Contacts of the strand formed by residues 387 - 389 (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 VAL 387 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J ILE* 3.7 17.0 - - + +
187J TYR* 3.5 35.0 - - + +
227J PHE* 4.6 8.7 - - + -
279J HIS* 5.2 0.2 - - + -
312J GLN* 4.6 10.8 - - + +
363J PHE* 3.6 35.2 - - + -
364J PRO 2.7 9.1 + - - -
365J THR* 3.3 27.6 - - + +
366J SER* 2.8 29.8 + - - -
386J ILE* 1.3 73.6 - - - +
388J LEU* 1.3 62.6 + - - +
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Residues in contact with LEU 388 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156J PRO* 4.3 13.0 - - + -
157J ILE 2.7 18.4 + - - +
158J TYR* 3.5 4.9 - - + -
159J GLY 3.0 17.0 + - - -
187J TYR* 2.8 18.7 + - - -
366J SER* 3.8 17.3 - - - +
370J LEU* 4.2 15.0 - - + -
375J ILE* 4.5 21.1 - - + -
378J VAL* 4.4 7.6 - - + -
379J ILE* 4.1 26.5 - - + -
386J ILE* 4.0 23.5 + - + -
387J VAL* 1.3 75.2 - - - +
389J GLN* 1.3 55.3 + - - +
390J LEU* 4.1 12.3 - - + -
408J VAL* 6.1 0.4 - - + -
412J ILE* 4.7 11.2 - - + -
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Residues in contact with GLN 389 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159J GLY 3.4 6.3 - - - +
160J VAL 3.6 0.2 - - - -
161J VAL* 2.8 47.8 + - + +
187J TYR* 3.3 17.0 - - + +
189J KCX 4.5 8.7 - - + +
314J HIS* 5.3 0.4 - - + -
365J THR* 4.8 6.5 - - + -
366J SER 3.3 8.1 + - - +
367J SER* 2.9 43.1 + - - +
370J LEU* 4.1 5.5 - - - +
388J LEU* 1.3 72.6 - - - +
390J LEU* 1.3 65.8 + - - +
391J GLY* 2.8 15.8 + - - -
600J CAP 2.9 25.9 + - - -
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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