Contacts of the helix formed by residues 179 - 195 (chain B) in PDB entry 2HJ9
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 179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B TYR* 3.8 24.2 + - + +
161B THR* 2.5 30.1 + - - +
162B THR* 3.9 13.7 - - - +
178B PHE* 1.3 67.6 - - - +
180B HIS* 1.3 66.5 + - - +
181B ALA* 3.7 11.3 + - - +
182B GLU* 3.1 33.0 + - + +
183B GLY 3.2 18.0 + - - -
185B ARG* 4.6 3.6 + - - -
210B TYR* 5.3 0.5 + - - -
337B SER* 2.9 20.4 + - - +
340B PHE* 3.3 10.5 - - + -
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Residues in contact with HIS 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ASN* 2.8 48.7 + - - -
160B ILE* 4.7 0.9 - - - -
161B THR* 5.4 1.6 - - - -
178B PHE 3.1 10.2 + - - -
179B ASP* 1.3 73.5 + - - +
181B ALA* 1.3 58.0 + - - +
184B SER* 2.9 32.9 + - - -
210B TYR* 3.6 30.7 - + - +
211B ILE* 3.3 14.5 - - + +
214B VAL* 3.5 26.0 - - + -
215B ARG* 2.9 42.9 + - + -
289B TRP* 3.3 9.7 - - - -
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Residues in contact with ALA 181 (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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179B ASP* 3.3 10.4 + - - +
180B HIS* 1.3 75.7 - - - +
182B GLU* 1.3 60.5 + - - +
184B SER 3.5 0.3 + - - -
185B ARG* 2.9 52.8 + - - +
214B VAL* 3.7 17.8 + - + +
218B THR* 3.9 16.7 - - + +
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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
----------------------------------------------------------
179B ASP* 3.1 29.5 + - + +
181B ALA* 1.3 76.2 - - - +
183B GLY* 1.3 63.3 + - - +
185B ARG* 3.0 32.7 + - - +
186B GLU* 2.7 62.9 + - - +
340B PHE* 4.1 9.9 - - + -
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Residues in contact with GLY 183 (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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179B ASP 3.2 10.3 + - - -
182B GLU* 1.3 76.6 - - - +
184B SER* 1.3 54.8 + - - +
186B GLU* 3.4 4.5 + - - +
187B LEU* 3.1 30.8 + - - +
289B TRP* 3.7 20.2 - - - -
308B VAL* 3.7 13.8 - - - +
340B PHE* 3.6 16.6 - - - -
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Residues in contact with SER 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 HIS 2.9 17.0 + - - -
181B ALA 3.9 3.8 - - - -
183B GLY* 1.3 73.0 - - - +
185B ARG* 1.3 60.6 + - - +
187B LEU* 3.4 4.3 + - - +
188B ALA* 2.8 30.2 + - - +
215B ARG* 3.1 29.5 + - - -
218B THR* 4.1 14.4 - - - -
219B PHE* 3.8 7.5 - - - -
262B TYR* 3.1 21.3 + - - -
289B TRP* 3.4 6.0 + - - +
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Residues in contact with ARG 185 (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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32B GLN* 5.7 6.9 - - - +
179B ASP* 4.6 3.6 + - - -
181B ALA* 2.9 42.3 + - - +
182B GLU* 3.0 40.0 + - - +
184B SER* 1.3 76.1 - - - +
186B GLU* 1.3 56.0 + - - +
188B ALA* 3.3 1.4 + - - -
189B THR* 2.8 34.7 + - - +
218B THR* 4.0 15.6 - - + +
222B GLN* 3.1 28.3 + - + +
225B ARG* 6.2 1.8 - - - +
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Residues in contact with GLU 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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182B GLU* 2.7 44.3 + - - +
183B GLY 3.6 7.4 - - - +
184B SER 3.2 0.2 - - - -
185B ARG* 1.3 73.9 - - + +
187B LEU* 1.3 65.0 + - - +
189B THR* 3.2 7.7 + - - -
190B GLU* 3.2 27.5 + - - +
308B VAL* 3.7 5.7 - - + +
340B PHE* 3.4 39.7 + - - +
341B GLU* 4.9 0.2 - - - -
342B ILE* 3.9 25.4 + - + +
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Residues in contact with LEU 187 (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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183B GLY 3.1 12.8 + - - +
184B SER 3.7 6.3 - - - +
186B GLU* 1.3 74.1 - - - +
188B ALA* 1.3 62.1 + - - +
190B GLU* 3.3 3.4 + - - +
191B PHE* 3.0 32.0 + - + -
219B PHE* 3.8 3.1 - - + -
262B TYR* 3.5 15.7 - - + +
287B ASN* 3.4 32.8 - - + +
288B GLY 3.9 4.3 - - - +
289B TRP* 3.5 27.6 - - + +
306B ILE* 4.2 13.5 - - + -
307B THR* 3.8 10.8 - - - -
308B VAL* 3.8 29.4 - - + +
342B ILE* 4.1 8.3 - - + -
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Residues in contact with ALA 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B SER 2.8 21.9 + - - +
185B ARG* 3.5 5.6 - - - +
187B LEU* 1.3 74.7 - - - +
189B THR* 1.3 56.5 + - - +
191B PHE 3.9 0.2 - - - -
192B GLY* 2.9 26.9 + - - -
219B PHE* 3.4 24.8 - - + +
222B GLN* 3.6 32.8 - - + +
223B VAL* 4.0 12.6 - - + +
227B ASN* 4.3 2.6 - - - +
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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 ARG* 2.8 27.0 + - - +
186B GLU* 3.2 8.9 + - - -
188B ALA* 1.3 74.0 - - - +
190B GLU* 1.3 68.5 + - - +
192B GLY* 3.5 3.0 + - - -
193B LYS* 3.3 35.8 + - + +
222B GLN* 3.3 14.4 + - - +
227B ASN* 5.9 0.2 - - - -
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Residues in contact with GLU 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 GLU 3.2 14.6 + - - +
187B LEU 3.7 4.3 - - - +
188B ALA 3.2 0.2 - - - -
189B THR* 1.3 76.8 - - - +
191B PHE* 1.3 57.3 + - - +
193B LYS* 2.7 61.5 + - - +
194B PHE* 3.1 30.4 + - + -
306B ILE* 3.5 31.2 - - + -
342B ILE* 3.8 24.5 - - + +
344B THR* 5.6 0.7 - - - +
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Residues in contact with PHE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU* 3.0 30.8 + - + +
188B ALA 4.1 2.7 - - - +
190B GLU* 1.3 72.9 - - - +
192B GLY* 1.3 61.4 + - - +
193B LYS 3.0 1.6 + - - -
194B PHE* 3.1 16.1 + + - -
195B PHE* 3.2 28.3 + + - -
219B PHE* 3.8 29.6 - + + -
229B PHE* 3.7 8.2 - - + -
260B PHE* 3.4 49.6 - + + -
261B ILE 4.6 1.6 - - - -
262B TYR* 4.6 0.9 - + - -
285B MET* 3.8 18.2 - - + -
286B ILE 4.6 1.6 - - - -
287B ASN* 3.9 29.8 - - + -
306B ILE* 3.9 28.9 - - + -
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Residues in contact with GLY 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 ALA 2.9 15.2 + - - -
189B THR* 3.7 4.7 - - - -
190B GLU 3.2 0.4 + - - -
191B PHE* 1.3 74.2 - - - +
193B LYS* 1.3 57.5 + - - +
195B PHE 3.4 13.7 - - - +
227B ASN* 3.6 39.0 + - - -
229B PHE* 4.0 6.8 - - - -
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Residues in contact with LYS 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* 3.3 22.4 + - + +
190B GLU* 2.7 56.8 + - - +
192B GLY* 1.3 73.4 - - - +
194B PHE* 1.3 70.4 + - + +
195B PHE 3.3 2.4 + - - +
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Residues in contact with PHE 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 GLU* 3.7 37.5 - - + -
191B PHE* 3.1 5.8 + + - +
193B LYS* 1.3 86.6 - - + +
195B PHE* 1.3 80.0 + - + +
196B PRO* 4.5 2.4 - - - +
285B MET* 3.1 37.7 - - + -
306B ILE* 4.2 18.2 - - + -
344B THR* 4.7 16.4 - - + -
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Residues in contact with PHE 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 PHE* 3.2 19.4 + + - -
192B GLY 3.4 17.8 - - - +
193B LYS 3.3 2.1 - - - -
194B PHE* 1.3 89.2 - - + +
196B PRO* 1.4 71.6 - - + +
199B THR* 3.3 26.5 - - + +
227B ASN* 5.6 0.2 + - - -
229B PHE* 3.6 16.3 - - + -
259B ASP* 3.8 38.6 - - + -
260B PHE* 3.5 25.1 - + + -
285B MET* 3.5 36.1 - - + -
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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