Contacts of the strand formed by residues 251 - 255 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H VAL* 4.4 7.8 - - + +
149H MET* 3.2 33.8 - - + +
150H LEU* 5.0 0.9 - - + -
225H THR* 2.7 24.8 + - + +
226H TRP 3.4 27.1 + - - +
227H PHE* 3.5 30.6 - + + -
228H ALA 4.1 2.8 + - - -
244H LEU* 3.5 21.2 - - - +
249H LEU* 3.8 0.7 - - - +
250H LYS* 1.3 79.0 + - - +
252H ALA* 1.3 59.8 + - - +
253H MET 4.3 0.2 - - - -
276H LEU* 3.9 4.2 - - - +
277H ALA* 3.4 28.6 - - + +
279H HIS 4.8 4.0 - - - -
312H GLN* 2.8 32.3 + - - -
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Residues in contact with ALA 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228H ALA 3.9 4.5 - - - +
230H ILE* 4.7 5.6 - - + -
241H LEU* 3.7 29.8 - - + -
244H LEU* 3.8 10.1 - - + -
251H HIS* 1.3 75.8 - - - +
253H MET* 1.3 61.2 + - - +
254H VAL* 4.7 2.0 - - + -
271H ALA* 4.9 5.4 - - + -
276H LEU* 4.4 9.6 - - + +
277H ALA 2.9 10.5 + - - +
278H ILE* 3.3 8.7 - - + +
279H HIS* 2.8 25.6 + - - +
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Residues in contact with MET 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189H KCX 3.6 29.2 - - - +
190H ASP 3.2 27.8 - - - +
192H GLU* 3.4 29.2 - - + -
227H PHE* 3.8 16.8 - - + +
228H ALA 2.6 24.2 + - - +
229H ASN* 3.6 17.7 - - - +
230H ILE* 3.0 32.9 + - - +
252H ALA* 1.3 70.5 - - - +
254H VAL* 1.3 68.7 + - - +
255H ASP* 3.7 12.8 - - - +
279H HIS* 3.3 15.9 - - + +
281H HIS* 4.1 6.5 - - + -
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Residues in contact with VAL 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230H ILE* 3.7 25.1 - - + -
231H THR* 4.1 4.3 - - - +
237H MET* 5.3 3.4 - - - -
252H ALA* 4.5 3.4 - - + +
253H MET* 1.3 83.7 - - - +
255H ASP* 1.3 68.6 + - - +
256H VAL* 3.0 18.8 + - + +
259H THR* 3.4 25.1 - - + +
264H LEU* 4.4 10.1 - - + -
267H ILE* 4.3 14.1 - - + -
278H ILE* 4.3 17.5 - - + -
279H HIS 2.8 11.0 + - - +
280H GLY* 3.5 3.5 - - - -
281H HIS 2.8 24.7 + - - -
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Residues in contact with ASP 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ALA* 3.4 16.8 - - - +
192H GLU* 2.8 35.8 - - - +
231H THR* 3.0 36.4 + - + +
253H MET* 3.7 8.7 - - - +
254H VAL* 1.3 67.7 - - - +
256H VAL* 1.3 59.7 + - - +
257H VAL 3.5 1.3 - - - -
258H ILE* 3.4 15.3 + - + -
259H THR* 2.9 30.7 + - - -
281H HIS* 3.3 26.1 - - - +
283H ALA* 4.8 3.1 - - + +
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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