Contacts of the strand formed by residues 251 - 255 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C VAL* 4.5 7.4 - - + -
149C MET* 3.2 32.7 - - + +
150C LEU* 5.2 1.1 - - + -
225C THR* 2.8 23.3 + - + +
226C TRP 3.4 26.9 + - - +
227C PHE* 3.4 31.3 - + + -
228C ALA* 4.0 4.7 + - - +
244C LEU* 3.4 18.8 - - - +
249C LEU* 3.8 1.5 - - - +
250C LYS* 1.3 77.6 + - - +
252C ALA* 1.3 59.8 + - - +
253C MET 4.2 0.2 - - - -
276C LEU* 4.5 3.6 - - - +
277C ALA* 3.4 24.5 - - + +
279C HIS* 4.6 5.2 - - + -
312C GLN* 2.7 36.1 + - - -
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Residues in contact with ALA 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C ALA 3.9 0.7 - - - -
230C ILE* 4.7 5.4 - - + -
241C LEU* 3.6 30.3 - - + -
244C LEU* 3.8 12.6 - - + -
251C HIS* 1.3 73.2 - - - +
253C MET* 1.3 61.0 + - - +
254C VAL* 4.8 2.2 - - + -
271C ALA* 4.9 5.2 - - + -
276C LEU* 4.4 10.7 - - + +
277C ALA 2.9 10.7 + - - +
278C ILE* 3.4 9.7 - - + +
279C HIS* 2.9 24.2 + - - +
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Residues in contact with MET 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C KCX 3.5 28.3 - - - +
190C ASP 3.2 26.9 - - - +
192C GLU* 3.5 23.6 - - - -
227C PHE* 3.8 24.0 - - + +
228C ALA 2.7 23.8 + - - +
229C ASN* 3.6 15.7 - - + +
230C ILE* 3.0 26.7 + - - +
252C ALA* 1.3 73.0 - - - +
254C VAL* 1.3 70.6 + - - +
255C ASP* 3.8 11.4 - - - +
279C HIS* 3.3 16.2 - - + +
281C HIS* 3.9 9.4 - - + -
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Residues in contact with VAL 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C ILE* 3.7 24.0 - - + -
231C THR* 4.2 3.8 - - - +
237C MET* 5.1 4.5 - - - -
252C ALA* 4.6 8.1 - - + +
253C MET* 1.3 81.7 - - - +
255C ASP* 1.3 69.0 + - - +
256C VAL* 3.0 19.9 + - + +
259C THR* 3.3 27.1 - - + +
264C LEU* 4.4 6.5 - - + -
267C ILE* 4.2 16.6 - - + -
278C ILE* 4.6 11.0 - - + -
279C HIS 2.9 8.5 + - - +
280C GLY* 3.5 4.0 - - - -
281C HIS 2.8 24.4 + - - -
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Residues in contact with ASP 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C GLU* 2.8 35.8 - - - +
229C ASN* 3.7 6.2 - - - +
231C THR* 2.9 35.0 + - + +
253C MET* 3.8 2.8 - - - +
254C VAL* 1.3 68.9 - - - +
256C VAL* 1.3 58.1 + - - +
257C VAL 3.4 3.0 + - - -
258C ILE* 3.4 14.9 + - + +
259C THR* 2.8 31.5 + - - -
281C HIS* 3.3 24.4 - - - +
283C ALA* 4.9 2.9 - - + -
106F ALA* 3.5 15.8 - - - +
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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