Contacts of the strand formed by residues 387 - 389 (chain E) 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 VAL 387 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E VAL* 5.8 0.2 - - + -
157E ILE* 3.8 21.8 - - + -
187E TYR* 3.6 35.0 - - + +
227E PHE* 4.6 8.5 - - + -
279E HIS* 5.1 0.2 - - + -
312E GLN* 4.6 11.0 - - - +
363E PHE* 3.6 32.3 - - + -
364E PRO 2.8 10.6 + - - +
365E THR* 3.3 24.1 - - + +
366E SER* 2.9 27.4 + - - -
386E ILE* 1.3 72.3 - - - +
388E LEU* 1.3 63.9 + - - +
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Residues in contact with LEU 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E PRO* 4.0 24.7 - - + -
157E ILE 2.7 17.3 + - - +
158E TYR* 3.4 5.0 - - + -
159E GLY 3.0 18.2 + - - +
187E TYR* 2.8 13.5 + - - -
366E SER* 3.8 17.5 - - - +
370E LEU* 4.4 9.2 - - + -
375E ILE* 4.8 13.5 - - + -
378E VAL* 4.3 10.1 - - + -
379E ILE* 4.2 17.7 - - + -
386E ILE* 3.8 26.0 - - + -
387E VAL* 1.3 73.4 - - - +
389E GLN* 1.3 59.5 + - - +
390E LEU* 3.9 14.6 - - + -
408E VAL* 5.8 0.7 - - + -
412E ILE* 4.4 15.5 - - + -
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Residues in contact with GLN 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159E GLY 3.5 3.8 - - - +
160E VAL 3.6 0.2 - - - -
161E VAL* 2.8 49.3 + - + +
187E TYR* 3.3 17.5 - - + +
189E KCX 4.4 9.2 - - + +
314E HIS* 5.3 0.4 - - - +
365E THR* 4.8 6.1 - - + -
366E SER 3.2 13.6 + - - +
367E SER* 2.9 43.8 + - - +
370E LEU* 4.1 6.8 - - - +
387E VAL 4.0 0.4 + - - -
388E LEU* 1.3 72.3 - - - +
390E LEU* 1.3 69.6 + - - +
391E GLY* 2.9 14.7 + - - -
600E CAP 3.2 25.6 + - - -
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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
------------------------------------------------------------
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