Contacts of the helix formed by residues 221 - 236 (chain C) in PDB entry 1VI9
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 GLY 221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C ALA* 4.7 1.1 - - - -
21C ALA* 4.4 7.6 - - - -
220C VAL* 1.3 77.7 - - - +
222C VAL* 1.3 65.3 + - - +
223C GLY 3.3 2.9 - - - -
224C ASP* 3.1 24.0 + - - +
225C VAL* 2.9 28.8 + - - +
266C LEU* 3.6 6.5 - - - -
298C SO4 3.0 13.5 + - - -
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Residues in contact with VAL 222 (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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194C PHE* 5.1 10.3 - - + -
209C ARG* 4.1 13.7 - - - +
218C GLN* 5.3 5.2 - - - +
219C PRO 4.3 11.0 - - - +
220C VAL 3.6 0.4 - - - -
221C GLY* 1.3 75.7 - - - +
223C GLY* 1.3 53.8 + - - +
225C VAL* 3.4 4.0 + - - +
226C THR* 2.6 39.2 + - - +
251C VAL* 4.1 20.6 - - + +
255C MSE 3.5 37.7 - - + -
266C LEU* 3.7 9.4 - - + +
298C SO4 3.0 12.1 + - - +
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Residues in contact with GLY 223 (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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112C ASP* 3.4 5.9 - - - +
182C LYS* 4.1 22.7 - - - +
222C VAL* 1.3 78.4 - - - +
224C ASP* 1.3 58.0 + - - +
226C THR* 3.7 5.2 - - - -
227C SER* 3.0 34.5 + - - -
298C SO4 2.8 17.9 + - - -
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Residues in contact with ASP 224 (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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9C GLN* 3.7 16.3 + - - +
17C ALA* 4.0 1.9 - - - +
18C GLY* 2.8 46.4 + - - +
21C ALA* 4.1 3.8 - - + -
22C ALA* 3.7 12.0 - - - +
80C LEU* 5.7 0.7 - - - +
82C GLY* 5.3 0.2 - - - -
83C TYR* 5.2 4.2 + - - +
112C ASP* 4.4 8.2 - - - +
114C VAL* 4.8 10.6 - - - +
220C VAL* 5.1 1.4 - - - +
221C GLY* 3.1 20.5 + - - +
223C GLY* 1.3 76.2 - - - +
225C VAL* 1.3 62.2 + - - +
227C SER* 4.0 2.4 - - - -
228C GLY 3.2 17.5 + - - -
298C SO4 3.7 6.9 + - - -
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Residues in contact with VAL 225 (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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21C ALA* 3.3 31.0 - - + +
22C ALA* 4.6 5.6 - - - +
25C PRO* 4.2 10.1 - - + -
221C GLY 2.9 20.1 + - - +
222C VAL* 3.8 4.5 - - - +
224C ASP* 1.3 74.8 - - - +
226C THR* 1.4 64.4 + - - +
228C GLY 3.4 0.2 + - - -
229C LEU* 2.9 46.4 + - + +
251C VAL* 4.2 8.5 - - + -
254C ILE* 4.0 19.7 - - + -
266C LEU* 4.1 14.4 - - + -
268C VAL* 4.5 6.1 - - + -
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Residues in contact with THR 226 (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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180C LEU* 3.9 23.3 - - + -
182C LYS* 4.8 6.7 - - + -
194C PHE* 6.1 0.3 - - - -
196C MSE 4.0 18.5 - - + -
209C ARG* 5.1 2.3 + - - +
222C VAL* 2.6 27.8 + - - +
223C GLY* 3.7 8.2 - - - -
225C VAL* 1.4 76.9 - - - +
227C SER* 1.3 62.6 + - - +
230C LEU* 3.1 23.6 + - - +
247C VAL* 3.7 20.7 - - + +
251C VAL* 3.7 23.7 - - + +
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Residues in contact with SER 227 (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 LEU* 4.5 6.5 - - - -
110C PHE* 3.4 39.0 - - - -
112C ASP* 2.8 33.6 + - - -
144C ALA* 3.9 7.9 - - - +
180C LEU* 5.4 1.5 - - - +
182C LYS* 4.8 2.6 - - - +
223C GLY 3.0 11.6 + - - -
224C ASP* 4.0 3.6 - - - -
226C THR* 1.3 77.6 - - - +
228C GLY* 1.3 64.4 + - - +
230C LEU* 3.5 0.6 + - - -
231C LEU* 3.0 19.9 + - - +
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Residues in contact with GLY 228 (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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22C ALA* 4.8 2.0 - - - -
26C MSE 3.6 36.1 - - - +
80C LEU* 4.3 9.8 - - - +
224C ASP 3.2 13.8 + - - -
225C VAL* 3.9 2.0 - - - -
227C SER* 1.3 80.4 - - - +
229C LEU* 1.4 61.5 + - - +
231C LEU* 3.4 5.0 + - - +
232C VAL* 3.0 19.1 + - - +
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Residues in contact with LEU 229 (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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25C PRO* 3.5 31.6 - - + +
26C MSE 3.9 5.4 - - + +
29C LEU* 3.5 26.4 - - + +
225C VAL* 2.9 38.7 + - + +
226C THR 4.2 1.1 - - - +
228C GLY* 1.4 75.8 - - - +
230C LEU* 1.3 57.3 + - - +
232C VAL* 3.2 4.6 + - - +
233C LYS* 2.9 32.4 + - - +
246C HIS* 6.2 0.2 - - + -
247C VAL* 3.7 16.4 - - + +
250C ALA* 3.8 28.7 - - + -
251C VAL* 4.3 9.6 - - + +
254C ILE* 5.0 0.7 - - + -
275C ILE* 4.2 9.2 - - + -
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Residues in contact with LEU 230 (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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110C PHE* 4.0 15.5 - - + -
142C ILE* 4.8 3.4 - - + -
180C LEU* 3.7 44.6 - - + -
198C LEU* 4.1 18.4 - - + -
226C THR 3.1 18.7 + - - +
227C SER 3.7 4.0 - - - +
229C LEU* 1.3 71.8 - - - +
231C LEU* 1.3 66.9 + - - +
233C LYS* 3.4 1.4 + - - +
234C LEU* 3.0 53.6 + - + +
243C ALA* 4.0 18.6 - - + -
244C LEU* 5.1 1.6 - - + +
247C VAL* 3.4 16.9 - - + +
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Residues in contact with LEU 231 (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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5C ILE* 3.7 33.2 - - + -
26C MSE 4.1 4.9 - - + -
78C ALA* 4.1 13.9 - - + -
80C LEU* 3.8 20.2 - - + -
108C LYS* 5.5 1.1 - - + -
110C PHE* 3.7 30.5 - - + +
142C ILE* 4.1 15.0 - - + -
227C SER 3.0 18.3 + - - +
228C GLY* 3.6 4.0 - - - +
230C LEU* 1.3 78.1 - - - +
232C VAL* 1.4 63.2 + - - +
234C LEU* 3.8 3.9 - - + -
235C LEU* 3.0 50.4 + - + +
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Residues in contact with VAL 232 (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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5C ILE* 4.5 0.7 - - + -
26C MSE 3.5 43.1 - - + -
29C LEU* 3.9 23.1 - - + -
31C ALA* 3.6 22.7 - - + -
228C GLY 3.0 11.6 + - - +
229C LEU* 3.2 7.1 + - - +
231C LEU* 1.4 77.6 - - - +
233C LYS* 1.3 64.9 + - - +
235C LEU* 3.2 6.4 + - - +
236C GLN* 2.9 52.7 + - + +
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Residues in contact with LYS 233 (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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29C LEU* 4.1 13.9 - - + -
229C LEU 2.9 20.6 + - - +
230C LEU* 3.9 2.9 - - - +
231C LEU 3.4 0.2 - - - -
232C VAL* 1.3 75.1 - - - +
234C LEU* 1.3 61.6 + - - +
236C GLN* 3.2 22.3 + - - +
238C ALA* 3.0 41.5 + - - +
242C GLU* 4.4 6.7 + - - +
243C ALA* 3.7 22.0 - - + +
246C HIS* 3.1 42.3 + - + +
247C VAL* 4.1 15.0 - - + -
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Residues in contact with LEU 234 (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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142C ILE* 4.2 24.9 - - + -
178C ILE* 4.2 32.1 - - + -
198C LEU* 5.2 0.7 - - + -
230C LEU* 3.0 47.9 + - + +
231C LEU* 3.8 4.9 - - - +
233C LYS* 1.3 75.7 - - - +
235C LEU* 1.3 58.9 - - + +
237C GLY* 3.0 18.4 + - - -
238C ALA 4.2 12.6 + - - +
240C LEU* 4.4 15.7 - - + -
243C ALA* 4.1 16.2 - - + -
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Residues in contact with LEU 235 (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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3C LYS* 3.5 44.0 + - + +
5C ILE* 3.4 39.9 - - + -
77C ASP* 4.1 26.2 - - + +
78C ALA* 3.9 14.6 - - + -
108C LYS* 4.9 12.1 - - + -
142C ILE* 6.2 0.9 - - + -
231C LEU* 3.0 28.0 + - + +
232C VAL* 3.7 3.8 - - - +
234C LEU* 1.3 77.2 - - + +
236C GLN* 1.3 57.7 + - - +
237C GLY* 3.1 4.0 + - - -
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Residues in contact with GLN 236 (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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3C LYS* 4.7 14.9 - - + +
29C LEU* 3.4 25.1 + - - +
30C GLY 3.9 16.4 + - - -
31C ALA* 4.0 3.6 - - - +
232C VAL* 2.9 38.4 + - + +
233C LYS* 3.7 18.2 + - - +
234C LEU 3.2 0.8 - - - -
235C LEU* 1.3 76.2 - - - +
237C GLY* 1.3 60.2 + - - +
238C ALA* 3.4 1.8 - - + -
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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