Contacts of the helix formed by residues 186 - 201 (chain B) in PDB entry 2XBM
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 MET 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLU* 3.2 41.1 - - - +
154B PRO* 3.8 23.8 - - + +
155B THR* 3.8 28.9 - - + -
158B GLU* 3.3 34.3 - - + +
183B ASN* 3.2 25.9 + - - +
184B PRO 3.5 0.6 - - - -
185B TYR* 1.3 80.6 - - + +
187B PRO* 1.4 73.5 - - + +
188B THR 3.4 0.2 - - - -
189B VAL* 3.1 22.2 + - + +
190B ILE* 3.2 11.5 + - - +
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Residues in contact with PRO 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 4.1 9.6 - - + -
11B GLU* 3.8 19.1 - - - +
158B GLU* 4.3 3.6 - - - +
185B TYR 3.6 5.1 - - - +
186B MET* 1.4 88.3 - - + +
188B THR* 1.3 65.7 + - + +
190B ILE* 3.2 19.9 + - + +
191B GLU* 3.3 15.3 + - - +
151D SER* 5.0 2.7 + - - +
156D VAL* 4.5 21.8 - - + -
160D ARG* 4.0 22.6 + - - +
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Residues in contact with THR 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLU* 3.1 26.6 + - - +
162B ILE* 3.4 15.6 - - - +
186B MET 3.4 0.6 - - - -
187B PRO* 1.3 77.8 - - + +
189B VAL* 1.3 63.5 + - - +
191B GLU* 3.5 17.9 + - - +
192B HIS* 3.1 36.5 + - - -
160D ARG* 5.5 3.8 - - - +
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLU* 3.8 25.6 - - + +
161B THR* 3.4 32.3 - - + -
162B ILE* 4.2 4.7 - - + -
165B LEU* 4.4 4.7 - - + -
181B VAL* 4.4 3.4 - - + -
183B ASN 3.2 23.8 - - - +
184B PRO* 4.0 4.3 - - + -
186B MET* 3.1 13.6 + - + +
188B THR* 1.3 76.0 - - - +
190B ILE* 1.3 59.5 + - - +
192B HIS* 3.2 5.3 + - - +
193B LEU* 2.9 49.2 + - + +
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Residues in contact with ILE 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 6.3 0.2 - - - -
184B PRO 3.4 19.5 - - - +
185B TYR* 3.6 26.9 - - - +
186B MET 3.2 6.8 + - - +
187B PRO* 3.2 12.1 + - + +
189B VAL* 1.3 77.8 - - - +
191B GLU* 1.3 61.5 + - - +
193B LEU* 4.6 4.7 - - + -
194B GLU* 3.1 23.6 + - - +
227B ILE* 3.9 11.0 - - + +
228B VAL* 4.3 18.2 - - + +
231B VAL* 5.0 12.1 - - + -
151D SER* 4.3 6.5 - - - +
152D PRO* 3.7 28.7 - - + -
153D SER* 4.4 12.1 - - - +
156D VAL* 5.7 2.9 - - + -
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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
----------------------------------------------------------
187B PRO 3.3 11.1 + - - +
188B THR* 3.7 26.8 - - - +
189B VAL 3.3 0.4 - - - -
190B ILE* 1.3 77.6 - - - +
192B HIS* 1.3 63.3 + - + +
194B GLU* 3.6 3.3 + - - +
195B ARG* 3.3 42.9 + - - +
149D GLU* 2.6 30.0 - - - +
150D SER 2.8 18.7 - - - +
151D SER* 4.7 2.0 - - - +
152D PRO* 3.8 23.3 - - + -
160D ARG* 4.9 8.0 + - - -
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Residues in contact with HIS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ILE* 3.9 34.8 + - + +
165B LEU* 4.4 16.7 - - + +
166B LYS* 4.0 21.8 - - - +
188B THR* 3.1 25.5 + - - +
189B VAL* 3.2 9.3 + - - +
191B GLU* 1.3 78.7 - - + +
193B LEU* 1.3 65.2 + - - +
195B ARG* 3.2 34.4 + - - +
196B LEU* 3.0 32.1 + - + +
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 3.8 22.7 - - + -
181B VAL* 4.0 26.7 - - + -
184B PRO* 4.2 9.6 - - + +
189B VAL* 2.9 39.4 + - + +
190B ILE* 4.1 1.3 - - + +
192B HIS* 1.3 75.5 - - - +
194B GLU* 1.3 58.5 + - - +
196B LEU* 3.3 8.3 + - + +
197B GLN* 2.9 31.0 + - - +
204B LEU* 3.7 31.4 - - + -
219B TRP* 5.2 10.6 - - + -
227B ILE* 3.5 20.4 - - + +
231B VAL* 5.5 0.2 - - + -
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Residues in contact with GLU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ILE 3.1 19.9 + - - +
191B GLU 3.6 4.9 - - - +
192B HIS 3.2 0.2 - - - -
193B LEU* 1.3 78.4 - - - +
195B ARG* 1.3 62.8 + - + +
197B GLN* 3.4 9.6 + - - +
198B ARG* 3.1 50.2 + - - +
227B ILE* 3.7 21.0 + - - +
18D ASN* 2.8 49.2 - - - +
152D PRO* 3.6 24.4 - - + +
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Residues in contact with ARG 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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191B GLU* 3.3 24.0 + - - +
192B HIS* 3.2 46.9 + - - +
194B GLU* 1.3 80.4 - - + +
196B LEU* 1.3 62.9 + - + +
198B ARG* 3.5 13.4 - - - +
199B LYS* 3.4 38.1 + - - +
22D ARG* 5.7 10.7 - - - +
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Residues in contact with LEU 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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165B LEU* 3.9 45.1 - - + +
169B GLU* 3.4 36.3 - - + +
192B HIS* 3.0 22.7 + - + +
193B LEU* 3.6 7.4 - - - +
194B GLU 3.2 0.2 - - - -
195B ARG* 1.3 74.4 - - + +
197B GLN* 1.3 56.1 + - - +
198B ARG 3.2 1.3 - - - -
199B LYS* 3.1 8.5 + - - +
200B HIS* 2.7 46.3 + - + +
219B TRP* 3.6 25.8 - - + -
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Residues in contact with GLN 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 LEU 2.9 17.6 + - - +
194B GLU* 3.9 12.1 + - - +
196B LEU* 1.3 76.6 - - - +
198B ARG* 1.3 59.2 + - - +
201B GLY* 2.7 42.5 + - - +
202B GLY 3.1 28.9 - - - +
203B MET* 4.4 1.3 - - - +
219B TRP* 4.3 5.9 - - - +
224B THR* 5.7 0.7 - - - -
225B GLY 2.9 29.6 + - - +
227B ILE* 3.7 19.1 - - + +
18D ASN 3.7 21.4 + - - -
19D GLN* 4.8 4.8 - - - +
20D LEU 5.3 2.2 + - - -
21D SER* 5.7 0.9 - - - -
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Residues in contact with ARG 198 (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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194B GLU* 3.1 49.5 + - - +
195B ARG* 3.5 15.4 - - - +
197B GLN* 1.3 81.3 - - - +
199B LYS* 1.3 59.7 + - - +
201B GLY 4.8 0.2 + - - -
17D LEU* 2.7 36.4 + - - +
18D ASN* 3.6 4.8 + - - +
20D LEU 3.5 22.4 + - - +
21D SER* 4.2 4.4 - - - +
22D ARG* 3.3 55.4 + - + +
25D PHE* 3.4 44.9 - - - -
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Residues in contact with LYS 199 (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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169B GLU* 3.9 22.8 + - + +
195B ARG* 3.4 27.2 + - - +
196B LEU* 3.1 11.8 + - - +
198B ARG* 1.3 82.7 - - - +
200B HIS* 1.3 81.0 + - + +
201B GLY 3.6 0.7 - - - -
22D ARG* 4.7 29.4 - - + +
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Residues in contact with HIS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B GLU* 3.6 27.7 + - + +
172B LEU* 3.5 40.7 + - + +
173B LYS* 4.9 5.6 + - - -
177B PHE* 3.8 21.5 - - + -
196B LEU* 2.7 31.2 + - + +
199B LYS* 1.3 95.4 + - + +
201B GLY* 1.3 62.8 + - - +
202B GLY 3.9 0.3 + - - -
219B TRP* 3.9 17.5 - + + -
221B SER 5.3 1.2 - - - +
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Residues in contact with GLY 201 (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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177B PHE* 4.0 0.4 - - - -
197B GLN* 2.7 27.4 + - - -
198B ARG 4.7 0.2 - - - -
199B LYS 3.6 1.2 - - - -
200B HIS* 1.3 83.2 - - - +
202B GLY* 1.3 62.9 + - - -
219B TRP* 3.0 23.0 + - - -
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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