Contacts of the helix formed by residues 182 - 197 (chain D) in PDB entry 2WJZ
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 SER 182 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123D TRP* 3.4 16.4 - - - -
137D TYR* 3.5 18.6 - - - +
138D ALA 3.0 20.6 + - - -
178D HIS 2.6 22.2 + - - -
179D PRO* 3.1 10.8 + - - -
180D GLU 3.6 0.2 - - - -
181D ALA* 1.3 76.5 - - - +
183D SER* 1.3 73.4 + - - +
185D ILE* 3.2 11.4 - - - +
186D GLY* 3.1 18.7 + - - -
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Residues in contact with SER 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C SER* 3.5 23.8 + - - -
74C ASP* 3.2 35.8 + - - +
75C ILE* 4.2 9.6 - - - -
249C ARG* 4.0 21.8 + - - -
123D TRP* 3.9 5.4 - - - -
179D PRO 4.6 1.2 - - - +
181D ALA 3.5 0.6 + - - -
182D SER* 1.3 83.5 - - - +
184D LYS* 1.3 77.2 + - - +
185D ILE* 4.7 0.4 - - - -
186D GLY* 3.2 5.7 + - - -
187D ARG* 3.3 11.7 + - - +
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Residues in contact with LYS 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C SER 5.5 0.2 - - - +
41C GLU* 4.8 19.3 - - - +
74C ASP* 4.5 1.0 + - - -
251C GLU* 5.9 10.1 - - + -
183D SER* 1.3 86.9 + - - +
185D ILE* 1.3 56.0 + - - +
187D ARG* 3.2 10.6 + - - +
188D LYS* 3.0 26.7 + - - +
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Residues in contact with ILE 185 (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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249C ARG* 5.7 3.1 - - - +
123D TRP* 5.1 0.4 - - + -
133D PRO* 3.8 14.1 - - + +
134D ASN 3.5 25.1 - - - +
135D GLY* 3.6 17.7 - - - -
136D TYR 3.5 20.2 - - - +
137D TYR* 3.6 28.6 + - + +
182D SER 3.2 11.9 - - - +
183D SER* 4.7 0.4 - - - -
184D LYS* 1.3 77.6 - - - +
186D GLY* 1.3 64.3 + - - +
188D LYS* 3.6 6.3 - - + +
189D LEU* 2.9 27.2 + - - +
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Residues in contact with GLY 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D TYR* 4.3 1.8 - - - -
179D PRO* 3.3 30.2 - - - +
182D SER* 3.1 19.8 + - - -
183D SER 3.2 1.7 + - - -
185D ILE* 1.3 75.2 - - - +
187D ARG* 1.3 59.8 + - - +
189D LEU* 3.1 6.9 + - - +
190D LEU* 2.8 34.2 + - - +
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Residues in contact with ARG 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ASP* 5.8 2.0 - - - +
19D GLY 5.3 1.3 - - - +
22D ARG* 3.6 41.4 + - + +
23D ALA* 3.7 20.3 + - + +
25D GLU* 3.5 24.0 + - - +
26D ASN* 3.5 22.4 - - - +
179D PRO 4.3 0.8 + - - -
183D SER 3.3 9.4 + - - +
184D LYS* 3.2 13.2 + - - +
186D GLY* 1.3 76.8 - - - +
188D LYS* 1.3 56.2 + - - +
190D LEU* 3.3 9.9 + - - +
191D GLU* 2.6 72.5 + - - +
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Residues in contact with LYS 188 (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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133D PRO* 4.4 17.3 - - + +
184D LYS 3.0 13.2 + - - +
185D ILE* 3.6 12.6 - - + +
186D GLY 3.2 0.2 - - - -
187D ARG* 1.3 73.1 - - - +
189D LEU* 1.3 60.8 + - - +
191D GLU* 3.5 15.9 + - - +
192D LYS* 3.0 28.4 + - - +
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Residues in contact with LEU 189 (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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128D PHE* 4.0 11.7 - - + -
132D PHE* 3.4 39.5 - - + -
133D PRO* 3.9 11.0 - - + +
137D TYR* 3.9 23.6 - - + +
175D PHE* 4.1 18.2 - - + -
177D PHE* 4.3 3.6 - - + -
179D PRO* 4.4 12.1 - - + -
185D ILE 2.9 15.2 + - - +
186D GLY* 3.1 8.3 + - - +
188D LYS* 1.3 76.6 - - - +
190D LEU* 1.3 68.3 + - + +
192D LYS* 3.2 5.3 + - - +
193D VAL* 3.0 38.0 + - + +
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Residues in contact with LEU 190 (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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16D LEU* 4.8 7.2 - - + -
19D GLY* 3.7 33.7 - - - +
20D VAL* 4.2 10.1 - - + +
23D ALA* 3.8 12.3 - - + -
47D PHE* 4.6 25.7 - - + -
83D VAL* 6.1 1.6 - - + -
175D PHE* 6.4 0.9 - - + -
179D PRO* 3.8 35.4 - - + +
180D GLU* 4.6 2.2 - - - +
186D GLY 2.8 20.4 + - - +
187D ARG* 3.7 6.3 - - - +
189D LEU* 1.3 79.8 - - + +
191D GLU* 1.3 64.5 + - - +
193D VAL* 3.2 8.1 + - + +
194D ILE* 3.0 26.4 + - + +
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Residues in contact with GLU 191 (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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23D ALA* 3.9 21.9 - - + +
26D ASN* 4.6 4.9 + - - -
27D PHE* 4.5 8.7 - - + -
187D ARG* 2.6 58.2 + - - +
188D LYS* 3.5 16.5 - - + +
189D LEU 3.3 0.2 - - - -
190D LEU* 1.3 72.5 - - - +
192D LYS* 1.3 56.9 + - - +
194D ILE* 3.1 8.5 + - - +
195D GLU* 2.8 48.8 + - - +
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Residues in contact with LYS 192 (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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131D THR* 3.7 43.1 - - + +
132D PHE* 3.8 13.7 - - + -
133D PRO* 5.2 3.8 - - + -
188D LYS 3.0 14.5 + - - +
189D LEU* 3.5 9.0 - - - +
191D GLU* 1.3 76.4 - - - +
193D VAL* 1.3 56.5 + - - +
195D GLU* 3.2 27.6 + - + +
196D CYS* 3.0 32.3 + - - -
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Residues in contact with VAL 193 (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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45D LEU* 3.9 20.1 - - + +
47D PHE* 4.1 15.0 - - + -
79D TYR* 5.4 2.9 - - + -
81D VAL* 4.1 17.0 - - + -
132D PHE* 3.7 20.4 - - + -
173D LEU* 4.5 5.6 - - + -
175D PHE* 3.8 23.8 - - + -
189D LEU* 3.0 23.0 + - + +
190D LEU* 3.2 13.0 + - + +
192D LYS* 1.3 73.8 - - - +
194D ILE* 1.3 66.4 + - - +
196D CYS* 3.3 13.5 + - - +
197D SER* 3.3 13.7 + - - -
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Residues in contact with ILE 194 (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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1D MET* 4.2 17.7 - - + -
3D ILE* 4.2 12.3 - - + -
20D VAL* 4.6 6.5 - - + +
23D ALA* 4.2 12.1 - - + +
24D SER* 4.0 36.6 - - - +
27D PHE* 4.2 28.5 - - + -
30D VAL* 5.6 1.1 - - + -
45D LEU* 4.1 16.8 - - + -
47D PHE* 5.8 1.8 - - + -
190D LEU* 3.0 17.0 + - + +
191D GLU* 3.4 6.3 - - - +
193D VAL* 1.3 77.5 - - + +
195D GLU* 1.3 63.1 + - - +
197D SER* 2.8 24.5 + - - -
198D LEU* 3.6 10.5 - - + +
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Residues in contact with GLU 195 (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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27D PHE* 3.5 26.5 - - + -
191D GLU* 2.8 39.5 + - - +
192D LYS* 3.2 38.4 + - + +
194D ILE* 1.3 72.0 - - - +
196D CYS* 1.3 61.0 + - - +
198D LEU* 3.8 26.8 - - + +
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Residues in contact with CYS 196 (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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79D TYR* 3.5 35.4 + - + +
131D THR* 4.0 25.6 - - - -
132D PHE* 4.5 9.4 - - + -
171D ARG* 4.6 2.1 + - - -
173D LEU* 5.7 2.0 - - + -
192D LYS* 3.0 26.3 + - - +
193D VAL* 3.5 8.3 - - - +
194D ILE 3.0 0.2 - - - -
195D GLU* 1.3 75.5 - - - +
197D SER* 1.3 52.7 + - - +
198D LEU* 2.7 22.7 + - - +
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Residues in contact with SER 197 (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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1D MET* 3.1 20.1 - - - +
44D ASP* 4.3 13.6 - - - +
45D LEU* 3.8 14.9 - - - +
79D TYR* 3.5 34.3 - - - -
193D VAL 3.3 6.8 + - - -
194D ILE* 2.8 23.4 + - - -
196D CYS* 1.3 74.5 - - - +
198D LEU* 1.3 68.8 + - - +
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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