Contacts of the strand formed by residues 251 - 255 (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 HIS 251 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146J VAL* 4.4 7.0 - - + -
149J MET* 3.9 20.6 - - - -
150J LEU* 5.0 1.6 - - + -
225J THR* 3.0 28.1 + - + +
226J TRP* 3.3 26.2 + - - +
227J PHE* 3.6 30.1 - + + -
228J ALA 4.3 1.9 + - - -
244J LEU* 3.4 21.0 - - - +
249J LEU* 4.8 1.6 - - - +
250J LYS* 1.3 80.9 + - - +
252J ALA* 1.3 60.0 + - - +
253J MET 4.3 0.2 - - - -
276J LEU* 4.4 4.6 - - - +
277J ALA* 3.4 27.9 - - + +
279J HIS* 4.7 4.7 - - + -
312J GLN* 2.8 37.1 + - - -
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Residues in contact with ALA 252 (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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228J ALA 3.8 4.7 - - - -
230J ILE* 4.5 6.1 - - + -
241J LEU* 3.5 31.0 - - + -
244J LEU* 3.8 10.1 - - + -
251J HIS* 1.3 76.0 - - - +
253J MET* 1.3 61.1 + - - +
254J VAL* 4.7 2.0 - - + -
271J ALA* 5.2 2.9 - - + -
276J LEU* 4.4 8.1 - - + -
277J ALA 2.8 12.6 + - - +
278J ILE* 3.3 10.1 - - + +
279J HIS* 2.8 24.6 + - - -
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Residues in contact with MET 253 (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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189J KCX 3.6 25.6 - - - +
190J ASP 3.3 23.3 - - - +
192J GLU* 3.5 32.8 - - - -
227J PHE* 3.8 17.0 - - + +
228J ALA 2.7 22.6 + - - +
229J ASN* 3.6 17.5 - - - +
230J ILE* 3.0 27.2 + - - +
252J ALA* 1.3 72.8 - - - +
254J VAL* 1.3 70.1 + - - +
255J ASP* 3.5 13.7 - - - +
279J HIS* 3.3 18.4 - - + +
281J HIS* 3.8 9.6 - - + -
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Residues in contact with VAL 254 (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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230J ILE* 3.6 25.6 - - + -
231J THR* 4.0 4.7 - - - +
237J MET* 4.9 7.4 - - - -
241J LEU* 6.0 0.2 - - + -
252J ALA* 4.5 3.6 - - + +
253J MET* 1.3 80.6 - - - +
255J ASP* 1.3 63.4 + - - +
256J VAL* 2.9 17.5 + - + +
259J THR* 3.2 31.6 - - + +
264J LEU* 4.5 9.2 - - + -
267J ILE* 4.2 13.0 - - + -
278J ILE* 4.3 15.9 - - + -
279J HIS 2.8 12.2 + - - +
280J GLY* 3.5 2.4 - - - -
281J HIS 2.8 24.2 + - - -
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Residues in contact with ASP 255 (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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106D ALA* 3.5 15.4 - - - +
192J GLU* 2.8 29.6 - - - +
231J THR* 2.9 32.7 + - + +
253J MET* 3.5 26.2 - - - +
254J VAL* 1.3 69.9 - - - +
256J VAL* 1.3 55.4 + - - +
257J VAL 3.4 2.6 + - - -
258J ILE* 3.5 16.7 + - + +
259J THR* 2.7 35.5 + - - -
281J HIS* 3.3 16.0 - - - +
283J ALA* 5.0 2.9 - - + +
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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
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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