LEU 3.8 2.9 - - - +
400D GLU* 1.3 70.6 - - - +
402D GLY* 1.3 66.9 + - - +
404D TYR* 3.0 16.7 + - - +
405D PHE* 3.0 30.8 + - + -
412D ILE* 3.7 27.8 - - + -
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Residues in contact with GLY 402 (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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398D LEU 2.8 14.6 + - - -
399D GLU 3.6 1.6 - - - -
401D VAL* 1.3 76.2 - - - +
403D ALA* 1.3 57.8 + - - +
405D PHE 3.0 2.3 + - - -
406D GLY 2.8 25.8 + - - -
407D VAL 2.9 26.9 + - - +
408D THR 4.4 2.5 - - - -
409D ARG 4.8 0.2 - - - -
412D ILE* 3.3 22.6 - - - +
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Residues in contact with ALA 403 (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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436A PHE* 3.6 20.1 - - + -
437A LEU* 5.4 2.0 - - + -
399D GLU 2.9 13.4 + - - +
400D GLU* 3.4 12.3 - - - +
402D GLY* 1.3 78.1 - - - +
404D TYR* 1.3 60.5 + - - +
405D PHE 3.3 0.5 + - - -
406D GLY* 3.3 11.1 + - - +
407D VAL 4.8 0.9 - - - -
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Residues in contact with TYR 404 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A SER* 4.0 16.1 + - - -
369A LEU* 3.8 28.8 - - + +
433A LEU* 4.8 3.1 - - + -
436A PHE* 3.6 27.8 - + + -
437A LEU* 5.8 0.2 - - + -
382D MET* 4.0 11.9 - - + +
386D MET* 3.9 27.6 - - + -
400D GLU 3.0 13.1 + - - +
401D VAL 3.0 9.4 + - - +
403D ALA* 1.3 77.1 - - - +
405D PHE* 1.3 96.7 + + - +
406D GLY 3.8 0.3 + - - -
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Residues in contact with PHE 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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379D ARG* 3.5 46.8 + - + +
382D MET* 3.8 20.9 - - + -
383D VAL* 3.7 21.8 - - + -
386D MET* 5.0 0.7 - - - -
401D VAL* 3.0 34.0 + - + +
402D GLY 3.0 4.0 + - - +
404D TYR* 1.3 110.1 - + - +
406D GLY* 1.3 62.8 + - - +
407D VAL* 3.0 19.3 + - + +
412D ILE* 3.9 10.1 - - + -
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Residues in contact with GLY 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 GLY 2.8 5.4 + - - -
403D ALA* 3.3 11.4 + - - -
404D TYR 3.5 1.0 + - - -
405D PHE* 1.3 77.6 - - - +
407D VAL* 1.3 61.0 + - - +
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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