Contacts of the helix formed by residues 180 - 198 (chain B) in PDB entry 4R1Z
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 LEU 180 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B MET* 4.4 16.1 - - + +
169B VAL* 6.6 0.2 - - + -
170B LEU* 4.1 33.2 - - + -
178B VAL* 3.3 35.2 + - + +
179B ASP* 1.3 77.8 + - - +
181B GLY* 1.3 67.6 + - - +
182B PRO* 2.7 4.5 - - - +
183B GLU* 2.7 19.8 + - - +
184B LEU* 3.3 14.6 + - + -
326B ILE* 5.0 19.5 - - + -
470B ILE* 6.2 2.7 - - + -
476B LEU* 5.0 8.3 - - + -
502B VAL* 3.5 24.7 - - + +
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Residues in contact with GLY 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ASP* 3.1 9.6 + - - -
180B LEU* 1.3 75.3 - - - +
182B PRO* 1.3 69.1 - - - -
184B LEU* 3.0 10.6 + - - +
185B THR* 2.8 32.3 + - - +
323B LYS* 4.2 27.2 - - - +
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Residues in contact with PRO 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ASP* 3.4 39.9 - - + +
180B LEU 3.3 1.6 - - - +
181B GLY* 1.3 82.4 - - - +
183B GLU* 1.3 60.1 + - + +
185B THR* 3.0 20.9 + - + +
186B ARG* 3.9 5.2 + - - +
208B PHE* 4.6 6.2 - - - -
212B LEU* 5.8 0.2 - - - +
499B LYS* 6.4 0.2 - - + -
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Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B MET* 3.9 14.0 - - + +
169B VAL* 3.3 35.9 - - + +
180B LEU 2.7 12.7 + - - +
182B PRO* 1.3 75.6 - - + +
184B LEU* 1.3 64.6 + - - +
185B THR 3.0 2.0 - - - -
186B ARG* 2.9 41.3 + - - +
187B ALA* 3.0 15.8 + - - +
203B ARG* 2.9 42.7 + - - +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B MET* 3.4 31.7 - - + +
180B LEU* 3.3 20.1 + - + +
181B GLY* 3.0 11.0 + - - +
183B GLU* 1.3 75.8 - - - +
185B THR* 1.3 62.3 + - - +
187B ALA* 3.4 2.4 + - - +
188B VAL* 3.2 26.9 + - - +
319B THR* 3.9 6.7 - - + -
322B LEU* 4.0 41.1 - - + -
323B LYS* 4.2 14.8 - - + -
326B ILE* 4.2 25.4 - - + -
466B PHE* 5.3 5.6 - - + -
470B ILE* 4.9 12.1 - - + -
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Residues in contact with THR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLY 2.8 23.4 + - - +
182B PRO* 3.0 15.3 + - + +
183B GLU 3.0 0.2 - - - -
184B LEU* 1.3 78.0 - - - +
186B ARG* 1.3 54.9 + - - +
188B VAL* 3.4 2.1 + - - +
189B THR* 2.6 38.8 + - - -
208B PHE* 3.8 12.0 - - - -
212B LEU* 4.0 16.7 - - + +
315B VAL* 4.7 6.9 - - + +
319B THR* 3.4 28.3 + - + -
323B LYS* 3.9 13.5 - - - +
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Residues in contact with ARG 186 (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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162B GLU* 5.0 1.4 + - - -
165B SER* 4.9 13.5 + - - -
182B PRO 4.4 0.7 - - - +
183B GLU* 2.9 44.1 + - - +
185B THR* 1.3 80.3 + - - +
187B ALA* 1.3 55.5 + - - +
189B THR* 3.1 1.3 + - - -
190B ASN* 2.7 49.0 + - - +
201B TYR* 2.9 29.2 + - + +
202B LYS* 3.7 3.9 - - - +
203B ARG* 3.5 45.4 - - - +
204B GLY 5.2 0.2 - - - +
208B PHE* 3.9 38.6 - - + -
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Residues in contact with ALA 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B GLU* 3.7 43.8 - - + +
165B SER* 6.0 0.2 - - - -
166B MET* 4.4 11.0 - - + -
183B GLU 3.0 13.7 + - - +
184B LEU* 3.9 4.3 - - + +
186B ARG* 1.3 79.7 - - - +
188B VAL* 1.3 59.2 + - - +
191B VAL* 3.3 24.3 + - - +
466B PHE* 3.8 15.7 - - + -
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Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU 3.2 17.7 + - - +
185B THR 3.8 1.8 - - - +
187B ALA* 1.3 74.8 - - - +
189B THR* 1.3 67.2 + - - +
191B VAL* 3.3 7.6 + - - +
192B VAL* 3.2 18.4 + - - +
314B GLY 3.0 27.1 - - - +
315B VAL 4.2 0.7 - - - +
318B THR* 3.6 12.1 - - + -
319B THR* 3.5 24.2 - - - +
322B LEU* 3.7 27.8 - - + -
462B GLU* 3.3 21.4 - - - +
466B PHE* 4.6 5.2 - - + -
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Residues in contact with THR 189 (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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185B THR* 2.6 24.4 + - - -
186B ARG* 3.4 7.6 - - - -
188B VAL* 1.3 76.7 - - - +
190B ASN* 1.3 52.4 + - - +
192B VAL* 2.8 13.5 + - - +
193B CYS* 2.5 36.1 + - + +
201B TYR* 4.0 16.2 - - + -
208B PHE* 4.0 9.2 - - + -
211B MET* 3.6 26.6 - - + +
212B LEU* 6.0 0.2 - - - +
311B PHE* 3.9 17.3 - - + -
315B VAL* 3.5 21.8 - - + +
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Residues in contact with ASN 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ARG* 4.0 6.9 + - - +
162B GLU* 3.2 40.4 + - + +
186B ARG* 2.7 36.6 + - - +
187B ALA 4.1 0.2 - - - +
189B THR* 1.3 73.4 - - - +
191B VAL* 1.3 56.8 + - - +
193B CYS* 3.6 5.6 - - - +
194B ALA* 3.0 29.6 + - - +
199B SER 4.0 0.7 - - - +
200B SER* 3.2 10.1 - - - -
201B TYR* 2.6 50.3 + - - +
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Residues in contact with VAL 191 (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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148B PHE* 6.1 0.2 - - - -
155B ILE* 4.7 7.5 - - + +
158B ILE* 3.9 10.6 - - + +
159B ILE* 3.9 40.4 - - + -
162B GLU* 4.4 5.2 - - + -
187B ALA 3.3 17.0 + - - +
188B VAL 3.3 7.8 + - - +
189B THR 3.1 0.8 - - - -
190B ASN* 1.3 79.0 - - - +
192B VAL* 1.3 61.6 + - + +
194B ALA* 3.2 3.1 + - - +
195B LEU* 3.0 26.9 + - + +
458B LEU* 4.1 13.7 - - + -
462B GLU* 3.8 27.8 - - - +
466B PHE* 4.5 6.5 - - + -
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B VAL 3.2 9.2 + - - +
189B THR* 2.8 22.7 + - - +
191B VAL* 1.3 77.3 - - + +
193B CYS* 1.3 63.1 + - - +
195B LEU* 3.8 9.2 - - + -
196B CYS* 3.2 24.2 + - - +
310B ILE* 3.6 43.3 - - + +
311B PHE* 4.1 19.1 - - + +
314B GLY* 4.0 25.6 - - - +
315B VAL* 4.2 1.3 - - + +
458B LEU* 5.3 7.4 - - + -
462B GLU* 5.5 3.1 - - - +
600B HEM 5.3 0.9 - - + -
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Residues in contact with CYS 193 (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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189B THR* 2.5 26.3 + - + +
190B ASN* 3.6 10.3 - - - +
192B VAL* 1.3 71.8 - - - +
194B ALA* 1.3 56.5 + - - +
197B PHE* 2.7 48.9 + - - +
198B ASN 3.4 0.3 + - - -
199B SER* 3.0 39.9 + - - +
200B SER 3.9 5.8 - - - -
201B TYR* 3.8 29.8 - - - -
311B PHE* 4.3 7.9 - - + -
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Residues in contact with ALA 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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148B PHE* 3.5 20.9 - - + -
158B ILE* 3.7 27.1 - - + -
161B ARG* 4.5 8.3 - - - +
190B ASN 3.0 19.0 + - - +
191B VAL 3.6 3.8 - - - +
193B CYS* 1.3 73.9 - - - +
195B LEU* 1.3 65.5 + - - +
198B ASN* 3.3 15.3 + - - +
199B SER 3.2 17.9 + - - +
274B ASP* 3.8 0.7 - - - +
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Residues in contact with LEU 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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141B VAL* 5.6 4.5 - - + +
144B ALA 4.4 3.8 - - - +
145B LEU* 3.9 40.2 - - + +
148B PHE* 4.1 31.4 - - + -
155B ILE* 4.8 6.7 - - + -
191B VAL* 3.0 16.8 + - + +
192B VAL* 3.9 12.1 - - + +
193B CYS 3.2 0.2 - - - -
194B ALA* 1.3 76.7 - - - +
196B CYS* 1.3 67.0 + - - +
274B ASP* 3.2 4.2 - - - +
275B LEU* 2.9 46.4 + - + +
310B ILE* 4.7 7.4 - - + -
458B LEU* 4.8 11.0 - - + -
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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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192B VAL* 3.2 22.4 + - - +
195B LEU* 1.3 82.2 - - - +
197B PHE* 1.3 83.5 + - + +
274B ASP* 3.1 18.1 - - - +
275B LEU* 4.1 15.5 - - - -
276B LEU* 3.4 14.0 + - - +
307B VAL* 4.0 14.4 - - + -
310B ILE* 3.7 34.8 - - - -
311B PHE* 4.3 7.0 - - - -
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Residues in contact with PHE 197 (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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193B CYS* 2.7 23.8 + - - +
196B CYS* 1.3 83.6 - - + +
198B ASN* 1.3 60.6 + - - +
199B SER* 2.6 30.6 + - - +
201B TYR* 5.3 0.7 - - - -
255B LEU* 4.7 7.2 - - + -
256B LEU* 4.1 22.4 - - + -
259B LYS* 4.0 43.1 - - + -
263B HIS* 3.4 13.2 + - - -
274B ASP* 2.7 10.0 - - - +
276B LEU* 4.1 9.9 - - + -
307B VAL* 3.4 32.5 - - + -
311B PHE* 3.6 41.1 - + + -
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Residues in contact with ASN 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B PHE* 4.7 10.0 - - - -
194B ALA* 3.3 20.8 + - - +
197B PHE* 1.3 79.3 - - - +
199B SER* 1.3 57.3 + - - +
263B HIS* 4.9 1.8 - - + -
273B ARG* 3.9 37.5 - - + +
274B ASP* 2.8 16.4 + - + +
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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
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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