Contacts of the helix formed by residues 426 - 433 (chain D) in PDB entry 1K79
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 PRO 426 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360D GLY* 3.5 36.1 - - - +
361D TRP* 3.7 38.8 - - + +
419D GLN* 4.3 10.1 - - - +
425D THR* 1.3 84.5 - - - +
427D GLU* 1.3 69.8 - - - +
429D LEU* 3.1 1.9 + - - +
430D HIS* 2.7 48.5 + - + +
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Residues in contact with GLU 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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358D GLY 5.4 1.9 - - - +
360D GLY 5.3 3.3 + - - -
425D THR* 3.8 10.8 + - - +
426D PRO* 1.3 94.3 - - - +
428D GLU* 1.3 58.9 + - + +
430D HIS* 3.1 13.5 + - - +
431D ALA* 2.8 32.6 + - - +
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Residues in contact with GLU 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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423D GLY 4.4 2.9 - - - +
424D TYR* 3.6 22.6 - - + -
425D THR* 3.0 42.9 + - - +
427D GLU* 1.3 80.5 - - + +
429D LEU* 1.3 63.4 + - - +
431D ALA* 3.5 5.9 + - - +
432D MET* 3.1 23.6 + - - +
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Residues in contact with LEU 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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346D THR* 4.8 14.4 - - + +
356D TRP* 3.7 37.9 - - + +
361D TRP* 3.9 17.5 - - + -
422D LEU* 4.6 12.6 - - + -
424D TYR* 4.2 33.6 - - + +
425D THR 3.0 14.6 + - - +
426D PRO 3.7 5.2 - - - +
428D GLU* 1.3 73.4 - - - +
430D HIS* 1.3 68.8 + - - +
432D MET* 3.3 10.9 + - - +
433D LEU* 2.9 40.6 + - + +
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Residues in contact with HIS 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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356D TRP* 3.8 39.9 - + + +
358D GLY* 3.9 30.0 + - - -
360D GLY 3.2 26.6 + - - -
361D TRP* 5.3 2.0 - + - -
426D PRO* 2.7 39.1 + - + +
427D GLU* 3.5 11.9 - - - +
429D LEU* 1.3 73.5 - - + +
431D ALA* 1.3 51.6 + - - +
433D LEU* 3.1 2.0 + - - -
434D ASP 2.6 32.1 + - - -
435D VAL* 2.9 37.1 + - + +
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Residues in contact with ALA 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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427D GLU 2.8 21.3 + - - +
428D GLU* 3.7 6.7 - - - +
430D HIS* 1.3 72.4 - - - +
432D MET* 1.3 63.5 + - - +
434D ASP* 2.9 20.1 + - - +
435D VAL 5.0 0.4 - - - +
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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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348D LYS* 3.8 15.8 + - - +
424D TYR* 3.1 46.2 - - + +
428D GLU 3.1 11.9 + - - +
429D LEU* 3.3 11.9 + - - +
431D ALA* 1.3 80.5 - - - +
433D LEU* 1.3 66.5 + - + +
434D ASP* 3.5 0.7 + - - +
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Residues in contact with LEU 433 (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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345D LEU 3.0 25.1 - - - +
346D THR* 3.1 31.6 - - - +
347D ASP 4.7 0.2 - - - -
348D LYS* 3.4 33.4 - - + +
351D GLN* 2.8 25.9 + - + +
356D TRP* 3.4 18.8 - - + +
429D LEU* 2.9 38.5 + - + +
430D HIS 3.9 1.8 - - - +
432D MET* 1.3 82.0 - - + +
434D ASP* 1.3 73.0 + - - +
435D VAL* 3.9 6.1 - - + -
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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