Contacts of the helix formed by residues 239 - 245 (chain B) in PDB entry 1UK0
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 MET 239 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B THR* 2.9 25.1 - - - +
161B HIS 3.5 12.8 - - - +
162B ALA* 4.8 0.9 - - + -
200B TRP* 3.4 15.5 - - - -
237B ALA* 3.6 3.6 - - - +
238B ASP* 1.4 88.0 - - - +
240B VAL* 1.3 69.3 + - - +
241B SER* 3.6 4.3 - - - +
242B LYS* 3.6 25.3 - - + +
243B SER* 3.4 10.2 + - - -
293B THR* 3.7 34.1 - - + +
295B PRO* 3.4 23.1 - - + -
313B GLY* 4.7 4.9 - - - -
325B TYR* 3.8 31.0 - - + -
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Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B VAL* 3.3 48.2 - - + +
160B THR* 2.6 16.7 + - - -
161B HIS* 3.5 23.6 - - + +
170B LEU* 4.3 8.5 - - + -
200B TRP* 3.5 39.2 - - + +
239B MET* 1.3 78.0 - - - +
241B SER* 1.4 48.0 + - - +
243B SER* 2.8 20.6 + - - -
244B ALA* 2.8 14.3 + - - +
258B ILE* 3.7 20.4 - - + -
344B LEU* 4.5 4.3 - - + -
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Residues in contact with SER 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B THR 3.5 4.3 + - - -
161B HIS* 3.3 36.9 - - - -
162B ALA* 3.1 21.1 + - - +
165B HIS* 3.3 25.4 + - - -
168B TYR* 3.1 14.4 - - - -
239B MET* 3.6 2.9 - - - +
240B VAL* 1.4 63.9 - - - +
242B LYS* 1.4 60.0 + - - -
243B SER 2.7 7.7 + - - -
244B ALA* 2.4 26.1 + - - +
245B ASN* 2.8 15.0 + - - +
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Residues in contact with LYS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B HIS* 3.1 12.8 + - + -
237B ALA* 4.4 14.8 - - + -
239B MET* 3.6 19.7 - - + +
240B VAL 3.5 0.8 + - - -
241B SER* 1.4 75.6 + - - +
243B SER* 1.3 66.2 + - - +
245B ASN* 4.3 3.9 + - - +
246B TYR* 2.9 34.4 - - + +
322B SER 5.2 0.4 + - - -
323B LEU* 4.4 11.7 - - - +
324B LEU* 3.5 36.7 - - + +
325B TYR* 3.3 47.4 + - + +
327B GLU* 4.8 9.2 - - - +
502B FRM 4.7 11.2 - - + -
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Residues in contact with SER 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B TRP* 2.9 27.5 + - - -
202B GLY* 2.7 45.2 + - - -
237B ALA* 4.7 7.2 - - - -
239B MET 3.4 10.8 + - - -
240B VAL 2.8 10.1 + - - -
241B SER 2.7 1.4 - - - -
242B LYS* 1.3 88.3 - - - +
244B ALA* 1.3 57.5 - - - +
245B ASN 3.4 0.2 - - - -
246B TYR* 3.6 6.6 - - - -
258B ILE* 4.5 0.7 - - - -
502B FRM 2.5 31.4 + - - -
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Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B TYR* 3.6 7.4 - - - +
170B LEU* 4.0 14.6 - - + -
240B VAL 3.0 21.8 - - - +
241B SER* 2.4 25.0 + - - +
243B SER* 1.3 72.3 - - - +
245B ASN* 1.4 52.2 + - - +
247B CYS* 2.5 45.6 + - - +
248B HIS 4.1 0.5 + - - -
258B ILE* 4.2 14.6 - - + -
344B LEU* 4.4 0.4 - - + -
346B PHE* 4.1 15.1 - - + -
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Residues in contact with ASN 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B HIS* 3.0 34.3 + - - +
168B TYR* 2.6 31.0 + - - -
241B SER 2.8 8.2 + - - +
242B LYS* 4.5 3.6 - - - +
244B ALA* 1.4 74.7 - - - +
246B TYR* 1.3 66.2 + - + +
247B CYS 2.8 6.9 + - - -
248B HIS* 2.9 27.4 + - - +
249B THR 6.1 0.2 - - - +
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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