Contacts of the helix formed by residues 188 - 200 (chain B) in PDB entry 2Q4E
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 ALA 188 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B PHE* 3.3 49.1 - - + +
161B SER* 5.4 0.2 - - - -
162B PHE* 5.7 2.0 - - + -
184B ALA* 2.8 17.1 + - + +
187B ASP* 1.3 81.0 - - + +
189B GLY* 1.3 66.4 + - - +
190B TRP 3.0 2.6 + - - -
191B TYR* 3.2 17.2 + - - +
192B ALA* 3.8 5.4 + - - +
241B CYS* 3.8 4.7 - - + -
242B SER 4.8 5.2 - - - +
243B PHE* 5.6 2.9 - - + -
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Residues in contact with GLY 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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184B ALA 2.8 14.5 + - - -
185B LEU* 3.0 16.1 + - - -
188B ALA* 1.3 73.2 - - - +
190B TRP* 1.3 64.8 + - - +
191B TYR 3.2 0.5 + - - -
192B ALA* 3.3 9.9 + - - +
193B ILE* 3.0 29.3 + - - +
239B ILE* 5.0 4.9 - - - -
241B CYS* 3.4 18.2 - - - +
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Residues in contact with TRP 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LYS* 3.4 33.0 - - + +
103B PRO* 3.4 19.7 - - + -
104B VAL* 3.8 13.7 - - + -
127B ASP* 3.7 14.8 - - - -
129B THR* 2.9 22.5 + - + +
185B LEU 2.6 11.7 + - - +
186B GLY 3.1 21.8 - - - +
188B ALA 3.0 2.2 + - - +
189B GLY* 1.3 73.7 - - - +
191B TYR* 1.3 81.9 + + + +
193B ILE* 3.2 5.7 + - - +
194B ARG* 3.1 17.1 + - + +
336B SER 4.2 0.7 - - - -
339B THR* 3.2 37.6 + - + -
340B GLN* 2.7 47.1 - - + -
343B VAL* 4.0 17.9 - - + -
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Residues in contact with TYR 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LYS* 2.5 39.9 + - + +
128B GLY 5.5 1.1 + - - -
129B THR* 4.3 9.4 - - + -
130B MSE 5.5 4.0 - - + -
131B TRP* 3.8 24.5 - + - +
160B PHE* 3.7 12.1 - + - -
187B ASP 3.1 22.7 - - - -
188B ALA 3.2 13.1 + - - +
190B TRP* 1.3 80.7 - + - +
192B ALA* 1.3 55.0 + - - +
193B ILE 2.5 1.7 + - - -
194B ARG* 2.3 36.7 + - - -
195B ALA 2.9 8.7 + - - -
265B PHE* 3.9 10.3 - - + -
266B ILE* 3.6 44.5 - - + +
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Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B SER* 3.5 35.2 - - - +
159B CYS* 4.1 9.9 - - - +
160B PHE* 5.5 0.2 - - - +
188B ALA 3.8 4.5 + - - +
189B GLY* 3.3 12.5 + - - +
191B TYR* 1.3 77.2 - - - +
193B ILE* 1.3 60.8 + - - +
195B ALA* 3.6 4.0 + - - +
196B THR* 3.2 27.2 + - - +
239B ILE* 3.4 22.3 - - + +
240B TYR 4.6 1.8 - - - +
265B PHE* 4.1 3.6 - - - -
266B ILE* 5.2 0.6 - - - +
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Residues in contact with ILE 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 4.6 9.0 - - + -
189B GLY 3.1 13.5 - - - +
190B TRP 3.2 6.1 - - - +
191B TYR 2.5 4.8 + - - -
192B ALA* 1.3 71.4 - - - +
194B ARG* 1.3 58.7 + - - +
196B THR* 2.4 25.4 + - - +
197B LEU* 2.9 29.4 + - + +
229B LEU* 5.4 3.1 - - + -
239B ILE* 4.0 20.0 - - + -
339B THR* 4.3 7.9 - - - +
342B VAL* 4.0 30.5 - - + -
343B VAL* 3.4 44.4 - - + +
346B VAL* 5.1 3.6 - - + -
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Residues in contact with ARG 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASP* 3.0 20.6 + - - -
129B THR* 3.7 29.0 + - + +
131B TRP* 3.8 25.1 - - + +
132B VAL* 4.2 13.3 - - + +
190B TRP* 3.1 11.8 + - - +
191B TYR* 2.3 29.8 + - - +
193B ILE* 1.3 69.0 - - - +
195B ALA* 1.3 52.8 + - - +
196B THR 3.1 0.2 + - - -
197B LEU* 3.2 5.8 + - - -
198B LEU* 2.6 64.0 + - + +
332B TRP* 5.5 1.8 - - - -
335B ILE* 2.8 48.6 + - - +
339B THR* 2.9 27.5 + - - +
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Residues in contact with ALA 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B TRP* 3.8 15.0 - - + -
156B VAL* 4.2 4.6 - - - +
158B SER* 3.9 19.3 - - - +
191B TYR 2.9 5.0 + - - +
192B ALA 3.7 8.7 - - - +
194B ARG* 1.3 79.4 - - - +
196B THR* 1.3 57.5 + - - +
198B LEU* 3.8 2.3 - - - +
199B ALA* 3.1 26.3 + - - +
251B ILE* 4.0 18.5 - - + +
265B PHE* 4.0 20.4 - - + -
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Residues in contact with THR 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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156B VAL* 3.7 30.5 - - - +
158B SER* 4.7 1.3 - - - -
192B ALA 3.2 13.8 + - - +
193B ILE* 2.4 34.3 + - - +
195B ALA* 1.3 74.5 - - - +
197B LEU* 1.3 67.1 + - - +
199B ALA* 2.8 3.6 + - - +
200B ASN* 2.8 31.4 + - - -
229B LEU* 4.3 14.5 - - + +
231B TRP* 5.2 1.6 - - - -
237B ALA* 3.9 20.4 - - + -
238B THR 4.7 1.8 - - - +
239B ILE* 3.9 14.1 - - + -
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ILE* 2.9 25.6 + - + +
194B ARG* 3.7 4.9 - - - +
196B THR* 1.3 80.0 + - - +
198B LEU* 1.3 60.1 + - + +
200B ASN* 3.1 10.9 + - - +
202B PHE* 2.7 36.6 + - - +
203B GLU 3.9 6.7 - - - +
204B LEU* 3.7 39.5 - - + +
205B PRO* 4.4 8.3 - - + -
229B LEU* 5.8 1.3 - - + -
231B TRP* 5.3 2.7 - - + -
335B ILE* 5.3 4.7 - - + -
338B LYS* 3.6 13.9 - - + +
339B THR* 3.5 41.3 - - - +
342B VAL* 4.7 3.1 - - + -
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Residues in contact with LEU 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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131B TRP* 3.4 33.0 - - + -
132B VAL* 3.6 20.4 - - + -
137B THR* 4.4 10.3 - - + -
141B LYS* 4.6 17.0 - - + +
144B LEU* 5.4 1.5 - - - +
194B ARG* 2.6 42.3 + - - +
195B ALA* 3.8 5.6 - - - +
197B LEU* 1.3 73.2 - - - +
199B ALA* 1.3 63.3 + - - +
200B ASN 3.3 0.3 + - - -
201B ASN* 3.3 12.6 + - - -
202B PHE* 3.1 38.6 + - + -
331B TYR* 4.1 3.8 - - - +
335B ILE* 3.7 6.1 - - + -
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Residues in contact with ALA 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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144B LEU* 4.1 31.7 - - + +
150B PHE* 6.1 0.2 - - - -
153B LEU* 3.2 25.1 - - + +
156B VAL* 3.5 26.2 - - + -
195B ALA 3.1 14.9 + - - +
196B THR 2.8 8.3 + - - +
198B LEU* 1.3 76.0 - - - +
200B ASN* 1.3 57.6 + - - +
201B ASN 3.1 4.7 + - - -
253B ALA* 5.2 0.2 - - + -
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Residues in contact with ASN 200 (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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153B LEU* 3.5 19.1 - - - +
156B VAL* 3.9 12.5 - - - +
196B THR 2.8 26.9 + - - +
197B LEU 3.1 3.1 + - - +
199B ALA* 1.3 74.5 - - - +
201B ASN* 1.3 57.5 + - - +
202B PHE 3.0 1.8 - - - -
203B GLU* 2.7 44.5 + - - +
231B TRP* 3.5 30.6 - - + -
235B ARG* 3.1 39.4 + - - +
237B ALA* 5.0 0.2 - - - +
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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