Contacts of the helix formed by residues 237 - 254 (chain C) in PDB entry 3DVA
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 237 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLN* 3.6 1.4 - - - +
25C ILE* 2.6 33.8 + - - -
26C LEU* 2.7 26.8 + - - +
83C ALA* 3.8 2.7 - - - -
234C ASP* 3.0 16.7 + - - +
235C GLY 3.3 0.6 - - - -
236C MET* 1.3 78.3 - - - +
238C PRO* 1.3 70.6 - - - +
239C LEU* 3.1 12.6 + - - +
240C ALA* 3.1 12.5 + - + +
241C VAL* 3.0 24.9 + - - +
298C ARG* 3.7 14.4 - - - +
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Residues in contact with PRO 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 5.0 1.1 - - + -
49C LEU* 4.0 18.4 - - + -
53C MET* 3.8 26.7 - - + -
83C ALA* 3.6 6.7 - - + -
87C ALA* 3.3 18.2 - - + +
236C MET 3.5 10.1 - - - +
237C ASP* 1.3 89.1 - - - +
239C LEU* 1.3 57.0 + - - +
241C VAL 3.3 1.0 + - - -
242C TYR* 2.9 29.1 + - - +
295C PRO 4.3 4.5 - - - +
298C ARG* 4.5 8.3 - - + -
299C PHE* 3.7 31.9 - - + -
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Residues in contact with LEU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ILE* 3.8 18.8 - - + -
26C LEU* 3.6 30.1 - - + -
38C MET* 3.8 30.3 - - + -
39C PRO* 4.0 11.6 - - + +
41C LEU* 3.9 27.6 - - + -
46C LEU* 4.1 7.6 - - + -
49C LEU* 4.9 2.7 - - + -
237C ASP* 3.1 4.5 + - - +
238C PRO* 1.3 79.4 - - - +
240C ALA* 1.3 56.8 + - - +
242C TYR* 3.4 3.7 + - - +
243C ALA* 2.8 32.6 + - - +
299C PHE* 3.8 22.0 - - + -
302C PHE* 4.0 11.2 - - + -
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Residues in contact with ALA 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 3.6 33.6 - - + +
25C ILE* 3.6 17.0 - - + +
233C VAL* 4.8 2.0 - - + -
234C ASP 4.3 4.7 - - - +
237C ASP* 3.1 33.1 + - + +
239C LEU* 1.3 75.5 - - - +
241C VAL* 1.3 65.0 + - - +
244C ALA* 3.0 26.3 + - - +
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Residues in contact with VAL 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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83C ALA 3.5 30.7 - - - +
84C SER* 3.9 7.4 - - - +
87C ALA* 4.1 0.2 - - + -
88C SER* 3.7 25.1 - - - +
233C VAL* 4.4 13.5 - - + -
234C ASP 3.7 13.9 - - - +
235C GLY* 4.1 13.5 - - - -
237C ASP 3.0 18.4 + - - +
238C PRO 3.8 2.5 - - - +
240C ALA* 1.3 75.4 - - - +
242C TYR* 1.3 64.1 + - - +
244C ALA* 3.3 1.8 + - - +
245C VAL* 3.0 31.2 + - + +
261C ILE* 6.1 1.1 - - + -
263C THR* 4.6 9.6 - - + -
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Residues in contact with TYR 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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39C PRO* 3.6 30.1 - - + -
40C GLU 4.7 3.2 + - - -
41C LEU* 3.5 28.4 - - + +
45C GLN* 5.5 1.9 + - - -
49C LEU* 5.3 3.1 - - + -
87C ALA* 3.6 25.5 - - + +
90C PHE* 3.5 27.3 + + + -
91C ALA* 3.5 26.9 - - + +
238C PRO 2.9 18.6 + - - +
239C LEU* 3.7 4.7 - - - +
241C VAL* 1.3 76.6 - - - +
243C ALA* 1.3 55.6 + - - +
245C VAL* 3.2 2.6 + - - +
246C LYS* 2.8 70.1 + - + +
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Residues in contact with ALA 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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5A PHE* 5.7 3.5 - - + -
7A PHE* 4.3 3.4 - - + -
23C PHE* 4.0 16.4 - - + -
25C ILE* 4.9 0.4 - - + -
37C ALA 4.1 18.8 - - - +
39C PRO* 4.4 11.2 - - + -
239C LEU 2.8 22.0 + - - +
240C ALA* 3.7 3.8 - - - +
242C TYR* 1.3 80.6 - - - +
244C ALA* 1.3 56.9 + - - +
246C LYS* 3.8 4.1 - - - +
247C ALA* 3.0 30.1 + - - +
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Residues in contact with ALA 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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7A PHE* 4.0 20.4 - - + -
23C PHE* 4.4 0.4 - - - -
231C ILE* 4.3 7.8 - - + +
233C VAL* 3.7 25.4 - - + -
240C ALA 3.0 17.7 + - - +
241C VAL 3.7 3.8 - - - +
243C ALA* 1.3 77.1 - - - +
245C VAL* 1.3 58.8 + - - +
247C ALA* 3.6 2.3 + - - +
248C ALA* 3.1 27.2 + - - +
261C ILE* 3.6 17.2 - - + +
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Residues in contact with VAL 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C SER* 3.5 42.0 - - - +
91C ALA* 3.8 10.3 - - + -
92C LEU* 4.2 9.9 - - + -
168C ILE* 4.5 4.7 - - + -
196C ILE* 3.9 17.2 - - + +
198C VAL* 5.0 8.7 - - + -
241C VAL* 3.0 20.4 + - + +
242C TYR 3.8 2.2 - - - +
244C ALA* 1.3 74.1 - - + +
246C LYS* 1.3 57.0 + - - +
248C ALA* 3.2 3.4 + - - +
249C ARG* 2.8 32.7 + - + +
261C ILE* 3.9 20.2 - - + -
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Residues in contact with LYS 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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90C PHE 5.1 1.0 + - - -
91C ALA* 2.8 39.5 + - + +
93C GLU* 3.4 22.0 + - - +
242C TYR* 2.8 49.0 + - + +
243C ALA* 3.8 5.2 - - - +
245C VAL* 1.3 72.0 - - - +
247C ALA* 1.3 58.4 + - - +
249C ARG* 3.2 14.6 + - - +
250C GLU* 2.9 32.4 + - + +
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Residues in contact with ALA 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 4.6 12.8 - - + +
6A GLN* 6.1 0.2 - - - -
7A PHE* 3.8 26.0 - - + +
9A PHE* 5.8 4.3 - - + -
243C ALA 3.0 18.3 + - - +
244C ALA 3.8 3.8 - - - +
246C LYS* 1.3 76.9 - - - +
248C ALA* 1.3 58.5 + - - +
250C GLU* 3.1 13.8 + - - +
251C ARG* 2.8 32.1 + - - +
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Residues in contact with ALA 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 6.0 1.7 - - - -
196C ILE* 4.0 16.4 - - + +
231C ILE* 5.3 0.9 - - + -
244C ALA 3.1 17.7 + - - +
245C VAL 3.2 5.1 + - - +
247C ALA* 1.3 74.7 - - - +
249C ARG* 1.3 57.1 + - - +
251C ARG* 3.5 5.3 + - - +
252C ALA* 2.9 30.8 + - - +
257C GLY 4.9 0.2 - - - +
259C THR* 3.8 37.1 + - + -
261C ILE* 4.2 8.7 - - + -
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Residues in contact with ARG 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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91C ALA 3.5 21.1 - - - +
92C LEU* 4.4 2.2 - - - +
93C GLU* 3.4 30.1 + - - +
95C GLU* 3.7 6.9 + - - -
96C ASP* 2.7 39.5 + - - -
164C LYS 3.6 19.6 + - - -
165C ALA* 4.1 0.4 - - - +
166C VAL* 4.0 15.9 - - + +
196C ILE* 3.7 11.8 - - + +
245C VAL* 2.8 21.8 + - + +
246C LYS* 3.5 15.0 - - + +
247C ALA 3.2 0.2 - - - -
248C ALA* 1.3 70.7 - - - +
250C GLU* 1.3 61.5 + - - +
252C ALA* 3.1 1.2 + - - -
253C ILE* 2.9 51.1 + - - +
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Residues in contact with GLU 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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4A THR* 3.2 36.8 + - - +
5A PHE 5.1 1.9 - - - +
6A GLN* 3.7 13.8 + - - +
246C LYS* 2.9 17.6 + - + +
247C ALA* 3.5 12.2 - - - +
249C ARG* 1.3 75.7 - - - +
251C ARG* 1.3 63.0 + - - +
253C ILE* 3.5 11.6 - - + +
254C ASN* 2.9 45.7 + - - +
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Residues in contact with ARG 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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9A PHE* 4.0 31.1 - - + +
13A LEU* 5.5 6.9 - - - +
229C PRO* 3.4 34.7 - - - +
247C ALA 2.8 20.2 + - - +
248C ALA* 3.7 5.2 - - - +
250C GLU* 1.3 76.0 - - - +
252C ALA* 1.3 59.4 + - - +
254C ASN* 3.6 8.9 + - - +
255C GLY 3.6 0.2 + - - -
256C GLU* 3.0 81.4 + - + +
257C GLY 4.5 4.2 + - - +
258C PRO 4.2 3.8 + - - -
259C THR* 3.8 16.4 + - - -
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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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166C VAL* 3.5 23.1 - - + -
194C PRO* 3.6 29.4 - - + +
195C ALA 4.6 0.9 - - - +
196C ILE* 5.0 3.8 - - + -
248C ALA 2.9 19.3 + - - +
251C ARG* 1.3 76.4 - - - +
253C ILE* 1.3 60.9 + - - +
255C GLY* 3.0 19.2 + - - -
256C GLU 4.1 0.2 + - - -
257C GLY 3.5 21.9 + - - +
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Residues in contact with ILE 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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164C LYS* 3.7 62.7 - - + +
165C ALA* 3.7 7.6 - - - +
166C VAL* 3.7 15.7 - - + -
249C ARG* 2.9 43.9 + - - +
250C GLU* 3.5 14.1 - - + +
252C ALA* 1.3 69.1 - - - +
254C ASN* 1.3 86.8 + - - +
255C GLY* 2.9 10.1 + - - -
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Residues in contact with ASN 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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250C GLU* 2.9 43.2 + - - +
251C ARG* 3.8 7.4 - - - +
252C ALA 3.2 0.4 - - - -
253C ILE* 1.3 89.1 - - - +
255C GLY* 1.3 60.2 + - - +
256C GLU* 3.4 20.0 + - - +
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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
------------------------------------------------------------
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