Contacts of the helix formed by residues 245 - 250 (chain C) in PDB entry 1XHU
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 245 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C ARG* 2.9 45.0 + - - +
242C ALA 3.9 4.9 - - - +
243C ILE 2.8 0.6 + - - -
244C SER* 1.3 78.3 + - - +
246C ILE* 1.3 60.6 + - - +
249C PHE* 3.0 54.2 + - + +
250C VAL* 3.8 2.1 + - - +
202D TRP* 4.9 9.6 - - + -
238D ALA* 4.4 13.2 - - - +
241D ARG* 3.6 20.0 - - + -
242D ALA* 3.5 21.3 - - + -
245D MET* 3.2 42.2 - - + +
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Residues in contact with ILE 246 (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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242C ALA 3.1 17.9 - - - +
243C ILE* 2.5 20.9 + - + +
245C MET* 1.3 68.3 - - - +
247C ASP* 1.3 61.4 + - - +
248C LYS 3.0 10.1 + - - -
250C VAL* 3.1 35.5 + - + +
251C LYS* 3.0 30.6 + - + +
238D ALA 4.0 3.6 - - - +
239D GLU* 4.2 15.0 - - + +
242D ALA* 3.5 27.6 - - + -
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Residues in contact with ASP 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C ILE* 3.1 24.8 + - + +
244C SER* 3.7 8.0 + - - +
246C ILE* 1.3 79.9 - - - +
248C LYS* 1.3 58.2 + - - +
251C LYS* 4.5 12.2 - - - +
252C PRO* 3.9 14.0 - - - +
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Residues in contact with LYS 248 (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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241C ARG* 5.2 2.5 - - - +
244C SER* 3.0 19.4 + - - +
245C MET 4.2 1.3 - - - +
246C ILE 3.0 1.2 - - - -
247C ASP* 1.3 79.8 - - - +
249C PHE* 1.3 80.3 + - + +
250C VAL 3.7 0.4 - - - -
252C PRO* 3.6 16.7 - - - +
253C PHE* 3.9 5.5 - - - -
146D TYR* 3.8 27.5 + - - +
4I G 5.1 7.2 - - - -
5I G 3.0 40.4 - - - +
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Residues in contact with PHE 249 (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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241C ARG* 3.5 30.5 - - - -
245C MET* 3.0 41.6 + - + +
248C LYS* 1.3 94.7 - - + +
250C VAL* 1.3 62.5 + - - +
253C PHE* 3.0 23.8 - - - -
146D TYR* 3.5 48.7 - + + -
202D TRP* 4.3 8.1 - + + -
206D MET* 3.4 25.8 - - + -
234D PHE* 3.2 28.7 - + + -
235D VAL* 4.0 2.9 - - - +
238D ALA* 4.1 11.9 - - + +
5I G 4.3 4.5 - - - -
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Residues in contact with VAL 250 (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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245C MET 4.0 1.8 - - - +
246C ILE* 3.1 45.6 + - + +
249C PHE* 1.3 76.8 - - - +
251C LYS* 1.3 68.8 + - - +
252C PRO 3.4 0.7 - - - -
253C PHE* 2.9 7.3 + - - +
254C LYS* 2.8 26.9 + - + +
235D VAL* 3.5 24.3 - - + +
238D ALA* 3.3 28.3 - - + -
239D GLU* 3.8 23.8 - - + +
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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