Contacts of the helix formed by residues 221 - 236 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D HIS 4.4 1.6 - - - -
17D ALA* 4.4 0.4 - - - -
21D ALA* 4.1 10.9 - - - +
220D VAL* 1.3 78.0 - - - +
222D VAL* 1.3 64.4 + - - +
223D GLY 3.3 2.9 - - - -
224D ASP* 3.1 15.5 + - - +
225D VAL* 3.0 27.5 + - - +
266D LEU* 3.5 8.3 - - - -
298D SO4 3.0 16.9 + - - -
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Residues in contact with VAL 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D PHE* 4.2 17.5 - - + -
209D ARG* 4.2 12.6 - - - +
219D PRO* 3.7 18.4 - - + +
220D VAL 3.4 0.6 - - - -
221D GLY* 1.3 76.1 - - - +
223D GLY* 1.4 65.4 + - - +
225D VAL* 3.2 4.3 + - - +
226D THR* 3.0 29.3 + - - +
251D VAL* 3.9 22.6 - - + +
255D MSE 3.7 32.3 - - + -
266D LEU* 3.6 10.1 - - + +
298D SO4 3.0 7.4 + - - +
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Residues in contact with GLY 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ASP* 4.2 5.8 - - - -
182D LYS* 3.9 19.3 - - - +
222D VAL* 1.4 79.0 - - - +
224D ASP* 1.3 55.9 + - - +
226D THR* 3.4 5.6 + - - -
227D SER* 3.0 33.8 + - - -
298D SO4 3.0 26.6 + - - -
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Residues in contact with ASP 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLN* 3.8 16.6 + - - +
17D ALA* 3.9 0.7 - - - -
18D GLY* 2.9 45.5 + - - +
21D ALA* 4.5 1.6 - - + -
22D ALA* 3.5 11.5 - - + +
83D TYR* 5.0 2.1 + - - +
112D ASP* 4.0 13.0 - - - +
114D VAL* 4.1 9.0 - - - +
221D GLY* 3.1 12.4 + - - +
223D GLY* 1.3 76.8 - - - +
225D VAL* 1.3 63.2 + - - +
227D SER* 4.0 1.7 - - - -
228D GLY* 3.1 18.5 + - - -
298D SO4 3.5 7.6 + - - -
300D BME 3.3 23.5 + - - -
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Residues in contact with VAL 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ALA* 3.8 24.9 - - + +
22D ALA* 4.4 6.5 - - - +
25D PRO* 4.3 9.4 - - + -
26D MSE 5.6 0.2 - - - +
221D GLY 3.0 15.0 + - - +
222D VAL* 3.8 5.4 - - - +
224D ASP* 1.3 75.9 - - - +
226D THR* 1.3 58.0 + - - +
228D GLY 3.8 0.3 - - - -
229D LEU* 2.9 46.5 + - + +
251D VAL* 3.8 20.6 - - + -
254D ILE* 4.0 15.9 - - + -
266D LEU* 3.9 17.9 - - + -
268D VAL* 4.5 6.5 - - + -
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Residues in contact with THR 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D LEU* 3.8 16.4 - - + -
182D LYS* 4.7 5.4 + - + -
194D PHE* 5.6 1.6 - - - -
196D MSE 3.6 31.2 - - + -
209D ARG* 5.5 1.0 + - - -
222D VAL* 3.0 25.5 + - - +
223D GLY* 3.6 7.3 - - - -
225D VAL* 1.3 77.8 - - - +
227D SER* 1.3 62.3 + - - +
230D LEU* 3.0 22.7 + - - +
247D VAL* 3.5 25.2 - - + +
251D VAL* 3.8 14.0 - - - +
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Residues in contact with SER 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D LEU* 4.3 7.2 - - - -
110D PHE* 3.5 31.5 - - - -
112D ASP* 2.9 32.9 + - - -
144D ALA* 3.6 15.6 - - - +
180D LEU* 5.0 2.7 - - - +
182D LYS* 4.3 4.0 - - - +
223D GLY 3.0 11.5 + - - -
224D ASP* 4.0 3.1 - - - -
226D THR* 1.3 75.0 - - - +
228D GLY* 1.3 63.2 + - - +
230D LEU* 3.2 3.0 + - - -
231D LEU* 3.0 21.1 + - - +
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Residues in contact with GLY 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLN* 6.0 0.2 - - - -
22D ALA* 4.7 1.3 - - - -
26D MSE 3.6 34.4 - - - +
80D LEU* 4.2 9.1 - - - +
224D ASP 3.1 14.2 + - - -
225D VAL 3.9 0.4 - - - -
227D SER* 1.3 79.7 - - - +
229D LEU* 1.3 61.2 + - - +
231D LEU* 3.3 1.9 + - - +
232D VAL* 3.1 24.6 + - - +
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Residues in contact with LEU 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D PRO* 3.5 35.9 - - + +
26D MSE 3.8 9.4 - - + +
29D LEU* 3.7 21.5 - - + +
225D VAL* 2.9 36.7 + - + +
226D THR 4.1 0.7 - - - +
228D GLY* 1.3 72.4 - - - +
230D LEU* 1.4 65.9 + - - +
232D VAL* 3.4 4.0 + - + +
233D LYS* 3.0 28.2 + - - +
246D HIS* 6.0 0.2 - - + -
247D VAL* 3.5 16.8 - - + +
250D ALA* 3.9 28.7 - - + -
251D VAL* 4.5 6.3 - - + -
254D ILE* 5.5 0.4 - - + -
275D ILE* 4.3 9.2 - - + -
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Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D PHE* 4.1 13.9 - - + -
142D ILE* 5.0 2.9 - - + -
180D LEU* 4.0 35.0 - - + -
198D LEU* 4.0 24.2 - - + -
226D THR 3.0 18.2 + - - +
227D SER* 3.7 4.3 - - - +
229D LEU* 1.4 76.8 - - - +
231D LEU* 1.3 62.1 + - - +
233D LYS* 3.2 3.4 + - - +
234D LEU* 2.9 43.4 + - + +
243D ALA* 3.9 32.8 - - + -
244D LEU* 4.2 10.3 - - + +
247D VAL* 3.4 12.9 - - + +
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Residues in contact with LEU 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 3.6 41.1 - - + -
26D MSE 4.9 0.4 - - + -
78D ALA* 3.9 23.8 - - + -
80D LEU* 3.9 23.1 - - + -
108D LYS* 5.3 3.6 - - + -
110D PHE* 3.7 33.8 - - + -
142D ILE* 4.4 11.9 - - + -
227D SER 3.0 9.9 + - - +
228D GLY 3.8 5.6 - - - +
230D LEU* 1.3 76.9 - - - +
232D VAL* 1.3 61.6 + - - +
234D LEU* 3.8 5.5 - - + +
235D LEU* 2.9 34.6 + - + +
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Residues in contact with VAL 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LYS* 6.4 0.4 - - - -
5D ILE* 3.9 13.5 - - + -
26D MSE 3.9 25.8 - - + -
29D LEU* 4.1 18.8 - - + -
31D ALA* 3.7 26.0 - - + -
228D GLY 3.1 16.2 + - - +
229D LEU* 3.6 8.3 - - - +
230D LEU 3.3 0.2 - - - -
231D LEU* 1.3 76.6 - - - +
233D LYS* 1.3 57.5 + - - +
235D LEU* 3.3 3.4 + - - +
236D GLN* 2.8 58.3 + - + +
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Residues in contact with LYS 233 (chain D).
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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29D LEU* 4.1 12.8 - - + -
229D LEU 3.0 21.3 + - - +
230D LEU 3.8 0.7 - - - +
232D VAL* 1.3 75.5 - - - +
234D LEU* 1.3 63.9 + - - +
236D GLN* 3.2 22.5 + - - +
238D ALA* 2.9 40.7 + - + +
242D GLU* 4.4 3.6 + - - +
243D ALA* 3.5 28.0 - - + +
246D HIS* 2.8 48.1 + - + +
247D VAL* 4.3 9.4 - - + -
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Residues in contact with LEU 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ILE* 3.9 28.5 - - + -
178D ILE* 4.3 15.7 - - + -
198D LEU* 5.4 0.7 - - + -
230D LEU* 2.9 46.7 + - + +
231D LEU* 3.8 5.8 - - + +
233D LYS* 1.3 76.8 - - - +
235D LEU* 1.3 63.4 + - + +
237D GLY* 2.9 16.8 + - - -
238D ALA 3.9 14.1 + - - +
239D THR 4.7 0.7 - - - +
240D LEU* 4.1 24.2 - - + -
243D ALA* 4.1 16.2 - - + -
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Residues in contact with LEU 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LYS* 3.6 38.6 + - + +
5D ILE* 3.5 37.2 - - + -
77D ASP* 4.0 31.2 - - + +
78D ALA* 3.7 16.4 - - + -
108D LYS* 5.0 10.8 - - + -
231D LEU* 2.9 26.2 + - + +
232D VAL* 3.7 3.6 - - - +
234D LEU* 1.3 77.6 - - + +
236D GLN* 1.3 60.4 + - - +
237D GLY* 3.2 1.7 + - - -
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Residues in contact with GLN 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LYS* 4.4 18.5 - - + +
29D LEU* 3.1 27.6 + - - +
30D GLY* 3.9 15.6 + - - -
31D ALA* 4.1 2.6 - - - +
232D VAL* 2.8 39.9 + - + +
233D LYS* 3.7 19.5 + - - +
234D LEU 3.1 0.4 - - - -
235D LEU* 1.3 75.6 - - - +
237D GLY* 1.3 57.2 + - - +
238D ALA* 3.6 1.3 - - + +
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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