Contacts of the helix formed by residues 182 - 197 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ASP 3.2 0.4 + - - -
123B TRP* 3.4 16.7 - - - -
137B TYR* 3.5 18.6 - - - +
138B ALA 3.0 20.1 + - - -
178B HIS 2.6 23.6 + - - -
179B PRO 3.1 11.0 + - - -
181B ALA* 1.3 77.2 - - - +
183B SER* 1.3 73.8 + - - +
185B ILE* 3.2 18.4 - - - +
186B GLY* 3.2 10.7 + - - -
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Residues in contact with SER 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A SER* 3.0 33.4 + - - -
74A ASP* 2.9 38.8 + - - +
75A ILE* 3.7 12.8 - - - -
249A ARG* 4.1 15.3 + - - -
123B TRP* 3.9 6.3 - - - -
179B PRO 4.6 0.9 - - - +
181B ALA 3.8 0.4 + - - -
182B SER* 1.3 82.4 - - - +
184B LYS* 1.3 72.7 + - - +
186B GLY* 3.2 5.5 + - - -
187B ARG* 3.3 10.2 + - - +
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Residues in contact with LYS 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A SER* 5.3 0.4 - - - +
41A GLU* 2.8 57.2 - - - +
74A ASP* 4.1 1.9 + - - +
183B SER* 1.3 86.5 + - - +
185B ILE* 1.3 57.0 + - - +
187B ARG* 3.2 10.9 + - - +
188B LYS* 3.0 27.5 + - - +
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Residues in contact with ILE 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ARG* 5.2 5.6 - - - +
251A GLU* 6.2 4.3 - - - -
123B TRP* 5.1 0.4 - - + -
133B PRO* 3.8 13.7 - - + +
134B ASN 3.5 24.9 - - - +
135B GLY* 3.6 17.5 - - - -
136B TYR 3.4 20.2 - - - +
137B TYR* 3.6 27.7 + - + +
182B SER 3.2 14.8 - - - +
183B SER* 4.7 0.2 - - - -
184B LYS* 1.3 77.3 - - - +
186B GLY* 1.3 65.2 + - - +
188B LYS* 3.5 6.3 + - + +
189B LEU* 2.9 26.5 + - - +
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Residues in contact with GLY 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B TYR* 4.3 2.0 - - - -
179B PRO* 3.3 28.4 - - - +
182B SER* 3.2 14.6 + - - -
183B SER 3.2 1.3 + - - -
185B ILE* 1.3 80.1 - - - +
187B ARG* 1.3 60.0 + - - +
189B LEU* 3.1 8.5 + - - +
190B LEU* 2.8 34.7 + - - +
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Residues in contact with ARG 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASP* 5.3 3.6 - - - +
19B GLY 5.3 1.1 - - - +
22B ARG* 3.6 41.7 + - + +
23B ALA* 3.7 19.8 + - + +
25B GLU* 3.5 24.4 + - - +
26B ASN* 3.5 22.4 - - - +
179B PRO 4.3 1.2 + - - -
183B SER 3.3 10.0 + - - +
184B LYS* 3.2 12.8 + - - +
186B GLY* 1.3 75.4 - - - +
188B LYS* 1.3 50.6 + - - +
190B LEU* 3.2 9.8 + - - +
191B GLU* 2.6 75.6 + - - +
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Residues in contact with LYS 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PRO* 4.4 17.3 - - + +
184B LYS 3.0 13.2 + - - +
185B ILE* 3.7 12.6 - - + +
186B GLY 3.3 0.2 - - - -
187B ARG* 1.3 75.5 - - - +
189B LEU* 1.3 57.4 + - - +
191B GLU* 3.5 22.2 + - - +
192B LYS* 3.0 28.2 + - - +
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Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 4.0 11.2 - - + -
132B PHE* 3.3 38.4 - - + -
133B PRO* 3.9 7.1 - - + +
137B TYR* 3.9 27.1 - - + +
175B PHE* 4.1 18.6 - - + -
177B PHE* 4.3 3.6 - - + -
179B PRO* 4.4 12.6 - - + -
185B ILE 2.9 15.7 + - - +
186B GLY 3.3 8.3 - - - +
188B LYS* 1.3 76.3 - - - +
190B LEU* 1.3 71.0 + - + +
192B LYS* 3.2 5.7 + - - +
193B VAL* 3.0 38.0 + - + +
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 4.8 7.2 - - + -
19B GLY* 3.7 32.8 - - - +
20B VAL* 4.3 9.6 - - + +
23B ALA* 3.8 12.3 - - + -
47B PHE* 4.6 25.7 - - + -
83B VAL* 6.1 1.8 - - + -
175B PHE* 6.4 0.4 - - + -
179B PRO* 3.8 34.8 - - + -
180B GLU* 4.6 2.0 - - - +
186B GLY 2.8 20.6 + - - +
187B ARG* 3.6 6.5 - - - +
189B LEU* 1.3 79.7 - - + +
191B GLU* 1.3 65.3 + - - +
193B VAL* 3.2 8.8 + - + +
194B ILE* 3.0 27.0 + - + +
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ALA* 3.8 22.8 - - + +
26B ASN* 4.5 5.1 + - - -
27B PHE* 4.2 9.4 - - + -
187B ARG* 2.6 58.0 + - - +
188B LYS* 3.6 24.4 - - + +
189B LEU 3.3 0.2 - - - -
190B LEU* 1.3 72.1 - - - +
192B LYS* 1.3 57.0 + - - +
194B ILE* 3.1 8.4 + - - +
195B GLU* 2.8 48.5 + - - +
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Residues in contact with LYS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B THR* 3.7 42.8 - - + +
132B PHE* 3.8 14.1 - - + -
133B PRO* 5.2 4.0 - - + -
188B LYS 3.0 15.0 + - - +
189B LEU* 3.2 9.4 + - - +
191B GLU* 1.3 76.1 - - - +
193B VAL* 1.3 57.3 + - - +
195B GLU* 3.2 27.6 + - + +
196B CYS* 3.0 31.4 + - - -
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 3.9 20.4 - - + -
47B PHE* 4.1 14.4 - - + -
79B TYR* 5.4 2.7 - - + -
81B VAL* 4.2 17.9 - - + -
132B PHE* 3.7 19.3 - - + -
173B LEU* 4.5 4.9 - - + -
175B PHE* 3.8 24.2 - - + -
189B LEU* 3.0 22.6 + - + +
190B LEU* 3.2 13.4 + - + +
192B LYS* 1.3 72.7 - - - +
194B ILE* 1.3 65.6 + - - +
196B CYS* 3.3 14.7 + - - +
197B SER* 3.3 13.9 + - - -
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 4.2 17.5 - - + -
3B ILE* 4.2 12.3 - - + -
20B VAL* 4.6 6.1 - - + +
23B ALA* 4.2 11.9 - - + +
24B SER* 4.0 37.0 - - - +
27B PHE* 4.2 29.2 - - + -
45B LEU* 4.1 17.7 - - + -
47B PHE* 5.8 1.8 - - + -
190B LEU* 3.0 17.9 + - + +
191B GLU* 3.4 7.0 - - - +
193B VAL* 1.3 77.5 - - + +
195B GLU* 1.3 61.6 + - - +
197B SER* 2.8 24.0 + - - -
198B LEU* 3.6 10.1 - - + +
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Residues in contact with GLU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PHE* 3.5 28.0 - - + -
191B GLU* 2.8 41.0 + - - +
192B LYS* 3.2 39.2 + - + +
194B ILE* 1.3 71.7 - - - +
196B CYS* 1.3 61.0 + - - +
198B LEU* 3.8 26.7 - - + +
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Residues in contact with CYS 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B TYR* 3.4 34.5 + - + +
131B THR* 4.1 24.9 - - - -
132B PHE* 4.6 8.3 - - + -
173B LEU* 5.7 2.9 - - + -
192B LYS* 3.0 27.4 + - - +
193B VAL* 3.5 8.3 - - - +
194B ILE 3.0 0.2 - - - -
195B GLU* 1.3 74.2 - - - +
197B SER* 1.3 53.4 + - - +
198B LEU* 2.7 22.7 + - - +
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Residues in contact with SER 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.1 19.9 - - - +
44B ASP* 4.3 13.1 - - - +
45B LEU* 3.8 16.0 - - - +
79B TYR* 3.5 32.3 - - - -
193B VAL 3.3 7.8 + - - -
194B ILE* 2.8 21.0 + - - -
196B CYS* 1.3 76.0 - - - +
198B LEU* 1.3 67.9 + - - +
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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
------------------------------------------------------------
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