Contacts of the helix formed by residues 239 - 256 (chain C) in PDB entry 1UMD
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 ASP 239 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C ARG* 3.6 1.2 - - - -
18C LEU 2.7 25.4 + - - -
19C ILE* 2.8 30.3 + - - +
75C ALA* 4.1 0.4 - - - -
236C ASP* 3.1 17.4 + - + +
238C MET* 1.3 78.5 - - - +
240C VAL* 1.3 61.9 + - - +
241C LEU* 3.0 6.9 + - - +
242C ALA* 2.9 26.0 + - + -
243C SER* 2.9 27.5 + - - -
299C ARG* 3.3 20.4 + - - +
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Residues in contact with VAL 240 (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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19C ILE* 4.3 2.1 - - + +
41C LEU* 4.4 21.5 - - + -
45C MET* 3.9 23.8 - - + -
75C ALA* 3.7 30.9 - - + +
78C VAL* 4.7 2.9 - - + -
79C ALA* 3.7 10.8 - - + +
238C MET 3.8 1.4 + - - -
239C ASP* 1.3 73.1 + - - +
241C LEU* 1.3 65.4 + - + +
244C TYR* 3.0 27.0 + - - +
296C PRO 6.0 0.2 - - - +
300C PHE* 3.5 47.7 - - + +
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Residues in contact with LEU 241 (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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18C LEU* 3.8 13.9 - - + -
19C ILE* 3.9 15.7 - - + -
25C TRP* 3.8 18.2 - - + -
31C LEU* 4.5 3.8 - - + -
33C LEU* 4.1 11.2 - - + -
38C LEU* 3.9 21.5 - - + -
41C LEU* 4.0 19.1 - - + -
239C ASP* 3.0 6.9 + - - +
240C VAL* 1.3 74.6 - - + +
242C ALA* 1.3 66.6 + - - +
244C TYR* 3.3 2.9 + - + -
245C TYR* 2.9 34.9 + - + -
300C PHE* 4.0 11.9 - - + -
303C PHE* 3.6 35.9 - - + -
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Residues in contact with ALA 242 (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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16C ILE* 3.6 27.8 - - + +
17C ARG* 3.8 0.9 - - - -
18C LEU* 3.6 22.4 - - + +
235C VAL* 3.8 7.2 - - + -
239C ASP* 2.9 30.4 + - + +
241C LEU* 1.3 75.7 - - - +
243C SER* 1.3 63.6 + - - +
245C TYR 4.0 0.2 - - - -
246C VAL* 3.0 32.1 + - - +
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Residues in contact with SER 243 (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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75C ALA 4.2 4.9 - - - -
76C ALA* 4.4 4.5 - - - -
79C ALA* 3.5 19.7 - - - -
235C VAL* 4.1 7.6 - - - -
236C ASP 3.5 11.6 + - - -
237C GLY* 3.6 16.3 + - - -
239C ASP 2.9 18.1 + - - -
240C VAL 3.9 0.7 - - - -
242C ALA* 1.3 77.1 - - - +
244C TYR* 1.3 62.2 + - - +
246C VAL* 4.3 0.4 - - - +
247C VAL* 3.1 32.1 + - - +
265C LEU* 3.8 15.9 - - - +
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Residues in contact with TYR 244 (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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33C LEU* 3.9 43.3 - - + +
41C LEU* 5.2 10.1 - - + -
79C ALA* 3.4 27.8 - - + +
82C HIS* 3.4 33.5 + - + -
83C ALA* 3.9 8.3 - - - +
240C VAL 3.0 20.4 + - - +
241C LEU* 3.6 4.3 - - - +
243C SER* 1.3 77.1 - - - +
245C TYR* 1.3 84.9 + + - +
247C VAL* 4.0 0.4 - - - -
248C LYS* 2.8 58.4 + - + +
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Residues in contact with TYR 245 (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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8C PHE* 3.5 23.9 - + + -
18C LEU* 3.5 14.4 - - + -
25C TRP* 3.8 18.2 - + - -
29C PHE* 3.7 22.4 - + - -
31C LEU* 3.4 14.2 - - + +
32C ASP* 2.5 44.7 + - - -
33C LEU* 3.4 14.9 - - + +
241C LEU* 2.9 31.6 + - + +
242C ALA 4.2 0.2 - - - +
244C TYR* 1.3 92.4 - + - +
246C VAL* 1.3 58.8 + - - +
248C LYS* 3.5 7.9 - - + +
249C GLU* 2.9 28.1 + - - +
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Residues in contact with VAL 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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8C PHE* 3.9 31.2 - - + -
16C ILE* 4.0 14.8 - - + -
233C TYR* 3.8 32.7 - - + -
235C VAL* 3.7 31.2 - - + -
242C ALA 3.0 18.3 + - - +
243C SER* 4.3 1.3 - - - +
245C TYR* 1.3 72.7 - - - +
247C VAL* 1.3 67.0 + - - +
249C GLU* 3.1 5.0 + - - +
250C ALA* 3.0 21.3 + - - +
263C VAL* 4.1 9.2 - - + -
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Residues in contact with VAL 247 (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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80C ILE* 4.5 14.6 - - + -
83C ALA* 3.8 18.2 - - + -
84C ILE* 5.6 0.4 - - + -
170C VAL* 5.4 0.9 - - + -
198C VAL* 5.0 2.2 - - + -
200C ILE* 3.8 30.3 - - + -
243C SER* 3.1 21.0 + - - +
244C TYR* 4.0 2.2 - - - +
246C VAL* 1.3 74.4 - - - +
248C LYS* 1.3 57.9 + - - +
250C ALA* 3.2 7.4 + - - +
251C VAL* 2.8 37.1 + - + +
263C VAL* 4.1 22.9 - - + -
265C LEU* 4.4 13.7 - - + -
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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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82C HIS 4.9 3.0 + - - -
83C ALA* 3.6 33.3 + - + +
84C ILE 5.9 0.6 + - - -
85C ARG* 6.0 3.4 - - - +
244C TYR* 2.8 47.0 + - + +
245C TYR* 3.5 11.9 - - + +
247C VAL* 1.3 77.7 - - - +
249C GLU* 1.3 57.6 + - - +
251C VAL* 3.2 4.4 + - + +
252C GLU* 2.9 61.2 + - + +
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Residues in contact with GLU 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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6C HIS 3.4 5.1 - - - +
7C ARG* 2.9 36.6 + - - +
8C PHE* 2.9 43.7 + - + +
233C TYR* 3.2 18.7 + - - -
245C TYR 2.9 14.8 + - - +
246C VAL* 3.1 8.9 + - - +
248C LYS* 1.3 76.7 - - - +
250C ALA* 1.3 56.1 + - - +
252C GLU* 3.2 14.3 + - - +
253C ARG* 2.9 48.6 + - - +
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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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198C VAL* 3.6 26.0 - - + +
233C TYR* 4.9 1.8 - - + -
246C VAL 3.0 12.3 + - - +
247C VAL 3.6 7.6 - - - +
249C GLU* 1.3 76.2 + - - +
251C VAL* 1.3 57.5 + - - +
253C ARG* 3.3 17.9 + - - +
254C ALA* 2.9 29.1 + - - +
261C SER* 3.9 19.9 + - - -
263C VAL* 4.1 10.5 - - + -
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Residues in contact with VAL 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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83C ALA 3.9 16.2 - - - +
84C ILE* 4.1 19.7 - - + -
168C VAL* 3.7 10.0 - - + +
170C VAL* 4.2 5.4 - - + -
198C VAL* 3.9 17.3 - - + -
247C VAL* 2.8 35.2 + - + +
248C LYS* 3.5 4.9 - - + +
250C ALA* 1.3 76.2 - - - +
252C GLU* 1.3 60.0 + - + +
254C ALA* 3.2 3.4 + - - +
255C ARG* 2.8 57.0 + - - +
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Residues in contact with GLU 252 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C ARG* 5.8 0.5 + - - -
248C LYS* 2.9 51.1 + - + +
249C GLU* 3.7 13.2 - - - +
251C VAL* 1.3 75.1 - - + +
253C ARG* 1.3 65.1 + - - +
255C ARG* 3.8 10.2 - - - +
256C ARG* 3.0 47.4 + - - +
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Residues in contact with ARG 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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7C ARG* 3.2 26.0 - - - +
231C PRO* 4.2 14.2 - - - +
233C TYR* 2.6 32.5 + - - -
249C GLU* 2.9 21.0 + - - +
250C ALA* 3.5 26.7 - - - +
251C VAL 3.2 0.2 - - - -
252C GLU* 1.3 77.1 - - - +
254C ALA* 1.3 62.3 + - - +
256C ARG* 3.2 21.0 - - - +
258C GLU* 3.0 60.4 + - + +
259C GLY 4.0 8.5 - - - +
261C SER* 3.0 28.4 + - - -
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Residues in contact with ALA 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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168C VAL* 4.1 6.1 - - + -
196C PRO* 3.4 42.9 - - + +
197C ALA 4.1 2.5 - - - +
198C VAL* 4.1 11.4 - - + -
250C ALA 2.9 13.8 + - - +
251C VAL 3.5 7.4 - - - +
253C ARG* 1.3 78.0 - - - +
255C ARG* 1.3 63.1 + - - +
257C GLY* 3.0 15.2 + - - -
259C GLY 3.7 17.7 + - - +
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Residues in contact with ARG 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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83C ALA 5.0 0.6 + - - -
84C ILE* 4.8 1.0 - - - +
85C ARG* 3.4 44.8 - - - +
88C PHE* 3.9 6.9 - - - -
89C ASP* 2.8 43.0 + - - -
166C GLY* 3.0 37.4 + - - +
167C GLN 5.0 1.1 - - - -
168C VAL* 3.6 14.2 - - + +
196C PRO* 4.9 1.6 - - - -
251C VAL* 2.8 39.8 + - - +
252C GLU* 3.3 9.9 + - - +
254C ALA* 1.3 74.0 - - - +
256C ARG* 1.3 57.5 + - - +
257C GLY 3.1 3.2 + - - -
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Residues in contact with ARG 256 (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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7C ARG* 2.7 35.8 - - - +
252C GLU* 3.0 36.7 + - - +
253C ARG* 3.2 34.5 - - - +
255C ARG* 1.3 75.4 - - - +
257C GLY* 1.3 57.8 + - - +
258C GLU* 2.9 31.5 + - + +
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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