Contacts of the helix formed by residues 184 - 200 (chain P) in PDB entry 1MVW
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 184 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127P ASN* 4.8 6.7 - - - -
180P GLU 4.4 0.2 + - - -
181P SER 4.6 2.8 + - - -
182P GLY* 3.1 6.3 + - - -
183P ALA* 1.3 78.8 - - - +
185P LYS* 1.3 65.0 + - - +
186P THR* 5.8 0.2 - - - -
187P VAL* 3.3 27.9 - - - +
188P ASN* 3.1 19.8 + - - -
240P ASN* 4.9 10.8 - - - -
674P CYS* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 185 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177P ILE* 3.6 20.0 - - + +
178P THR* 4.3 3.1 - - - -
179P GLY* 2.9 46.4 - - - +
180P GLU 3.9 10.9 + - - +
181P SER* 4.9 8.2 + - - +
183P ALA* 4.9 0.2 - - + -
184P GLY* 1.3 74.2 - - - +
186P THR* 1.3 55.6 + - - +
187P VAL 3.0 2.2 - - - -
188P ASN* 2.6 29.5 + - - +
189P THR* 2.5 24.7 + - - +
243P SER* 5.8 1.0 + - - -
244P SER* 4.6 19.0 + - - +
463P ASP* 4.4 17.1 + - - +
464P ILE 3.8 19.0 + - - +
465P ALA* 4.6 6.7 - - - +
674P CYS* 4.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184P GLY* 3.7 0.4 - - - -
185P LYS* 1.3 75.6 + - - +
187P VAL* 1.3 57.5 - - - +
189P THR* 3.1 6.8 + - - -
190P MLY 2.6 46.5 + - + +
230P GLU* 3.6 23.1 - - + +
234P ASN* 4.6 4.4 + - - +
240P ASN* 5.5 2.3 + - - -
242P ASN* 4.5 8.9 + - - -
244P SER* 3.7 29.1 + - - +
248P MLY 3.3 31.6 - - - -
463P ASP* 3.8 5.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135P TYR* 5.5 6.7 - - + +
184P GLY* 3.3 32.8 - - - +
186P THR* 1.3 78.3 - - - +
188P ASN* 1.3 62.7 + - - +
190P MLY 3.6 16.1 + - - +
191P ARG* 3.0 48.7 + - - +
240P ASN* 5.5 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 188 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116P TYR* 4.4 0.9 + - - -
125P THR* 4.2 15.0 - - - +
135P TYR* 3.9 16.8 + - - -
155P ILE* 3.3 31.1 - - + +
177P ILE* 4.8 8.1 - - + -
184P GLY 3.1 15.4 + - - -
185P LYS* 2.6 11.4 + - - +
187P VAL* 1.3 75.6 - - - +
189P THR* 1.3 55.1 + - - +
191P ARG* 2.8 7.1 + - - +
192P VAL* 2.6 41.9 + - + +
674P CYS* 2.9 35.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 189 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177P ILE* 4.4 9.8 - - + +
185P LYS* 2.5 25.9 + - - +
186P THR* 3.3 5.6 - - - -
188P ASN* 1.3 71.0 - - - +
190P MLY 1.3 66.4 + - - +
192P VAL* 3.0 10.0 + - - +
193P ILE* 2.9 30.0 + - + +
248P MLY 4.8 16.2 - - - -
250P ILE* 5.0 2.0 - - + -
461P VAL* 3.7 26.7 - - + +
463P ASP* 3.1 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MLY 190 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186P THR* 2.6 39.0 + - + +
187P VAL* 3.7 15.3 - - - +
189P THR* 1.3 71.3 - - - +
191P ARG* 1.3 102.3 + - - +
193P ILE* 2.8 25.7 + - - +
194P GLN* 2.9 21.3 + - - +
226P ASN* 4.1 29.4 - - + +
227P PRO* 6.1 2.2 - - - -
230P GLU* 2.8 43.1 - - - +
242P ASN* 4.0 8.3 - - - -
248P MLY 4.8 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 191 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135P TYR* 3.1 49.1 - - + -
155P ILE* 5.8 4.5 - - + -
156P PHE* 4.4 15.1 - - + -
187P VAL* 3.0 36.9 + - - +
188P ASN* 2.8 6.7 + - - +
190P MLY 1.3 113.8 + - - +
192P VAL* 1.3 61.0 + - - +
194P GLN* 3.6 29.1 + - + +
195P TYR* 3.3 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 192 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155P ILE* 4.4 26.9 - - + -
156P PHE* 5.9 0.2 - - - -
158P ILE* 6.5 0.7 - - + -
159P SER* 4.0 13.7 - - - -
175P ILE* 4.7 11.4 - - + -
177P ILE* 4.4 14.6 - - + -
188P ASN 2.6 24.8 + - - +
189P THR* 3.0 10.3 + - - +
191P ARG* 1.3 73.6 - - - +
193P ILE* 1.3 62.7 + - + +
195P TYR* 2.8 27.7 + - - +
196P PHE* 3.1 31.2 + - + -
461P VAL* 4.8 9.6 - - + -
672P VAL* 6.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 193 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189P THR* 3.0 19.7 - - + +
190P MLY 2.8 13.8 + - - +
192P VAL* 1.3 78.2 - - + +
194P GLN* 1.3 64.6 + - - +
196P PHE* 3.0 18.1 + - - +
197P ALA* 3.0 11.8 + - - +
222P ILE* 4.0 29.6 - - + +
223P ILE* 5.3 6.1 - - + -
226P ASN* 5.6 7.4 - - - +
248P MLY 5.6 3.1 - - - -
250P ILE* 3.1 37.2 - - + -
252P ILE* 3.9 24.7 - - + -
461P VAL* 4.7 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 194 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190P MLY 2.9 18.3 + - - +
191P ARG* 3.8 37.1 + - + +
192P VAL 3.3 0.2 - - - -
193P ILE* 1.3 73.4 - - - +
195P TYR* 1.3 54.8 + - - +
197P ALA* 2.9 5.2 + - - +
198P THR* 2.5 43.1 + - + +
223P ILE* 3.2 39.9 - - + +
226P ASN* 6.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 195 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140P VAL* 3.4 35.8 + - + -
143P TYR* 3.9 5.5 + - - +
144P ARG* 4.0 0.9 + - - -
156P PHE* 2.9 41.1 - + + -
159P SER* 2.8 34.5 - - - +
160P ASP* 2.4 32.3 + - + +
191P ARG 3.3 10.5 + - - +
192P VAL* 2.8 15.9 + - - +
194P GLN* 1.3 78.4 - - - +
196P PHE* 1.3 63.4 + + - +
198P THR* 3.0 13.5 + - - -
199P ILE* 2.9 55.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 196 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159P SER* 3.1 34.5 - - - -
162P ALA* 4.3 5.2 - - + -
163P TYR* 4.0 14.6 - + + -
175P ILE* 4.2 5.4 - - + -
192P VAL* 3.1 38.6 + - + -
193P ILE* 3.0 7.8 + - - +
195P TYR* 1.3 81.5 - + - +
197P ALA* 1.3 68.6 + - - +
199P ILE* 3.6 12.3 + - + +
200P ALA* 3.3 23.4 + - - +
252P ILE* 4.6 17.9 - - + -
254P PHE* 3.6 28.2 - + + -
260P LEU* 5.0 2.5 - - + -
459P ILE* 3.7 43.1 - - + -
461P VAL* 4.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193P ILE 3.0 10.7 + - - +
194P GLN* 2.9 11.5 + - - +
196P PHE* 1.3 79.2 - - - +
198P THR* 1.3 64.0 + - - +
200P ALA 3.8 0.2 - - - -
201P ALA* 3.0 27.6 + - - +
219P GLU* 4.3 23.8 - - + +
222P ILE* 5.2 6.3 - - + -
223P ILE* 4.9 6.7 - - + -
260P LEU* 3.9 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 198 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140P VAL* 5.1 12.3 - - + +
194P GLN* 2.5 33.0 + - + +
195P TYR* 3.0 12.0 + - - -
197P ALA* 1.3 75.6 - - + +
199P ILE* 1.3 61.1 + - - +
200P ALA 2.8 7.4 + - - -
201P ALA* 3.7 8.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 199 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140P VAL* 4.8 8.7 - - + +
144P ARG* 4.5 17.1 + - + -
160P ASP* 4.1 6.7 - - - +
163P TYR* 4.3 22.7 + - + -
195P TYR* 2.9 68.9 + - + +
196P PHE* 4.1 19.1 - - + +
198P THR* 1.3 75.5 - - - +
200P ALA* 1.3 64.3 + - + +
259P LYS* 4.5 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 200 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163P TYR* 3.1 35.7 - - + +
196P PHE 3.3 11.9 + - - +
197P ALA 3.8 3.1 - - - -
198P THR 2.8 9.3 + - - -
199P ILE* 1.3 78.9 - - + +
201P ALA* 1.3 59.2 + - - +
254P PHE* 4.3 5.6 - - + -
258P GLY 3.6 6.7 - - - +
259P LYS* 3.7 12.7 - - - +
260P LEU* 3.1 28.8 + - - +
----------------------------------------------------------
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