Contacts of the helix formed by residues 246 - 255 (chain C) in PDB entry 7UUT
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 ALA 246 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245C ASN* 1.3 76.0 - - - +
247C ASP* 1.3 63.0 + - - +
248C ILE 3.2 1.0 + - - -
249C MET* 3.2 14.7 + - - +
268C PHE* 4.0 13.9 - - + -
270C GLU 5.0 10.1 + - - +
271C GLY* 5.6 2.9 - - - -
273C VAL 3.8 12.6 - - - +
274C LEU* 3.9 11.2 - - + -
275C PRO* 3.3 31.9 - - + +
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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
----------------------------------------------------------
245C ASN* 3.7 23.0 + - - +
246C ALA* 1.3 78.8 - - - +
248C ILE* 1.3 82.1 + - - +
250C ALA* 3.1 17.5 + - + +
251C THR* 3.3 13.9 + - - +
275C PRO* 4.5 9.6 - - - -
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Residues in contact with ILE 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C LEU* 3.9 26.9 - - + -
197C VAL* 6.1 0.2 - - + -
223C ILE* 4.2 20.0 - - + -
241C ILE* 3.6 24.9 - - + +
243C GLY 3.6 20.6 - - - +
244C GLY* 4.5 5.6 - - - -
245C ASN 3.1 21.5 + - - +
247C ASP* 1.3 87.7 + - - +
249C MET* 1.3 59.6 + - - +
251C THR* 3.3 18.6 + - - +
252C ALA* 2.9 28.1 + - - +
268C PHE* 4.0 9.2 - - + -
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Residues in contact with MET 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C ILE* 4.0 25.8 - - + -
246C ALA 3.2 13.5 + - - +
247C ASP 3.1 0.6 - - - -
248C ILE* 1.3 78.9 - - + +
250C ALA* 1.3 64.6 + - - +
252C ALA* 3.3 1.0 + - - +
253C VAL* 3.1 31.1 + - + +
262C ILE* 4.2 6.7 - - + -
264C ASN* 4.7 11.9 - - + -
268C PHE* 4.9 7.4 - - + -
274C LEU* 4.6 27.1 - - + -
275C PRO 3.2 18.4 - - - +
276C VAL* 4.1 12.6 - - + -
290C ILE* 4.1 32.1 - - + -
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Residues in contact with ALA 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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247C ASP* 3.1 13.1 + - + +
249C MET* 1.3 77.4 - - - +
251C THR* 1.3 63.2 + - - +
253C VAL* 3.3 2.8 + - - +
254C LYS* 3.1 42.1 + - - +
275C PRO* 3.6 16.0 + - + +
277C PRO* 3.6 27.8 - - + +
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Residues in contact with THR 251 (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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173C LEU* 4.4 5.4 - - + -
223C ILE* 3.8 33.9 - - + +
224C GLU* 2.8 33.8 + - + +
247C ASP* 3.3 10.5 + - - +
248C ILE* 3.5 27.4 - - + +
249C MET 3.3 0.6 - - - -
250C ALA* 1.3 78.4 - - - +
252C ALA* 1.3 61.7 + - - +
254C LYS* 3.2 2.4 + - - +
255C ILE* 3.2 26.0 + - + +
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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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173C LEU* 3.8 16.3 - - + +
239C ALA* 4.2 5.4 - - + -
241C ILE* 3.7 24.0 - - + -
248C ILE 2.9 16.7 + - - +
249C MET 3.7 4.0 - - - +
250C ALA 3.3 0.2 - - - -
251C THR* 1.3 77.0 - - - +
253C VAL* 1.3 63.5 + - - +
255C ILE* 3.3 7.1 + - - +
256C VAL* 3.2 28.1 + - - +
262C ILE* 3.8 18.2 - - + -
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Residues in contact with VAL 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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249C MET* 3.1 22.3 + - - +
250C ALA 3.8 4.3 - - - +
252C ALA* 1.3 75.0 - - - +
254C LYS* 1.3 61.1 + - - +
255C ILE 3.4 0.3 + - - -
256C VAL 3.6 4.3 + - - +
262C ILE* 4.1 21.8 - - + -
276C VAL* 4.5 4.3 - - + -
277C PRO* 4.0 19.7 - - + -
280C GLU 3.7 26.2 - - - +
281C TRP* 3.8 19.1 - - + +
288C LYS* 3.0 30.6 + - + +
290C ILE* 4.3 18.8 - - + -
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Residues in contact with LYS 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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224C GLU* 4.0 30.7 + - + +
228C MET* 4.2 11.8 - - - +
250C ALA* 3.1 29.1 + - - +
251C THR 3.7 4.9 - - - +
252C ALA 3.2 0.4 - - - -
253C VAL* 1.3 78.3 - - - +
255C ILE* 1.3 60.2 + - - +
256C VAL 4.3 2.9 - - - +
277C PRO* 4.3 11.9 - - + -
280C GLU* 3.5 46.3 + - + +
288C LYS* 4.6 3.0 + - - +
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Residues in contact with ILE 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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171C ALA* 3.9 20.0 - - + -
173C LEU* 4.0 16.8 - - + -
224C GLU* 3.9 30.7 - - + +
227C ILE* 3.7 41.1 - - + -
228C MET* 4.2 8.1 - - - -
235C GLY* 3.2 10.2 - - - -
236C VAL* 2.9 29.9 + - + -
239C ALA* 4.2 8.5 - - + -
251C THR* 3.4 17.5 - - + +
252C ALA* 3.4 13.0 - - - +
254C LYS* 1.3 78.5 - - - +
256C VAL* 1.3 59.5 + - - +
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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