Contacts of the helix formed by residues 391 - 396 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160C VAL* 4.3 0.2 - - - -
161C VAL 3.3 23.3 - - - -
163C LYS* 3.9 8.3 - - - -
389C GLN* 3.1 7.9 + - - -
390C LEU* 1.3 68.9 - - - +
392C GLY* 1.3 61.1 + - - +
393C GLY 3.2 1.0 - - - +
394C THR 3.0 3.3 + - - -
395C LEU* 2.9 29.8 + - - +
600C CAP 2.9 21.9 + - - -
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Residues in contact with GLY 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C LYS* 3.7 7.0 - - - +
391C GLY* 1.3 65.9 - - - -
393C GLY* 1.3 57.5 + - - +
394C THR 2.8 5.7 + - - -
395C LEU* 4.4 2.0 - - - -
396C GLY* 2.7 35.7 + - - -
438C TRP* 3.7 1.2 - - - -
600C CAP 2.9 17.6 + - - -
54F THR* 4.1 6.7 - - - -
55F TRP* 4.1 1.6 - - - -
56F THR* 3.4 27.6 - - - +
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Residues in contact with GLY 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C LEU 3.4 23.9 + - - -
371C HIS* 4.1 7.6 - - - -
372C PRO* 3.6 14.1 - - - +
390C LEU* 4.5 5.6 - - - -
391C GLY 3.2 2.6 - - - +
392C GLY* 1.3 74.8 - - - +
394C THR* 1.3 58.8 + - - +
404C GLY* 5.2 1.7 - - - -
408C VAL* 4.3 3.1 - - - +
438C TRP* 3.5 23.4 - - - -
55F TRP* 3.8 15.2 - - - +
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Residues in contact with THR 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C TYR* 2.8 28.4 + - - +
160C VAL* 3.6 13.9 - - + +
180C LEU* 3.8 21.8 - - + -
390C LEU* 2.9 31.9 + - - +
391C GLY 3.0 2.3 + - - -
392C GLY 2.8 1.6 + - - -
393C GLY* 1.3 79.8 - - - +
395C LEU* 1.3 64.1 + - + +
396C GLY 3.0 5.0 + - - -
397C HIS* 3.2 20.6 + - - +
401C PRO* 4.0 4.7 - - - +
404C GLY* 3.9 6.9 - - - -
405C ALA 3.9 11.7 - - - +
408C VAL* 3.8 3.5 - - - +
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Residues in contact with LEU 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C VAL* 3.0 34.3 - - + -
161C VAL 4.0 0.7 - - - +
162C PRO* 3.4 9.6 - - + -
163C LYS* 2.6 54.5 - - + +
176C LEU* 4.1 21.8 - - + -
180C LEU* 4.2 8.5 - - + -
391C GLY 2.9 13.0 + - - +
392C GLY* 4.8 0.7 - - - -
394C THR* 1.3 77.3 - - + +
396C GLY* 1.3 57.7 + - - +
397C HIS 3.3 2.8 + - - +
401C PRO* 4.5 11.7 - - + +
58F LEU* 5.1 2.9 - - + -
59F TYR* 3.3 32.7 + - + +
61F TRP* 4.2 4.9 - - - +
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Residues in contact with GLY 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392C GLY* 2.7 24.1 + - - -
395C LEU* 1.3 72.5 - - - +
397C HIS* 1.3 64.8 + - - +
437C LYS* 2.7 27.6 + - - +
438C TRP* 3.3 14.0 - - - -
56F THR* 4.6 1.8 - - - -
57F THR 3.4 21.8 - - - -
58F LEU* 4.7 1.3 - - - -
59F TYR 4.9 0.2 - - - -
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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