Contacts of the helix formed by residues 391 - 396 (chain F) in PDB entry 3KDO
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 GLY 391 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160F VAL* 4.4 0.4 - - - -
161F VAL 3.4 23.6 - - - -
163F LYS* 3.9 9.2 - - - -
389F GLN* 3.0 8.8 + - - -
390F LEU* 1.3 68.6 - - - +
392F GLY* 1.3 58.7 + - - +
393F GLY 3.0 0.8 - - - +
394F THR* 2.9 18.9 + - - -
395F LEU* 2.9 16.1 + - - +
600F CAP 2.9 20.6 + - - -
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Residues in contact with GLY 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C THR* 4.3 1.6 - - - -
55C TRP* 4.0 2.2 - - - -
56C THR* 3.5 27.8 - - - +
58C LEU* 4.2 15.7 - - - -
163F LYS* 3.7 3.9 - - - +
391F GLY* 1.3 71.5 - - - +
393F GLY* 1.3 57.8 - - - +
394F THR 3.0 0.4 + - - -
396F GLY* 2.8 30.4 + - - -
438F TRP* 3.6 2.3 - - - -
600F CAP 2.9 18.5 + - - -
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Residues in contact with GLY 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TRP* 3.9 13.3 - - - +
370F LEU 3.3 26.8 + - - -
371F HIS* 4.2 6.3 - - - -
372F PRO* 3.7 20.3 - - - +
390F LEU* 4.3 5.2 - - - -
391F GLY 3.0 3.4 - - - +
392F GLY* 1.3 75.7 - - - +
394F THR* 1.3 60.0 + - - +
397F HIS* 5.7 0.3 - - - -
404F GLY* 4.8 2.4 - - - +
408F VAL* 4.2 5.0 - - - +
438F TRP* 3.8 12.6 - - - -
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Residues in contact with THR 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F TYR* 2.7 30.1 + - - +
160F VAL* 3.3 15.4 - - + +
180F LEU* 3.8 23.3 - - + -
390F LEU* 2.7 32.0 + - - +
391F GLY 2.9 2.9 + - - -
393F GLY* 1.3 80.6 + - - +
395F LEU* 1.3 63.2 + - - +
396F GLY 3.3 2.1 + - - -
397F HIS* 3.5 7.8 - - - +
401F PRO* 3.9 4.5 - - - +
404F GLY* 3.5 20.3 - - - -
405F ALA 3.8 10.5 - - - +
408F VAL* 3.9 2.3 - - - +
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Residues in contact with LEU 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C LEU* 4.3 13.7 - - + -
59C TYR* 3.2 30.5 + - - +
61C TRP* 3.4 22.4 - - + +
160F VAL* 4.2 9.6 - - + -
161F VAL 3.8 7.0 - - - +
162F PRO* 3.5 13.2 - - + -
163F LYS* 3.0 37.0 - - + +
176F LEU* 3.4 35.9 - - + -
180F LEU* 4.9 1.6 - - + -
391F GLY 2.9 11.8 + - - +
394F THR* 1.3 74.8 - - - +
396F GLY* 1.3 59.0 + - - +
397F HIS 3.2 6.3 + - - +
401F PRO* 3.7 17.7 - - + +
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Residues in contact with GLY 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C THR 3.3 22.7 - - - -
58C LEU* 4.3 3.1 - - - -
59C TYR 5.1 1.3 - - - -
392F GLY* 2.8 18.7 + - - -
395F LEU* 1.3 76.5 - - - +
397F HIS* 1.3 62.4 + - - +
398F PRO 3.5 0.7 - - - -
437F LYS* 2.6 27.9 + - - -
438F TRP* 3.4 13.2 - - - -
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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