Contacts of the helix formed by residues 246 - 261 (chain H) in PDB entry 1UW9
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 THR 246 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244H ALA* 3.3 1.5 - - - +
245H GLY* 1.3 81.6 - - - +
247H CYS* 1.3 64.5 - - - +
248H GLU* 3.4 9.7 + - - +
249H GLU* 3.2 28.4 + - + +
250H MET* 3.0 19.6 + - - +
111R GLY 5.6 1.1 - - - +
275R THR* 3.3 13.8 - - - +
278R THR* 3.7 21.3 - - + -
279R SER* 3.4 12.6 - - - +
282R ILE* 3.8 19.3 - - + -
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Residues in contact with CYS 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H THR* 1.3 69.9 - - - +
248H GLU* 1.3 58.1 + - - +
250H MET* 3.3 9.0 + - + +
251H MET* 2.9 38.1 + - + +
276H ALA* 4.1 4.5 - - - -
247R CYS* 2.1 50.5 - - + -
250R MET* 5.2 0.7 - - + -
251R MET* 6.0 0.9 - - + -
275R THR* 3.4 10.2 - - - +
276R ALA* 3.7 23.8 - - - -
279R SER* 2.7 19.1 + - - +
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Residues in contact with GLU 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H THR* 3.4 11.5 - - - +
247H CYS* 1.3 80.1 - - + +
249H GLU* 1.3 57.1 + - + +
251H MET* 3.6 5.5 + - - +
252H LYS* 3.1 34.5 + - + +
251R MET* 3.9 13.5 - - - +
279R SER* 2.6 37.6 + - - +
282R ILE* 5.7 4.3 - - - +
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Residues in contact with GLU 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H TRP* 3.9 9.4 + - - -
244H ALA* 3.6 20.0 - - + -
245H GLY 4.9 1.1 - - - +
246H THR* 3.2 21.2 + - + +
248H GLU* 1.3 76.0 - - + +
250H MET* 1.3 65.9 + - - +
252H LYS* 2.8 37.4 + - - +
253H ARG* 2.9 57.4 + - - +
109R GLU* 5.1 2.2 - - - +
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Residues in contact with MET 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242H ALA* 3.3 32.5 - - + +
243H THR* 5.2 0.2 - - - -
244H ALA* 3.5 5.9 - - + +
246H THR 3.0 13.1 + - - +
247H CYS* 3.5 19.1 - - + +
249H GLU* 1.3 76.7 - - - +
251H MET* 1.3 90.2 + - + +
253H ARG* 3.3 6.4 + - - +
254H ALA* 3.1 18.0 + - - +
267H HIS* 3.9 23.8 - - + +
276H ALA* 3.5 39.9 - - + +
279H SER* 4.5 1.8 - - - -
280H LEU* 3.9 21.8 - - + -
275R THR* 4.7 3.8 - - + -
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Residues in contact with MET 251 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247H CYS* 2.9 23.0 + - + +
248H GLU* 3.9 6.1 - - - +
249H GLU 3.3 0.2 - - - -
250H MET* 1.3 90.0 - - + +
252H LYS* 1.3 65.8 + - - +
254H ALA* 3.2 3.9 + - - +
255H VAL* 2.8 33.8 + - + +
279H SER* 3.8 42.0 - - - +
280H LEU* 4.1 7.4 - - - +
283H TYR* 4.3 27.1 - - + -
247R CYS* 6.0 1.3 - - + -
248R GLU* 3.9 12.6 - - - +
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Residues in contact with LYS 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H TRP* 3.9 17.8 - - + +
248H GLU* 3.1 21.1 + - + +
249H GLU* 2.8 40.1 + - - +
251H MET* 1.3 74.5 - - - +
253H ARG* 1.3 61.5 + - - +
255H VAL* 3.4 8.5 + - - +
256H SMC 3.1 23.7 + - - +
286V ASP* 3.4 37.4 + - - -
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Residues in contact with ARG 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207H ASN* 3.9 3.8 - - - +
208H SER* 3.8 12.3 - - - +
214H TRP* 3.5 51.4 - - + -
218H PHE* 3.3 21.7 - - + -
241H ASN 4.2 11.2 - - - -
242H ALA* 4.0 22.4 - - - -
243H THR 3.5 14.8 + - - -
244H ALA* 3.9 7.3 - - - +
249H GLU* 2.9 43.2 + - - +
250H MET 3.6 7.2 - - - +
251H MET 3.2 0.6 - - - -
252H LYS* 1.3 74.5 - - - +
254H ALA* 1.3 65.1 + - - +
256H SMC 3.3 1.7 + - - +
257H ALA* 3.2 17.7 + - - +
265H ILE* 5.6 0.2 - - - -
109R GLU* 2.7 43.0 + - - -
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Residues in contact with ALA 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242H ALA* 4.4 1.2 - - + +
250H MET 3.1 9.6 + - - +
251H MET* 3.6 8.5 - - - +
253H ARG* 1.3 75.5 - - - +
255H VAL* 1.3 63.0 + - - +
257H ALA* 3.3 6.9 + - - +
258H LYS* 3.0 19.6 + - - +
265H ILE* 4.0 17.0 - - + -
280H LEU* 3.7 29.6 - - + -
283H TYR* 3.8 21.1 - - + -
289H LEU* 3.7 7.0 - - + +
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Residues in contact with VAL 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251H MET* 2.8 23.4 + - + +
252H LYS* 3.6 8.1 - - - +
253H ARG 3.3 0.2 - - - -
254H ALA* 1.3 76.5 - - - +
256H SMC 1.3 58.0 + - - +
258H LYS* 3.1 5.6 + - + +
259H GLU* 2.9 57.1 + - + +
283H TYR* 3.4 29.2 - - + +
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Residues in contact with SMC 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H TRP* 3.6 36.1 - - + -
215H ARG* 3.8 36.6 - - + +
218H PHE* 3.8 10.8 - - - -
219H LEU* 5.4 1.3 - - + -
252H LYS 3.1 11.4 + - - +
253H ARG 3.7 1.6 - - - +
254H ALA 3.3 0.2 - - - -
255H VAL* 1.3 76.2 + - - +
257H ALA* 1.3 62.8 + - - +
259H GLU* 3.1 6.1 + - - +
260H LEU* 3.0 52.8 + - + +
63W VAL* 4.1 14.1 - - + -
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Residues in contact with ALA 257 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H PHE* 4.3 8.0 - - + -
240H LEU* 4.7 2.0 - - + -
253H ARG 3.2 10.0 + - - +
254H ALA 3.5 7.6 - - - +
256H SMC 1.3 77.1 + - - +
258H LYS* 1.3 62.4 + - - +
260H LEU* 3.2 14.0 + - - +
261H GLY 3.2 9.5 + - - -
262H VAL* 3.4 30.4 + - + +
265H ILE* 3.5 31.6 - - + -
289H LEU* 4.3 4.7 - - + -
65J CYS* 4.1 2.3 - - - -
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Residues in contact with LYS 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E ARG* 4.6 4.0 - - - +
259E GLU* 5.3 2.2 + - - -
254H ALA 3.0 7.6 + - - +
255H VAL* 3.1 11.2 + - + +
257H ALA* 1.3 76.2 - - - +
259H GLU* 1.3 64.9 + - + +
261H GLY* 3.1 16.3 + - - -
283H TYR* 3.3 26.9 - - + +
287H ASN* 2.8 34.4 + - + +
289H LEU* 4.2 9.5 - - + +
62J SER* 3.1 43.6 + - - +
63J VAL* 4.1 13.7 - - - +
64J SER* 5.3 0.3 + - - -
65J CYS* 3.6 22.2 + - - -
59W ARG 5.1 0.5 - - - +
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Residues in contact with GLU 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255H VAL* 2.9 38.8 + - + +
256H SMC 3.1 7.0 + - - +
258H LYS* 1.3 85.0 - - + +
260H LEU* 1.3 56.2 + - - +
261H GLY 3.3 0.2 - - - -
62J SER* 4.7 16.7 + - - +
258V LYS* 5.1 2.8 + - - -
59W ARG 4.0 0.4 - - - +
60W PHE* 3.2 8.8 - - - -
61W GLY* 2.8 31.7 + - - +
62W SER 5.3 4.0 + - - -
63W VAL* 3.3 36.5 - - + +
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Residues in contact with LEU 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H PHE* 4.0 18.6 - - + +
219H LEU* 3.8 24.0 - - + +
222H THR* 3.5 26.7 - - + +
226H TYR* 2.7 26.9 + - - -
240H LEU* 5.4 0.2 - - + -
256H SMC 3.0 43.0 + - + +
257H ALA* 3.2 7.6 + - - +
259H GLU* 1.3 75.8 - - - +
261H GLY* 1.3 52.1 + - - +
262H VAL* 3.3 5.5 + - + -
59W ARG* 4.1 0.7 - - - +
60W PHE* 3.4 37.4 - - + -
63W VAL* 3.8 18.8 - - + -
67W TYR* 5.4 0.2 - - + -
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Residues in contact with GLY 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226H TYR* 3.1 6.5 + - - -
257H ALA 3.2 0.8 + - - -
258H LYS 3.1 16.3 + - - -
259H GLU 3.3 1.6 + - - -
260H LEU* 1.3 77.3 - - - +
262H VAL* 1.3 63.4 + - - +
263H PRO* 4.0 1.6 - - - +
64J SER* 3.4 22.9 - - - -
65J CYS* 3.8 11.9 - - - -
66J LEU 4.4 0.3 + - - -
59W ARG* 3.0 26.4 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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