Contacts of the helix formed by residues 221 - 236 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA* 4.8 0.7 - - - -
21A ALA* 4.4 7.2 - - - -
220A VAL* 1.3 76.6 - - - +
222A VAL* 1.3 62.8 + - - +
223A GLY 3.2 2.5 - - - -
224A ASP* 3.2 16.7 + - - +
225A VAL* 3.0 27.9 + - - +
266A LEU* 3.5 7.9 - - - -
298A SO4 2.8 22.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A PHE* 5.1 8.7 - - + -
209A ARG* 3.9 15.3 - - - +
219A PRO 4.4 9.9 - - - +
221A GLY* 1.3 74.7 - - - +
223A GLY* 1.3 52.9 + - - +
225A VAL* 3.5 4.2 + - - +
226A THR* 2.6 40.4 + - - +
251A VAL* 3.9 22.0 - - + +
255A MSE 3.5 36.8 - - + -
266A LEU* 3.6 10.5 - - + +
298A SO4 2.7 12.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASP* 4.1 6.5 - - - -
182A LYS* 4.4 18.2 - - - +
222A VAL* 1.3 73.5 - - - +
224A ASP* 1.3 64.1 + - - +
226A THR* 3.3 6.4 + - - -
227A SER* 3.0 29.5 + - - -
298A SO4 2.5 24.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 3.7 17.6 + - - +
17A ALA* 4.1 1.6 - - - +
18A GLY* 2.8 45.8 + - - +
21A ALA* 4.3 3.1 - - + -
22A ALA* 3.7 11.7 - - + +
80A LEU* 5.7 0.7 - - - +
82A GLY* 5.2 0.5 - - - -
83A TYR* 4.9 10.2 + - - +
112A ASP* 4.8 6.4 - - - +
114A VAL* 5.1 5.5 - - - +
220A VAL* 5.1 1.2 - - - +
221A GLY* 3.2 15.6 + - - +
223A GLY* 1.3 77.5 - - - +
225A VAL* 1.3 62.6 + - - +
227A SER* 4.1 2.8 - - - -
228A GLY* 3.1 17.8 + - - -
298A SO4 3.2 13.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 3.5 30.1 - - + +
22A ALA* 4.7 5.6 - - - +
25A PRO* 4.1 9.0 - - + -
221A GLY 3.0 17.1 + - - +
222A VAL* 3.9 4.7 - - - +
224A ASP* 1.3 78.0 - - - +
226A THR* 1.3 62.1 + - - +
228A GLY* 3.4 0.9 + - - -
229A LEU* 2.9 46.6 + - + +
251A VAL* 4.2 8.3 - - + -
254A ILE* 3.9 20.6 - - + -
266A LEU* 4.1 13.2 - - + -
268A VAL* 4.4 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 3.8 23.8 - - + -
182A LYS* 4.8 7.0 - - + +
194A PHE* 6.1 0.9 - - - -
196A MSE 3.9 19.4 - - + -
209A ARG* 5.2 2.0 + - - +
222A VAL* 2.6 27.9 + - - +
223A GLY* 3.3 7.1 + - - -
225A VAL* 1.3 77.2 - - - +
227A SER* 1.3 57.0 + - - +
229A LEU 3.4 0.2 + - - -
230A LEU* 2.9 28.9 + - - +
247A VAL* 3.7 20.2 - - + +
251A VAL* 3.6 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 4.5 6.5 - - - -
110A PHE* 3.4 37.1 - - - -
112A ASP* 2.7 35.2 + - - +
144A ALA* 3.8 6.4 - - - +
180A LEU* 5.2 1.8 - - - +
182A LYS* 4.7 2.4 - - - +
223A GLY 3.0 11.0 + - - -
224A ASP* 4.1 3.6 - - - -
226A THR* 1.3 78.1 - - - +
228A GLY* 1.3 64.6 + - - +
230A LEU* 3.3 1.4 + - - -
231A LEU* 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 4.7 1.8 - - - -
26A MSE 3.5 31.3 - - - +
80A LEU* 4.2 11.4 - - - +
224A ASP 3.1 15.0 + - - -
225A VAL 3.9 0.7 - - - -
227A SER* 1.3 78.8 - - - +
229A LEU* 1.3 62.1 + - - +
231A LEU* 3.5 1.4 + - - +
232A VAL* 3.2 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PRO* 3.5 37.5 - - + +
26A MSE 3.9 4.7 - - + +
29A LEU* 3.7 21.3 - - + +
225A VAL* 2.9 40.9 + - + +
226A THR 4.1 0.9 - - - +
228A GLY* 1.3 75.6 - - - +
230A LEU* 1.3 57.6 + - - +
232A VAL* 3.4 4.5 + - - +
233A LYS* 3.0 31.9 + - - +
247A VAL* 3.6 16.6 - - + +
250A ALA* 4.0 27.8 - - + -
251A VAL* 4.4 8.5 - - + -
254A ILE* 5.1 0.9 - - + -
275A ILE* 4.4 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PHE* 3.9 14.1 - - + -
142A ILE* 4.7 3.4 - - + -
180A LEU* 3.7 40.6 - - + -
198A LEU* 4.0 21.5 - - + -
226A THR 2.9 18.7 + - - +
227A SER 3.7 4.0 - - - +
229A LEU* 1.3 74.0 - - - +
231A LEU* 1.3 61.1 + - - +
233A LYS* 3.3 1.3 + - - +
234A LEU* 2.9 54.7 + - + +
243A ALA* 3.8 24.9 - - + -
244A LEU* 4.9 2.2 - - + +
247A VAL* 3.5 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.8 32.5 - - + -
26A MSE 4.6 2.5 - - + -
78A ALA* 4.0 14.8 - - + -
80A LEU* 3.9 19.5 - - + -
108A LYS* 5.3 2.0 - - + -
110A PHE* 3.6 36.9 - - + -
142A ILE* 4.2 13.9 - - + -
227A SER 3.1 11.4 + - - +
228A GLY* 3.8 5.4 - - - +
230A LEU* 1.3 78.3 - - - +
232A VAL* 1.3 64.0 + - - +
234A LEU* 3.8 3.5 - - + -
235A LEU* 2.9 53.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.5 0.7 - - + -
26A MSE 3.5 41.1 - - + -
29A LEU* 3.8 23.3 - - + -
31A ALA* 3.6 19.1 - - + -
228A GLY 3.2 14.3 + - - +
229A LEU 3.7 7.4 - - - +
230A LEU 3.3 0.2 - - - -
231A LEU* 1.3 78.6 - - - +
233A LYS* 1.3 63.6 + - - +
235A LEU* 3.9 6.8 - - - +
236A GLN* 3.0 52.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.8 17.3 - - + -
229A LEU 3.0 21.5 + - - +
230A LEU* 3.3 4.9 + - - +
232A VAL* 1.3 77.5 - - - +
234A LEU* 1.3 60.1 + - - +
236A GLN* 3.3 18.9 + - - +
238A ALA* 3.0 41.9 + - + +
242A GLU* 4.5 4.1 + - - +
243A ALA* 3.7 22.7 - - + +
246A HIS* 2.7 42.9 + - + +
247A VAL* 4.0 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ILE* 4.2 23.8 - - + -
178A ILE* 4.1 31.2 - - + -
198A LEU* 5.2 0.9 - - + -
230A LEU* 2.9 50.8 + - + +
231A LEU* 3.8 5.2 - - - +
233A LYS* 1.3 68.2 - - - +
235A LEU* 1.3 69.1 + - + +
237A GLY* 3.0 14.9 + - - -
238A ALA 4.3 13.6 - - - +
240A LEU* 4.5 14.4 - - + -
243A ALA* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 3.4 41.3 + - + +
5A ILE* 3.4 41.1 - - + -
77A ASP* 4.1 25.4 - - + +
78A ALA* 4.0 5.8 - - + -
108A LYS* 4.9 12.1 - - + -
142A ILE* 6.0 0.7 - - + -
231A LEU* 2.9 44.4 + - + +
232A VAL* 3.9 3.4 - - - +
234A LEU* 1.3 74.6 - - + +
236A GLN* 1.3 58.2 + - - +
237A GLY 3.1 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 4.5 16.5 - - + +
29A LEU* 3.0 27.5 + - - +
30A GLY* 3.8 16.2 + - - -
31A ALA* 4.1 2.0 - - - +
232A VAL* 3.0 39.2 + - + +
233A LYS* 3.7 19.5 + - - +
234A LEU 3.2 0.6 - - - -
235A LEU* 1.3 75.7 - - - +
237A GLY* 1.3 59.0 + - - +
238A ALA* 3.5 1.7 + - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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