Contacts of the strand formed by residues 387 - 389 (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 VAL 387 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F VAL* 6.0 0.4 - - + -
157F ILE* 3.7 16.4 - - + +
187F TYR* 3.4 35.2 - - + +
227F PHE* 4.7 9.0 - - + -
279F HIS* 5.2 0.2 - - + -
312F GLN* 4.8 11.2 - - + +
363F PHE* 3.6 32.5 - - + -
364F PRO 2.7 9.7 + - - +
365F THR* 3.4 27.3 - - + +
366F SER* 2.8 30.5 + - - +
386F ILE* 1.3 73.8 - - - +
388F LEU* 1.3 63.2 + - - +
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Residues in contact with LEU 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156F PRO* 3.7 29.6 - - + -
157F ILE 2.6 15.1 + - - +
158F TYR* 3.5 4.6 - - + -
159F GLY 3.0 17.7 + - - +
187F TYR* 2.8 15.3 + - - -
366F SER* 3.8 3.4 - - - +
370F LEU* 4.2 21.8 - - + -
375F ILE* 4.3 19.1 - - + -
378F VAL* 4.5 8.7 - - + -
379F ILE* 4.2 14.6 - - + -
386F ILE* 3.9 23.3 - - + -
387F VAL* 1.3 74.1 - - - +
389F GLN* 1.3 59.7 + - - +
390F LEU* 4.0 10.8 - - + -
408F VAL* 6.0 0.4 - - + -
412F ILE* 4.3 17.5 - - + -
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Residues in contact with GLN 389 (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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159F GLY 3.5 4.7 - - - +
160F VAL 3.6 0.3 - - - -
161F VAL* 2.7 48.5 + - + +
187F TYR* 3.7 13.2 - - + +
189F KCX 4.3 11.0 - - + +
314F HIS* 5.1 0.7 - - + -
365F THR* 4.8 7.0 - - + -
366F SER 3.2 7.9 + - - +
367F SER* 2.9 48.8 + - - +
370F LEU* 4.2 6.1 - - - +
388F LEU* 1.3 74.0 - - - +
390F LEU* 1.3 67.3 + - - +
391F GLY 3.0 12.8 + - - -
600F CAP 3.0 34.0 + - - -
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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
------------------------------------------------------------
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