Contacts of the helix formed by residues 182 - 199 (chain P) in PDB entry 1JVP
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 THR 182 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119P HIS* 3.3 55.4 + - + +
122P ARG* 4.1 21.8 + - - +
124P LEU* 3.4 27.6 - - + +
181P SER* 1.3 79.8 - - - +
183P ALA* 1.3 64.9 + - - +
185P ASP* 3.1 14.0 + - - +
186P ILE* 3.6 4.2 + - - +
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Residues in contact with ALA 183 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172P GLU* 4.2 0.4 - - - +
181P SER* 2.9 15.7 + - - +
182P THR* 1.3 82.6 + - - +
184P VAL* 1.3 62.0 + - - +
185P ASP 3.1 0.2 - - - -
186P ILE* 3.2 10.2 + - - -
187P TRP 3.1 14.6 + - - -
271P PRO* 3.6 28.0 - - + +
274P ARG* 2.9 36.8 + - + +
275P ILE 6.0 0.2 - - - +
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Residues in contact with VAL 184 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124P LEU* 4.7 4.9 - - + -
126P ARG* 4.4 13.9 - - - -
170P ALA* 3.9 12.3 + - + +
172P GLU* 3.5 14.1 - - - +
173P ILE* 3.8 24.9 - - + -
180P TYR* 3.4 41.1 - - + -
181P SER 3.1 15.1 + - - +
183P ALA* 1.3 77.3 - - - +
185P ASP* 1.3 76.4 + - - +
187P TRP* 3.5 3.8 + - - +
188P SER* 3.1 26.6 + - - -
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Residues in contact with ASP 185 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115P LEU* 4.0 18.9 - - + +
119P HIS* 2.8 27.8 + - + +
124P LEU* 3.6 4.3 - - - +
125P HIS* 2.8 25.7 + - - -
126P ARG* 2.9 29.5 + - - -
127P ASP 4.6 0.5 + - - -
128P LEU* 5.1 3.8 + - - -
182P THR 3.1 10.1 + - - +
184P VAL* 1.3 81.8 - - - +
186P ILE* 1.3 64.2 + - - +
188P SER* 3.3 7.2 + - - -
189P LEU* 3.0 24.9 + - - +
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Residues in contact with ILE 186 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112P LEU* 4.1 14.4 - - + -
115P LEU* 4.1 9.6 - - + -
119P HIS* 4.6 4.9 - - + +
182P THR* 3.6 10.1 + - - +
183P ALA* 3.2 12.3 + - - +
185P ASP* 1.3 76.8 - - - +
187P TRP* 1.3 56.9 + - - +
189P LEU* 3.4 2.4 + - - -
190P GLY* 3.0 24.9 + - - -
266P MET* 3.6 38.5 - - + +
274P ARG* 4.1 4.9 - - + -
275P ILE* 3.4 26.2 - - + +
276P SER* 4.1 2.2 - - - +
277P ALA* 3.6 38.4 - - + +
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Residues in contact with TRP 187 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167P TRP 5.3 0.4 + - - -
168P TYR 3.5 11.8 + - - -
169P ARG 3.4 11.7 + - - -
170P ALA* 3.5 17.7 - - + -
171P PRO* 3.4 33.4 - - + -
183P ALA 3.1 5.5 + - - -
184P VAL 3.6 8.5 - - - +
185P ASP 3.2 0.2 - - - -
186P ILE* 1.3 77.3 - - - +
188P SER* 1.3 65.6 + - - +
190P GLY* 3.1 3.1 + - - -
191P CYS* 3.1 36.0 + - - -
203P PHE* 3.8 20.5 - + - -
215P ILE* 3.8 19.0 - - + +
219P LEU* 3.5 23.8 - - + -
266P MET 3.6 10.0 + - - -
267P LEU* 3.3 43.1 - - + +
268P HIS 4.1 3.8 - - - -
269P TYR* 4.9 2.9 - + - -
274P ARG* 3.8 26.4 - - - +
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Residues in contact with SER 188 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P ARG 5.3 3.8 + - - -
127P ASP* 5.6 0.3 - - - -
128P LEU* 4.0 23.7 + - - -
168P TYR* 2.7 39.0 + - - +
169P ARG* 4.9 0.2 - - - -
170P ALA 5.0 0.3 + - - -
184P VAL 3.1 12.5 + - - -
185P ASP* 3.3 10.7 + - - -
187P TRP* 1.3 78.6 - - - +
189P LEU* 1.3 63.0 + - - +
191P CYS* 3.2 5.2 + - - +
192P ILE* 3.1 27.5 + - - +
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Residues in contact with LEU 189 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108P LEU* 3.7 18.8 - - + -
111P LEU* 3.6 39.5 - - + -
112P LEU* 3.6 37.7 - - + +
115P LEU* 3.8 18.2 - - + -
133P LEU* 5.0 1.6 - - + -
143P LEU* 6.2 1.6 - - + -
185P ASP 3.0 17.0 + - - +
186P ILE 3.8 4.3 - - - +
188P SER* 1.3 73.5 - - - +
190P GLY* 1.3 61.5 + - - +
192P ILE* 3.1 20.4 + - + +
193P PHE* 2.8 30.4 + - - +
196P MET* 5.9 1.3 - - + -
266P MET* 3.9 3.1 - - + -
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Residues in contact with GLY 190 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186P ILE 3.0 15.6 + - - -
187P TRP 3.1 4.4 + - - -
189P LEU* 1.3 77.2 - - - +
191P CYS* 1.3 60.3 + - - +
193P PHE* 3.3 4.0 + - - +
194P ALA* 3.0 19.6 + - - +
263P LEU* 3.3 27.9 - - - +
266P MET* 3.6 17.0 - - - +
267P LEU* 4.3 4.5 - - - -
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Residues in contact with CYS 191 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167P TRP 4.2 9.6 - - - +
168P TYR* 3.7 19.2 - - + -
187P TRP* 3.1 44.4 + - - -
188P SER 3.2 7.4 + - - +
190P GLY* 1.3 75.3 - - - +
192P ILE* 1.3 58.7 + - - +
194P ALA* 3.4 2.9 + - - +
195P GLU* 3.0 27.5 + - - +
202P LEU* 4.1 18.1 + - + +
203P PHE* 3.9 25.6 - - - +
267P LEU* 4.3 3.8 - - - +
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Residues in contact with ILE 192 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87P LEU* 3.8 28.5 - - + -
91P MET* 5.5 0.7 - - + -
128P LEU* 4.1 5.6 - - - -
129P LYS* 3.7 29.6 - - - +
130P PRO* 4.0 10.1 - - + -
133P LEU* 3.8 19.3 - - + -
168P TYR* 3.6 19.7 - - + -
188P SER 3.1 19.1 + - - +
189P LEU* 3.1 16.6 + - + +
191P CYS* 1.3 73.4 - - - +
193P PHE* 1.3 58.7 + - - +
195P GLU* 3.2 8.6 + - + +
196P MET* 2.9 37.6 + - + +
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Residues in contact with PHE 193 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101P LEU* 5.7 0.7 - - + -
104P ILE* 3.9 18.8 - - + -
108P LEU* 3.6 34.5 - - + -
189P LEU* 2.8 13.7 + - - +
190P GLY* 3.3 9.4 - - - +
192P ILE* 1.3 77.1 - - - +
194P ALA* 1.3 61.5 + - - +
196P MET* 3.3 13.7 + - + +
197P VAL* 3.2 36.7 + - + +
259P GLY* 3.8 25.4 - - - -
262P LEU* 4.3 8.3 - - + -
263P LEU* 4.1 22.7 - - + -
266P MET* 4.4 7.6 - - - -
285P PHE* 3.7 31.6 - + - -
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Residues in contact with ALA 194 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190P GLY 3.0 10.8 + - - +
191P CYS 3.6 7.9 - - - +
193P PHE* 1.3 76.0 - - - +
195P GLU* 1.3 58.9 + - - +
197P VAL* 3.3 5.9 + - - +
198P THR* 2.9 41.1 + - + +
200P ARG 4.7 0.4 - - - -
202P LEU* 3.7 33.7 - - + -
251P VAL 6.0 1.6 - - - +
263P LEU* 4.3 17.5 - - + -
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Residues in contact with GLU 195 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91P MET* 3.6 29.8 - - + +
130P PRO* 4.2 1.5 - - - +
167P TRP* 5.0 3.3 - - - -
168P TYR* 2.6 39.7 + - - -
191P CYS 3.0 12.1 + - - +
192P ILE 3.2 9.6 + - - +
194P ALA* 1.3 74.9 - - - +
196P MET* 1.3 58.2 + - - +
199P ARG* 2.8 32.5 + - - -
200P ARG 3.4 26.0 - - - +
201P ALA* 3.6 20.3 + - - +
202P LEU 4.9 0.7 + - - +
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Residues in contact with MET 196 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87P LEU* 4.2 17.5 - - + -
91P MET* 4.0 21.1 - - - -
98P GLY* 5.3 0.2 - - - -
99P ILE* 4.1 28.7 + - + +
104P ILE* 3.5 47.5 - - + +
107P TYR* 4.4 22.7 - - + -
108P LEU* 4.9 8.7 - - + +
111P LEU* 5.6 4.5 - - + -
189P LEU* 5.9 0.9 - - + -
192P ILE* 2.9 22.0 + - + +
193P PHE* 3.3 25.5 + - + +
195P GLU* 1.3 76.8 - - - +
197P VAL* 1.3 60.9 + - - +
199P ARG* 4.1 10.0 + - - +
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Residues in contact with VAL 197 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101P LEU* 5.5 6.3 - - + -
104P ILE* 3.9 19.5 - - + -
193P PHE* 3.2 35.8 + - + +
194P ALA* 3.7 9.0 - - - +
195P GLU 3.2 0.2 - - - -
196P MET* 1.3 78.6 - - - +
198P THR* 1.3 68.6 - - + +
199P ARG* 4.8 7.1 + - - +
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Residues in contact with THR 198 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194P ALA* 2.9 19.5 + - + +
197P VAL* 1.3 86.2 - - + +
199P ARG* 1.3 71.6 + - - +
200P ARG* 3.1 32.0 + - - +
251P VAL 3.7 24.9 - - - +
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Residues in contact with ARG 199 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91P MET* 5.9 1.3 - - - +
94P SER 5.6 0.4 - - - -
95P ALA* 3.1 31.4 + - + +
96P LEU 3.1 26.5 + - - -
97P THR 3.3 18.0 + - - -
98P GLY* 3.4 21.6 - - - -
195P GLU* 2.8 20.5 + - - -
196P MET 4.4 8.1 - - - +
197P VAL 3.5 5.8 + - - +
198P THR* 1.3 76.3 + - - +
200P ARG* 1.3 64.4 + - - +
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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
------------------------------------------------------------
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