Contacts of the helix formed by residues 136 - 161 (chain D) in PDB entry 4WYV
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 ASP 136 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D TYR* 4.7 3.4 + - - +
85D TYR* 3.3 31.8 + - + +
88D HIS* 4.0 15.8 - - - +
134D HIS* 3.8 5.1 + - - +
135D LEU* 1.3 81.1 - - - +
137D VAL* 1.3 65.2 + - - +
138D GLU* 2.9 33.0 - - - +
139D ASP* 3.3 32.3 + - - +
140D TYR* 3.3 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D ARG* 4.1 28.6 - - - +
128D ASP* 5.6 1.3 - - - +
135D LEU 3.6 0.8 + - - -
136D ASP* 1.3 75.3 + - - +
138D GLU* 1.3 70.4 + - + +
140D TYR* 3.2 9.7 + - + +
141D LEU* 2.9 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D GLN* 4.9 0.4 - - - -
136D ASP* 2.9 30.3 - - - +
137D VAL* 1.3 85.3 + - + +
139D ASP* 1.3 57.1 + - - +
141D LEU* 3.5 2.5 + - - +
142D SER* 2.9 32.7 + - - +
188D ASN* 4.1 26.7 - - + +
191D LEU* 4.0 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D HIS* 2.8 27.7 + - - -
92D ARG* 3.6 15.3 - - - +
95D LEU* 3.6 19.2 - - + +
96D GLN* 3.2 38.0 + - + +
99D VAL* 3.9 8.9 - - - +
135D LEU* 4.1 11.9 - - + -
136D ASP* 3.3 23.2 + - + +
137D VAL 3.3 0.6 - - - -
138D GLU* 1.3 76.3 - - - +
140D TYR* 1.3 66.8 + - - +
142D SER 3.4 0.2 + - - -
143D GLY 3.2 14.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D VAL* 3.6 23.6 - - + +
113D LEU* 3.9 14.4 - - + +
114D VAL* 2.6 29.6 + - + -
115D THR* 3.8 1.4 - - - -
116D ARG* 3.6 56.4 + - + -
119D VAL* 4.1 11.7 - - + -
135D LEU* 4.3 6.3 - - + +
136D ASP 3.3 11.5 + - - +
137D VAL* 3.2 10.4 + - + +
139D ASP* 1.3 75.5 - - - +
141D LEU* 1.3 79.6 + - + +
143D GLY 3.0 12.3 + - - -
144D VAL* 3.2 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D VAL* 2.9 34.9 + - + +
138D GLU 3.8 4.3 - - - +
140D TYR* 1.3 92.3 - - + +
142D SER* 1.3 62.2 + - - +
144D VAL* 3.3 9.4 + - + +
145D LEU* 3.1 24.9 + - - +
181D PHE* 4.1 22.8 - - + -
184D LEU* 3.7 28.9 - - + -
186D LEU* 4.4 3.4 - - + -
191D LEU* 3.9 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D GLN* 3.0 42.3 + - - -
138D GLU* 2.9 21.5 + - - +
140D TYR 3.2 0.2 - - - -
141D LEU* 1.3 76.0 - - - +
143D GLY* 1.3 63.0 + - - +
145D LEU* 3.2 6.3 + - - +
146D ILE* 3.0 27.4 + - - +
191D LEU* 3.6 15.4 - - - +
194D ARG* 4.1 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D GLN 3.7 22.8 + - - -
99D VAL* 3.9 10.8 - - - -
100D PHE* 3.5 18.5 - - - +
103D ALA* 5.7 0.4 - - - -
139D ASP 3.2 4.0 + - - -
140D TYR 3.0 8.6 + - - -
142D SER* 1.3 80.3 - - - +
144D VAL* 1.3 55.3 + - - +
146D ILE* 3.3 6.3 + - - -
147D LEU* 2.9 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D VAL* 4.9 2.7 - - + -
103D ALA* 5.6 3.6 - - + -
113D LEU* 4.2 18.8 - - + -
140D TYR* 3.4 43.7 - - + +
141D LEU* 3.5 11.7 - - + +
142D SER 3.2 0.6 - - - -
143D GLY* 1.3 75.1 - - - +
145D LEU* 1.3 65.7 + - - +
147D LEU* 3.1 12.0 + - + +
148D ALA* 3.0 19.9 + - - +
177D LEU* 3.9 33.7 - - + +
181D PHE* 4.5 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D LEU 3.1 14.7 + - - +
142D SER* 3.2 6.3 + - - +
144D VAL* 1.3 77.8 - - - +
146D ILE* 1.3 62.0 + - - +
148D ALA* 3.2 8.6 + - - +
149D SER* 3.2 22.9 + - - -
181D PHE* 3.5 36.8 - - + -
191D LEU* 4.2 14.8 - - + +
194D ARG* 3.9 32.5 - - + +
195D TYR* 3.9 23.3 - - - +
198D LEU* 3.8 33.0 - - + +
201D ASP* 4.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D GLN* 4.4 20.9 - - + +
97D ARG* 5.0 8.5 - - + +
100D PHE* 3.5 31.9 - - + -
142D SER 3.0 22.7 + - - +
143D GLY* 3.6 11.0 - - - +
144D VAL 3.3 0.2 - - - -
145D LEU* 1.3 75.4 - - - +
147D LEU* 1.3 62.6 + - - +
149D SER* 3.3 9.1 + - - +
150D GLU* 3.1 20.3 + - - +
194D ARG* 3.9 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D PHE* 3.6 11.6 - - + -
103D ALA* 3.9 24.0 - - + +
104D PHE* 3.6 48.2 - - + +
107D TYR* 4.8 3.1 - - + -
113D LEU* 4.7 10.1 - - + -
143D GLY 2.9 14.1 + - - +
144D VAL* 3.2 13.5 - - + +
146D ILE* 1.3 74.0 - - - +
148D ALA* 1.3 52.3 + - - +
150D GLU* 2.8 5.4 + - - +
151D LEU* 2.7 47.0 + - + +
173D PHE* 4.0 27.6 - - + -
177D LEU* 5.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D VAL 3.0 11.7 + - - +
145D LEU* 3.3 11.7 - - - +
147D LEU* 1.3 75.0 - - - +
149D SER* 1.3 58.3 + - - +
151D LEU* 3.2 3.6 + - - +
152D SER* 2.9 26.3 + - - -
174D ILE* 3.6 18.2 - - + +
177D LEU* 4.3 13.4 - - + +
198D LEU* 3.5 33.0 - - + -
201D ASP* 3.9 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D LEU 3.2 9.3 + - - -
146D ILE* 3.6 11.2 - - - -
147D LEU 3.2 0.6 - - - -
148D ALA* 1.3 77.5 - - - +
150D GLU* 1.3 61.4 + - - +
152D SER* 3.0 16.5 + - - -
153D ARG* 3.3 9.9 + - - +
197D GLY 5.8 0.3 - - - -
201D ASP* 2.8 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D GLN* 3.1 34.7 + - - +
46D HIS* 2.6 29.4 + - - +
100D PHE* 3.5 35.2 - - + -
104D PHE* 3.8 24.5 - - + -
146D ILE* 3.1 5.3 + - - +
147D LEU* 2.8 9.2 + - - +
149D SER* 1.3 76.1 - - - +
151D LEU* 1.3 58.7 + - - +
153D ARG* 3.5 12.7 + - - +
154D LEU* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D PHE* 4.2 15.9 - - + -
107D TYR* 3.8 33.4 - - + -
147D LEU* 2.7 29.6 + - + +
148D ALA* 3.2 6.0 + - - +
150D GLU* 1.3 75.4 - - - +
152D SER* 1.3 59.5 + - - +
154D LEU* 3.0 24.0 + - + +
155D SER* 2.8 28.8 + - - -
170D ILE* 3.7 22.1 - - + +
173D PHE* 3.5 39.9 - - + -
174D ILE* 4.5 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D ALA 2.9 15.1 + - - -
149D SER 3.0 10.9 + - - -
151D LEU* 1.3 76.4 - - - +
153D ARG* 1.3 65.0 + - - +
155D SER* 3.2 15.4 - - - -
156D VAL* 3.4 13.8 - - - +
174D ILE* 4.4 1.2 - - - +
201D ASP* 3.3 28.2 + - - -
204D LYS* 4.8 10.5 - - - +
205D VAL* 3.6 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASN* 3.2 19.2 - - - +
178A ASP* 5.0 6.7 + - - -
182A ARG* 5.6 0.8 - - - +
202A VAL* 3.8 9.9 - - - +
206A GLU* 2.9 38.8 + - - +
43D GLN* 3.5 30.7 + - - +
46D HIS* 3.8 25.6 + - + +
149D SER 3.3 9.2 + - - +
150D GLU* 3.5 14.5 + - - +
151D LEU 3.2 0.2 - - - -
152D SER* 1.3 81.9 + - - +
154D LEU* 1.3 63.0 + - - +
156D VAL* 3.2 10.6 + - - +
157D ASN* 3.1 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D VAL* 3.9 26.0 - - + +
46D HIS* 3.5 23.3 - - + +
104D PHE* 4.4 7.4 - - + -
108D LEU* 4.4 21.3 - - + -
150D GLU 3.1 10.9 + - - +
151D LEU* 3.0 30.7 + - + +
153D ARG* 1.3 80.5 - - - +
155D SER* 1.3 55.1 + - - +
157D ASN* 4.4 0.9 - - + +
158D SER* 2.8 40.6 + - - +
166D ARG* 4.4 19.1 - - - +
170D ILE* 4.0 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D LEU 2.8 11.8 + - - -
152D SER* 3.2 16.8 - - - -
154D LEU* 1.3 77.7 - - - +
156D VAL* 1.3 61.6 + - - +
158D SER* 3.4 14.6 - - - -
159D VAL* 3.5 5.4 + - - +
167D PRO* 3.5 21.8 - - - +
170D ILE* 4.0 17.5 - - - +
205D VAL* 4.2 15.6 - - - +
208D VAL* 3.7 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLU* 4.4 10.8 - - + +
207A GLU* 4.6 14.1 - - + +
210A TYR* 3.5 44.2 - - + -
152D SER 3.4 15.5 - - - +
153D ARG* 3.2 9.4 + - - +
155D SER* 1.3 78.3 - - - +
157D ASN* 1.3 65.3 + - - +
158D SER 3.3 0.7 + - - -
159D VAL 3.3 9.5 + - - -
160D THR* 3.4 9.9 + - - -
204D LYS* 4.2 22.0 - - + +
208D VAL* 4.2 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLU* 3.3 54.6 + - - +
46D HIS* 3.2 49.9 + - - +
153D ARG* 3.1 18.4 + - - +
154D LEU* 3.3 4.0 + - + +
156D VAL* 1.3 74.9 - - - +
158D SER* 1.3 63.8 - - - +
160D THR* 3.3 11.6 + - - -
161D ALA* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D LEU* 2.8 23.1 + - - +
155D SER* 3.4 10.1 - - - -
157D ASN* 1.3 73.3 - - - +
159D VAL* 1.3 66.3 + - - +
161D ALA* 3.0 15.6 + - - +
162D GLY 3.2 0.2 + - - -
163D ASP* 3.1 38.5 + - - +
166D ARG* 3.3 29.8 - - - +
167D PRO* 3.6 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A TYR* 3.8 30.1 - - + -
213A SER* 4.5 3.5 - - - -
214A ILE* 4.1 24.0 - - + +
155D SER 3.5 1.1 + - - +
156D VAL 3.3 9.6 + - - +
158D SER* 1.3 77.2 + - - +
160D THR* 1.3 66.7 + - - +
162D GLY* 2.9 11.3 + - - -
163D ASP 3.9 5.8 - - - -
164D TYR* 3.4 27.5 + - + -
167D PRO* 3.9 22.4 - - + -
208D VAL* 4.0 5.8 - - + -
212D LEU* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLU 4.6 1.6 + - - -
209A VAL* 3.3 27.5 - - + +
210A TYR* 3.5 28.9 + - - +
213A SER* 3.6 18.9 + - - +
156D VAL 3.4 6.7 + - - -
157D ASN* 3.3 16.2 + - - -
158D SER 3.3 0.8 - - - -
159D VAL* 1.3 79.6 - - - +
161D ALA* 1.3 59.9 + - + +
162D GLY* 3.4 3.1 + - - -
164D TYR* 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D HIS 5.7 0.4 - - - +
47D GLN 4.4 18.2 - - - +
48D GLY* 4.9 9.0 - - - -
49D ALA* 5.1 4.9 - - + +
157D ASN 3.0 17.3 + - - +
158D SER* 3.0 6.0 + - - +
160D THR* 1.3 75.4 - - + +
162D GLY* 1.3 57.9 + - - +
163D ASP* 3.3 7.3 + - + +
----------------------------------------------------------
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