Contacts of the strand formed by residues 363 - 367 (chain J) 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 PHE 363 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143J ILE* 3.7 34.8 - - + +
146J VAL* 4.0 21.1 - - + -
147J ARG* 3.9 33.7 - - + -
157J ILE* 3.9 24.2 - - + -
311J ASP 2.7 10.9 + - - +
312J GLN* 3.2 20.0 - - + -
313J LEU 2.9 24.5 + - - -
337J LEU* 4.9 0.7 - - - -
362J ALA* 1.3 69.6 - - - +
364J PRO* 1.3 66.5 - - - +
365J THR* 3.7 2.4 + - - -
385J ASP* 3.3 36.6 - - - -
386J ILE 3.4 13.5 - - - -
387J VAL* 3.6 19.1 - - + -
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Residues in contact with PRO 364 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143J ILE* 4.4 0.2 - - + -
313J LEU 3.4 7.2 - - - +
315J VAL* 4.2 6.1 - - + -
334J VAL* 3.9 30.5 - - + -
337J LEU* 4.0 19.0 - - + -
338J ARG* 3.8 22.4 - - + -
362J ALA 2.8 18.8 - - - +
363J PHE* 1.3 78.7 - - + +
365J THR* 1.3 53.4 + - - +
382J LEU* 6.2 0.2 - - + -
385J ASP 3.5 17.9 - - - +
386J ILE* 3.3 11.3 - - + +
387J VAL 2.7 31.2 + - - -
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Residues in contact with THR 365 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187J TYR* 5.1 0.2 - - - +
279J HIS* 3.6 17.5 - - + -
312J GLN* 4.1 0.9 - - - +
313J LEU 2.7 19.5 + - - -
314J HIS* 3.1 39.2 - - + +
315J VAL* 2.9 28.4 + - - +
316J GLY 4.0 0.9 + - - -
363J PHE 3.7 6.9 + - - -
364J PRO* 1.3 72.9 - - - +
366J SER* 1.3 66.9 + - - +
367J SER* 4.0 2.1 + - - -
387J VAL* 3.3 32.3 - - + +
389J GLN* 4.8 6.5 - - + -
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Residues in contact with SER 366 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315J VAL* 5.3 0.7 - - - -
316J GLY 3.1 21.0 + - - -
317J THR* 3.5 11.1 - - - +
364J PRO 4.2 0.6 + - - -
365J THR* 1.3 71.0 - - - +
367J SER* 1.3 60.7 + - - +
370J LEU* 3.3 10.7 - - - +
378J VAL* 3.4 30.0 - - - +
382J LEU* 4.5 5.6 - - - -
386J ILE* 4.5 6.7 - - - +
387J VAL 2.8 10.6 + - - +
388J LEU* 3.8 9.7 - - - -
389J GLN 3.3 22.3 + - - -
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Residues in contact with SER 367 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314J HIS* 3.8 22.7 - - - -
316J GLY* 4.4 1.5 + - - -
317J THR* 3.0 21.1 + - - +
323J LEU* 4.6 2.1 - - - +
365J THR* 4.0 2.0 + - - -
366J SER* 1.3 77.6 + - - +
368J GLY* 1.3 61.9 + - - +
370J LEU* 3.8 5.6 - - - -
389J GLN* 2.9 35.5 + - - +
600J CAP 2.9 37.8 + - - -
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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