Contacts of the helix formed by residues 238 - 252 (chain C) in PDB entry 3V9G
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 238 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C GLN* 4.0 3.8 - - - +
151C GLN* 3.6 29.2 - - + +
209C PRO 4.5 3.1 - - - +
210C PHE* 3.9 17.3 - - - +
212C PHE 5.7 1.8 - - - +
213C THR* 5.8 1.6 - - - -
235C SER* 2.9 12.2 + - - +
237C THR* 1.3 79.3 - - - +
239C MET* 1.3 62.0 + - - +
240C LEU 3.3 3.4 + - - -
241C ALA* 3.4 4.9 + - - +
242C SER* 2.8 37.1 + - - +
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Residues in contact with MET 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ILE* 4.0 16.6 - - + -
81C GLN* 3.4 11.0 + - - +
92C ALA* 5.1 0.7 - - + -
94C PHE* 3.8 28.3 - - + -
234C PRO* 3.8 21.5 - - + +
235C SER 3.2 23.6 + - - +
236C ASP* 3.8 15.3 - - - +
237C THR 3.7 0.2 - - - -
238C ALA* 1.3 76.7 - - - +
240C LEU* 1.3 64.6 + - - +
242C SER* 3.7 2.6 - - - -
243C TYR* 2.9 28.6 + - - +
261C PHE* 3.8 21.8 - - - -
263C PRO* 3.6 35.9 - - + -
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Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LEU* 4.6 13.5 - - + -
62C GLU* 3.8 28.7 - - + -
64C ILE* 3.9 9.7 - - + +
81C GLN* 2.8 25.2 + - - +
91C VAL* 4.0 31.0 - - + +
92C ALA* 4.3 4.0 - - + -
146C LYS* 3.7 51.0 + - + +
149C VAL* 4.7 8.3 - - + -
150C GLY 4.8 0.4 - - - +
238C ALA 3.3 0.4 - - - -
239C MET* 1.3 74.6 - - - +
241C ALA* 1.3 62.9 + - - +
243C TYR* 3.6 3.5 + - - +
244C ALA* 3.3 18.2 + - - +
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Residues in contact with ALA 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C GLN* 5.5 0.2 - - - +
143C ILE* 4.3 3.6 - - + +
146C LYS* 4.0 18.8 + - + -
147C THR* 3.6 19.3 - - - +
151C GLN* 3.5 24.0 + - - +
213C THR* 3.9 12.8 - - + +
238C ALA 3.4 2.7 + - - +
239C MET 3.4 0.4 - - - -
240C LEU* 1.3 77.5 - - - +
242C SER* 1.3 63.5 + - - +
244C ALA* 3.2 6.8 + - - +
245C VAL* 3.0 25.5 + - - +
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Residues in contact with SER 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C SER* 5.3 1.2 + - - -
213C THR* 4.9 7.9 + - - +
216C GLY* 5.8 1.0 - - - -
232C TRP* 3.6 22.7 - - - -
234C PRO* 3.9 28.2 - - - +
235C SER 4.9 0.9 + - - -
238C ALA* 2.8 32.6 + - - +
239C MET* 3.7 3.6 - - - -
241C ALA* 1.3 75.9 - - - +
243C TYR* 1.3 58.9 + - - +
245C VAL* 3.2 8.9 + - - +
246C TYR* 2.9 23.2 + - - +
261C PHE* 3.9 3.1 - - - -
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Residues in contact with TYR 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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63C ALA 5.2 1.8 - - - -
64C ILE* 3.6 36.1 - - + -
65C PRO* 3.8 22.4 - - + +
67C VAL* 4.0 24.7 - - + +
72C GLU* 4.6 8.0 + - - -
146C LYS* 6.2 1.6 - - - -
239C MET 2.9 15.7 + - - +
240C LEU 4.0 2.2 - - - +
242C SER* 1.3 74.0 - - - +
244C ALA* 1.3 60.4 + - - +
246C TYR* 4.1 7.9 - + - -
247C ARG* 2.8 60.4 + - + +
261C PHE* 3.5 33.3 - + + -
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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
----------------------------------------------------------
139C ARG* 4.8 1.1 + - - +
142C GLU* 3.9 9.2 - - - +
143C ILE* 4.5 11.7 - - + -
146C LYS* 3.6 35.0 - - + +
240C LEU 3.3 8.4 + - - +
241C ALA* 3.2 10.9 + - - +
242C SER 3.2 0.2 - - - -
243C TYR* 1.3 78.3 - - - +
245C VAL* 1.3 63.8 + - - +
247C ARG* 4.1 5.0 - - - +
248C ILE* 3.2 32.3 + - + +
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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
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135C LEU* 5.2 2.7 - - + -
143C ILE* 4.1 9.2 - - + -
166C LEU* 3.6 32.8 - - + -
170C PHE* 4.7 6.1 - - + -
213C THR* 3.8 18.2 - - + +
217C GLY* 4.4 18.4 - - - -
232C TRP* 4.7 7.4 - - + -
241C ALA 3.0 14.7 + - - +
242C SER* 3.5 10.5 - - - +
244C ALA* 1.3 77.9 - - - +
246C TYR* 1.3 63.1 + - - +
248C ILE* 3.3 9.4 + - + +
249C LEU* 3.1 34.3 + - + +
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Residues in contact with TYR 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C VAL* 3.5 34.0 + - + +
69C GLY 4.3 1.2 + - - -
232C TRP* 4.0 9.4 - + + -
242C SER 2.9 9.3 + - - +
243C TYR* 3.3 19.0 + + - +
245C VAL* 1.3 77.3 - - - +
247C ARG* 1.3 68.1 + - - +
249C LEU* 3.3 10.8 + - + +
250C ARG* 3.1 64.7 + - + +
254C LEU* 5.2 0.7 - - + -
259C ILE* 2.8 50.3 + - + -
260C GLN* 4.9 0.2 + - - -
261C PHE* 3.6 39.9 - + + -
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Residues in contact with ARG 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C VAL* 5.6 5.4 - - - +
70C ASP* 6.0 0.2 + - - -
139C ARG* 5.1 5.2 - - - +
243C TYR* 2.8 61.9 + - + +
244C ALA* 4.1 5.8 - - - +
245C VAL 3.3 0.2 - - - -
246C TYR* 1.3 79.2 - - - +
248C ILE* 1.3 58.3 + - - +
250C ARG* 3.3 32.1 + - - +
251C GLU* 2.9 69.1 + - - +
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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
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131C ALA* 4.0 28.5 - - + +
134C MET* 3.9 20.4 - - + +
135C LEU* 3.4 31.2 - - + -
139C ARG* 3.5 44.9 - - + +
142C GLU* 5.3 2.2 - - - +
143C ILE* 4.9 5.4 - - + -
170C PHE* 6.1 0.4 - - + -
244C ALA* 3.2 24.3 + - + +
245C VAL* 3.3 6.5 + - + +
247C ARG* 1.3 78.1 - - - +
249C LEU* 1.3 52.9 + - + +
251C GLU* 3.2 3.3 + - - +
252C ALA* 2.8 31.9 + - - +
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Residues in contact with LEU 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ILE* 4.1 8.0 - - + +
128C PHE* 3.8 36.1 - - + -
131C ALA* 3.8 21.1 - - + -
170C PHE* 4.0 22.7 - - + -
217C GLY* 5.4 4.5 - - - +
220C ALA* 6.4 0.2 - - + -
221C GLY* 5.4 0.9 - - - -
232C TRP* 5.9 3.4 - - + -
245C VAL* 3.1 23.0 + - + +
246C TYR* 3.3 13.4 + - + +
248C ILE* 1.3 72.5 - - + +
250C ARG* 1.3 65.7 + - - +
252C ALA* 3.3 11.1 + - - +
253C GLY 3.3 1.2 + - - -
254C LEU* 3.1 33.2 + - + +
259C ILE* 4.5 18.8 - - + -
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Residues in contact with ARG 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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67C VAL* 4.4 3.2 - - - +
69C GLY 3.1 21.2 + - - -
70C ASP* 2.8 24.0 + - - +
246C TYR* 3.1 55.2 + - + +
247C ARG* 3.6 27.9 - - - +
249C LEU* 1.3 75.7 - - - +
251C GLU* 1.3 61.9 + - - +
253C GLY* 3.1 15.4 + - - -
254C LEU* 2.8 43.9 + - - +
255C PRO 4.0 0.9 + - - -
256C PRO* 3.3 30.7 - - - +
257C ASN 5.1 0.2 - - - +
259C ILE 5.0 1.0 + - - -
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Residues in contact with GLU 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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130C LYS* 5.0 5.5 + - - -
134C MET* 3.7 13.1 - - + +
139C ARG* 2.4 36.9 + - - -
247C ARG* 2.9 45.2 + - - +
248C ILE 3.7 3.6 - - - +
250C ARG* 1.3 72.0 - - - +
252C ALA* 1.3 61.8 + - - +
253C GLY* 3.0 7.1 + - - -
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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
----------------------------------------------------------
127C ILE* 3.4 37.1 - - + +
130C LYS* 3.6 30.1 - - + +
131C ALA* 3.6 14.6 - - + +
134C MET* 4.0 4.0 - - - -
248C ILE 2.8 17.3 + - - +
249C LEU* 3.6 7.4 - - - +
250C ARG 3.2 0.6 - - - -
251C GLU* 1.3 75.5 - - - +
253C GLY* 1.3 57.2 + - - +
254C LEU 3.8 0.2 - - - -
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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
------------------------------------------------------------
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