Contacts of the helix formed by residues 246 - 261 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A ALA* 3.3 2.7 - - - +
245A GLY* 1.3 83.6 - - - +
247A CYS* 1.3 63.9 + - - +
248A GLU* 3.4 10.0 + - - +
249A GLU* 3.2 27.0 + - + +
250A MET* 3.1 19.1 + - - +
111B GLY 5.6 1.1 - - - +
275B THR* 3.2 13.9 - - - +
278B THR* 3.8 21.1 - - + -
279B SER* 3.4 12.1 - - - +
282B ILE* 3.8 19.3 - - + -
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Residues in contact with CYS 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A THR* 1.3 70.9 - - - +
248A GLU* 1.3 60.1 + - - +
250A MET* 3.4 9.0 + - + +
251A MET* 2.9 35.5 + - + +
276A ALA* 4.0 12.3 - - - -
247B CYS* 3.4 39.9 - - + -
250B MET* 5.2 0.4 - - - -
251B MET* 6.0 0.9 - - + -
275B THR* 3.3 12.6 - - - +
276B ALA* 3.7 31.0 - - - -
279B SER* 2.8 17.4 + - - +
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Residues in contact with GLU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A THR* 3.4 11.9 - - - +
247A CYS* 1.3 80.3 - - + +
249A GLU* 1.3 57.2 + - + +
251A MET* 3.5 5.4 + - - +
252A LYS* 3.1 34.1 + - + +
251B MET* 3.9 18.7 - - - +
279B SER* 2.6 31.7 + - - +
282B ILE* 5.7 3.1 - - - +
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Residues in contact with GLU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A TRP* 3.9 9.4 + - - -
244A ALA* 3.5 20.4 - - + -
245A GLY 4.9 1.1 - - - +
246A THR* 3.2 19.9 + - + +
248A GLU* 1.3 74.9 - - + +
250A MET* 1.3 66.9 + - - +
252A LYS* 2.8 38.0 + - - +
253A ARG* 3.0 54.4 + - - +
109B GLU* 5.1 2.2 - - - +
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Residues in contact with MET 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ALA* 3.3 36.7 - - + +
244A ALA* 3.5 5.0 - - + +
246A THR 3.1 13.6 + - - +
247A CYS* 3.5 17.3 - - + +
249A GLU* 1.3 76.5 - - - +
251A MET* 1.3 92.7 + - + +
253A ARG* 3.3 5.4 + - - +
254A ALA* 3.1 20.1 + - - +
267A HIS* 3.9 23.6 - - + +
276A ALA* 3.5 39.0 - - + +
279A SER* 4.5 2.0 - - - -
280A LEU* 4.0 16.8 - - + -
275B THR* 4.7 3.6 - - + -
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Residues in contact with MET 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A CYS 2.9 21.7 + - - +
248A GLU* 3.9 5.8 - - - +
250A MET* 1.3 96.7 - - + +
252A LYS* 1.3 60.3 + - - +
254A ALA* 3.2 3.7 + - - +
255A VAL* 2.9 40.0 + - + +
279A SER* 3.8 33.9 - - - +
280A LEU* 4.1 7.0 - - - +
283A TYR* 4.2 29.2 - - + -
247B CYS* 4.5 5.4 - - - -
248B GLU* 4.0 13.2 - - - +
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Residues in contact with LYS 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A TRP* 3.8 17.0 - - + -
248A GLU* 3.1 20.9 + - + +
249A GLU* 2.8 42.2 + - - +
251A MET* 1.3 75.2 - - - +
253A ARG* 1.3 58.9 + - - +
255A VAL* 3.5 7.7 + - - +
256A SMC 3.1 27.0 + - - +
286O ASP* 3.3 38.6 + - - -
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Residues in contact with ARG 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ASN* 4.0 4.0 - - - +
208A SER* 3.8 13.1 - - - +
214A TRP* 3.5 50.5 - - + -
218A PHE* 3.3 23.9 - - + -
241A ASN 4.2 8.7 + - - -
242A ALA* 4.0 20.6 - - - -
243A THR 3.5 14.8 + - - -
244A ALA* 3.9 7.5 - - - +
249A GLU* 3.0 44.3 + - - +
250A MET 3.6 6.7 - - - +
252A LYS* 1.3 75.2 - - - +
254A ALA* 1.3 65.9 + - - +
256A SMC 3.3 1.7 + - - +
257A ALA* 3.1 18.0 + - - +
265A ILE* 5.6 0.4 - - - -
109B GLU* 2.7 42.4 + - - -
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Residues in contact with ALA 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ALA* 4.5 1.7 - - + +
250A MET 3.1 8.8 + - - +
251A MET* 3.2 9.2 + - - +
253A ARG* 1.3 77.4 - - - +
255A VAL* 1.3 56.5 + - - +
257A ALA* 3.3 6.3 + - - +
258A LYS* 3.0 24.4 + - - +
265A ILE* 4.0 18.4 - - + -
280A LEU* 3.8 29.2 - - + -
283A TYR* 3.8 20.4 - - + -
289A LEU* 3.7 7.5 - - + +
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Residues in contact with VAL 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A MET* 2.9 24.6 + - + +
252A LYS* 3.6 7.9 - - - +
254A ALA* 1.3 73.8 - - - +
256A SMC 1.3 60.1 + - - +
258A LYS* 3.1 5.1 + - + +
259A GLU* 2.9 57.9 + - + +
283A TYR* 3.5 29.8 - - + +
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Residues in contact with SMC 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A TRP* 3.6 35.4 - - + -
215A ARG* 3.7 36.6 - - - +
218A PHE* 3.8 10.5 - - - -
219A LEU* 4.5 2.7 - - + -
252A LYS 3.1 10.8 + - - +
253A ARG 3.3 2.7 + - - +
255A VAL* 1.3 73.2 + - - +
257A ALA* 1.3 63.3 + - - +
259A GLU* 3.1 8.3 + - - +
260A LEU* 3.0 52.3 + - + +
63T VAL* 4.0 13.7 - - + -
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Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A PHE* 4.3 9.1 - - + -
240A LEU* 4.6 2.2 - - + -
253A ARG 3.1 11.2 + - - +
254A ALA 3.3 6.3 + - - +
256A SMC 1.3 77.8 + - - +
258A LYS* 1.3 61.6 + - - +
260A LEU* 3.2 13.6 + - - +
261A GLY 3.2 9.4 + - - -
262A VAL* 3.5 31.1 + - + +
265A ILE* 3.5 32.1 - - + -
289A LEU* 4.4 5.8 - - + -
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Residues in contact with LYS 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A ALA 3.0 9.1 + - - +
255A VAL* 3.1 10.7 + - + +
257A ALA* 1.3 74.7 - - - +
259A GLU* 1.3 64.5 - - + +
261A GLY* 3.1 19.8 + - - -
283A TYR* 3.3 26.0 - - + +
287A ASN* 2.8 35.6 + - + +
289A LEU* 4.2 9.3 - - + +
62I SER* 3.1 41.2 + - - +
63I VAL* 4.2 13.9 - - - +
64I SER 5.4 0.2 + - - -
65I CYS* 3.6 18.7 + - - -
215K ARG* 4.6 2.8 - - - +
259K GLU* 5.5 1.2 + - - -
59T ARG 5.1 0.3 - - - +
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Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A VAL* 2.9 41.4 + - + +
256A SMC 3.1 7.8 + - - +
258A LYS* 1.3 83.5 - - + +
260A LEU* 1.3 57.9 + - - +
261A GLY 3.3 0.4 + - - -
62I SER* 4.8 16.2 + - - +
258O LYS* 5.2 2.3 + - - -
59T ARG 3.9 0.6 - - - +
60T PHE* 3.1 8.5 - - - -
61T GLY* 2.9 31.9 + - - +
62T SER 5.5 3.6 - - - -
63T VAL* 3.3 34.0 - - + +
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Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A PHE* 4.0 18.2 - - + +
219A LEU* 4.2 19.3 - - + -
222A THR* 3.4 28.5 - - + +
226A TYR* 2.7 25.6 + - - -
240A LEU* 5.4 1.6 - - + -
256A SMC 3.0 43.1 + - + +
257A ALA* 3.8 8.1 - - - +
258A LYS 3.2 0.4 - - - -
259A GLU* 1.3 77.2 - - - +
261A GLY* 1.3 52.3 + - - +
262A VAL* 3.4 4.6 + - + +
59T ARG 4.0 0.8 - - - +
60T PHE* 3.3 40.3 - - + -
63T VAL* 3.7 20.4 - - + +
67T TYR* 5.3 0.4 - - + -
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Residues in contact with GLY 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A TYR* 3.1 10.6 + - - -
257A ALA 3.2 0.6 + - - -
258A LYS 3.1 16.1 + - - -
259A GLU 3.3 1.2 - - - -
260A LEU* 1.3 73.7 - - - +
262A VAL* 1.3 62.6 + - - +
263A PRO* 4.1 0.9 - - - +
64I SER* 3.5 22.2 - - - -
65I CYS* 3.8 11.8 - - - -
66I LEU 4.4 0.3 + - - -
59T ARG* 2.9 27.2 + - - -
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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