Contacts of the helix formed by residues 175 - 195 (chain B) in PDB entry 3H44
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 ASP 175 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B MET* 4.0 3.7 - - - +
116B LEU 5.2 4.6 + - - +
124B GLU* 5.4 1.3 - - + -
173B LEU* 3.1 22.3 - - + +
174B PHE* 1.3 78.5 - - - +
176B GLU* 1.3 58.6 + - - +
177B SER* 2.8 34.3 + - - -
178B ALA* 3.0 22.8 + - + +
179B LYS* 3.0 26.9 + - - +
181B ARG* 4.8 0.6 + - - -
238B ARG* 4.7 1.8 - - - +
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Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B PHE 3.5 2.1 + - - -
175B ASP* 1.3 76.7 + - - +
177B SER* 1.3 60.7 + - - +
179B LYS* 2.7 32.6 + - - +
180B ASP* 3.2 30.2 + - - +
236B ASP* 5.0 6.2 - - - +
237B VAL 5.8 0.2 + - - -
238B ARG* 3.0 34.6 + - - +
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Residues in contact with SER 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ASP* 2.8 12.3 + - - -
176B GLU* 1.3 74.3 - - - +
178B ALA* 1.3 66.0 + - - +
179B LYS 3.2 0.4 - - - -
180B ASP* 3.6 10.3 + - - +
181B ARG* 3.1 45.8 + - - +
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Residues in contact with ALA 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B MET* 4.3 6.5 - - + -
116B LEU* 4.2 19.0 - - + +
124B GLU* 3.1 23.3 - - + +
175B ASP* 3.0 27.0 + - + +
177B SER* 1.3 76.5 + - - +
179B LYS* 1.3 57.7 + - - +
181B ARG* 3.4 11.4 + - - +
182B GLU* 2.9 34.5 + - - +
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Residues in contact with LYS 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PHE* 3.7 21.6 - - + -
113B MET* 3.9 15.4 - - + +
174B PHE 5.1 1.1 - - - +
175B ASP 3.0 17.8 + - - +
176B GLU* 2.7 45.8 + - - +
177B SER 3.2 0.2 - - - -
178B ALA* 1.3 76.7 - - - +
180B ASP* 1.3 89.2 + - - +
181B ARG 3.1 0.3 + - - -
183B VAL* 3.1 23.3 + - + +
226B LEU 5.9 0.7 - - - -
227B GLU* 6.5 1.1 - - - -
237B VAL* 4.1 25.4 - - + +
238B ARG* 3.8 25.8 - - + +
241B LEU* 4.7 6.7 - - + -
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Residues in contact with ASP 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLU* 3.2 20.5 + - - +
177B SER* 3.9 10.6 - - - +
178B ALA 3.5 0.2 - - - -
179B LYS* 1.3 97.8 + - - +
181B ARG* 1.3 58.1 + - + +
183B VAL* 3.2 21.9 - - - +
184B ASN* 3.4 7.6 - - - +
227B GLU* 4.2 14.9 - - - +
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Residues in contact with ARG 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLU* 2.9 40.9 + - - -
175B ASP* 4.8 1.0 + - - -
177B SER* 3.1 37.2 + - - +
178B ALA* 3.4 9.8 - - - +
179B LYS 3.1 0.8 - - - -
180B ASP* 1.3 77.9 - - + +
182B GLU* 1.3 59.5 + - - +
183B VAL 3.1 1.6 - - - -
184B ASN* 2.9 30.0 + - - +
825B THR* 3.5 16.0 + - - +
826B LYS* 3.3 36.1 - - - +
828B GLN* 3.1 24.7 - - + +
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Residues in contact with GLU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PHE* 4.0 3.4 - - + -
112B HIS* 3.1 31.8 + - + +
113B MET* 4.1 9.6 - - - -
116B LEU* 3.7 26.6 - - + +
178B ALA 2.9 21.6 + - - +
181B ARG* 1.3 71.0 - - - +
183B VAL* 1.3 64.4 + - - +
184B ASN 3.1 1.0 + - - -
185B ALA* 3.3 15.7 + - - +
186B VAL* 3.5 11.3 + - - +
824B ARG* 3.1 30.6 + - - -
825B THR* 4.3 13.9 - - - +
828B GLN* 3.0 20.9 + - - +
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PHE* 3.8 14.5 - - + -
179B LYS* 3.1 11.5 + - + +
180B ASP* 3.2 24.7 - - - +
181B ARG 3.0 0.6 + - - -
182B GLU* 1.3 76.2 - - - +
184B ASN* 1.3 57.9 + - - +
186B VAL* 3.3 4.9 + - - +
187B ASP* 3.0 25.9 + - - +
223B LYS* 4.0 28.3 - - - +
226B LEU* 3.8 33.0 - - + +
227B GLU* 3.5 27.6 - - + +
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Residues in contact with ASN 184 (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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180B ASP 3.4 11.6 - - - +
181B ARG* 2.9 21.9 + - - +
183B VAL* 1.3 75.4 - - - +
185B ALA* 1.3 56.0 + - - +
187B ASP* 3.3 6.9 + - - +
188B SER* 2.8 36.4 + - - -
223B LYS* 2.9 42.6 - - - +
828B GLN* 3.6 24.5 - - + +
830B GLY* 6.2 0.4 - - - -
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Residues in contact with ALA 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B HIS* 4.4 1.3 - - - +
182B GLU* 3.3 30.9 + - - +
184B ASN* 1.3 74.9 - - - +
186B VAL* 1.3 58.3 + - - +
188B SER* 3.4 7.8 - - - -
189B GLU* 2.8 31.4 + - - +
824B ARG* 3.5 26.0 - - - +
828B GLN* 3.2 18.7 - - - +
831B TYR* 3.6 7.7 - - + +
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Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B HIS* 3.9 7.9 - - + +
109B PHE* 4.0 18.6 - - + -
112B HIS* 3.9 33.7 - - + +
182B GLU 3.5 9.8 + - - +
183B VAL* 3.3 8.8 + - - +
184B ASN 3.2 0.6 - - - -
185B ALA* 1.3 74.1 - - - +
187B ASP* 1.3 65.7 + - - +
189B GLU* 3.0 19.5 + - - +
190B HIS* 3.0 12.5 + - - +
220B THR* 3.4 25.7 - - + +
221B GLY 3.7 6.7 - - - +
222B ASN* 4.3 0.4 - - - +
226B LEU* 3.6 22.4 - - + -
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Residues in contact with ASP 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B VAL 3.0 11.6 + - - +
184B ASN* 3.6 11.6 + - - +
186B VAL* 1.3 76.3 - - - +
188B SER* 1.3 50.7 + - - +
190B HIS* 3.3 4.0 + - - +
191B GLU* 2.8 45.1 + - - +
222B ASN* 3.4 15.7 - - - +
223B LYS* 3.0 47.8 + - + +
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Residues in contact with SER 188 (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 ASN 2.8 21.4 + - - -
185B ALA* 3.4 2.7 - - - -
187B ASP* 1.3 70.4 + - - +
189B GLU* 1.4 64.8 + - - +
191B GLU* 3.2 8.1 + - - +
192B LYS* 3.0 24.6 + - - +
788B ASN* 4.9 9.4 + - - -
830B GLY* 3.7 8.8 - - - -
831B TYR* 3.0 37.5 + - - +
851B GLN 4.9 2.3 + - - -
852B SER* 5.5 0.3 - - - -
853B GLU 5.9 0.2 + - - -
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Residues in contact with GLU 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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1B ZN 1.7 35.5 - - - -
108B HIS* 2.2 16.7 + - + -
112B HIS* 1.9 19.2 + - + -
185B ALA 2.8 16.3 + - - +
186B VAL* 3.0 8.1 + - - +
188B SER* 1.4 71.5 - - - +
190B HIS* 1.3 62.6 + - - +
192B LYS* 3.4 16.7 + - - +
193B ASN* 3.4 18.5 + - - +
220B THR* 4.5 5.8 - - + +
831B TYR* 3.2 40.1 + - + +
18D SER* 3.8 4.7 + - - -
19D ARG 2.6 23.7 + - - +
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Residues in contact with HIS 190 (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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186B VAL 3.0 7.3 + - - +
187B ASP* 3.7 7.9 - - - +
189B GLU* 1.3 73.8 - - - +
191B GLU* 1.3 71.4 + - - +
193B ASN* 2.9 15.0 + - - +
194B VAL* 2.9 30.3 + - + +
218B PHE* 3.2 34.9 - + - -
220B THR* 4.2 9.6 - - + +
221B GLY 3.7 17.9 - - - +
222B ASN* 3.5 26.8 + - + -
495B TRP 3.5 22.4 + - - -
496B TYR* 3.9 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
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187B ASP* 2.8 35.0 + - - +
188B SER* 3.2 9.8 + - - +
190B HIS* 1.3 74.0 - - - +
192B LYS* 1.3 64.9 + - - +
193B ASN 2.9 1.9 + - - -
194B VAL* 3.0 33.2 + - - +
195B MET* 4.2 2.8 + - - +
786B HIS* 5.1 3.5 + - - -
787B ASN* 4.2 11.8 + - - +
788B ASN* 3.6 28.7 - - - +
853B GLU* 6.1 1.0 - - + +
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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
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188B SER 3.0 9.0 + - - +
189B GLU* 3.4 11.5 + - - +
191B GLU* 1.3 77.0 - - - +
193B ASN* 1.3 84.3 + - - +
194B VAL 3.8 0.2 + - - -
195B MET 4.4 0.2 + - - -
196B ASN* 4.5 4.2 + - - +
199B TRP* 5.3 3.2 - - - +
677B GLN* 3.2 45.4 + - - +
679B HIS* 5.9 1.6 - - - -
786B HIS* 4.2 7.0 - - - -
788B ASN* 5.8 0.2 - - - -
831B TYR* 4.1 25.2 - - + -
832B ILE* 3.8 26.9 - - + -
851B GLN* 4.0 14.3 - - - +
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Residues in contact with ASN 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 GLU* 3.4 16.6 + - - +
190B HIS* 2.9 11.2 + - - +
192B LYS* 1.3 107.2 + - - +
194B VAL* 1.3 66.0 + - - +
195B MET 3.1 3.4 - - - -
196B ASN* 3.0 21.5 + - - +
199B TRP* 3.4 54.5 + - + +
220B THR* 5.1 7.1 + - - +
496B TYR* 3.5 16.6 + - + +
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Residues in contact with VAL 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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190B HIS* 2.9 40.8 + - + +
191B GLU* 3.0 31.3 + - - +
193B ASN* 1.3 76.7 - - - +
195B MET* 1.3 74.1 + - + +
200B ARG* 2.9 33.3 + - - +
495B TRP 4.7 2.7 - - - +
496B TYR* 3.7 31.9 - - - +
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Residues in contact with MET 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 4.2 2.3 + - - +
192B LYS 4.4 1.0 + - - -
193B ASN 3.1 0.8 - - - -
194B VAL* 1.3 91.4 - - + +
196B ASN* 1.3 60.2 + - - +
197B ASP* 3.8 0.9 + - - +
200B ARG* 4.2 14.1 - - - +
307B ILE* 3.5 39.2 - - - +
496B TYR 5.9 0.2 - - - +
675B ALA 5.1 2.4 - - - +
785B VAL* 3.7 28.3 - - + +
786B HIS* 3.3 37.9 + - + +
787B ASN 5.2 1.1 - - - +
961B ARG* 4.1 23.3 - - - +
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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