Contacts of the helix formed by residues 181 - 197 (chain B) in PDB entry 1GQF
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 GLY 181 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B ASN* 1.3 71.9 - - - +
182B THR* 1.3 62.6 + - - +
183B ASP 3.4 2.5 - - - -
184B LYS* 3.2 7.9 + - - +
185B ASP* 3.2 25.6 + - - -
344B GLY* 3.8 23.4 - - - -
346B GLY* 3.7 8.2 - - - -
1404B SO4 2.9 23.9 + - - -
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Residues in contact with THR 182 (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 ASN* 2.6 24.4 + - - +
170B ASN 4.2 6.2 + - - -
171B LYS* 3.3 31.2 - - + -
179B ARG 3.1 23.1 - - - -
180B ASN 3.3 3.8 + - - -
181B GLY* 1.3 74.3 - - - +
183B ASP* 1.3 62.9 + - - +
185B ASP* 2.9 12.8 + - - +
186B ALA* 2.7 35.3 + - - +
235B LEU* 3.7 18.2 + - - +
1404B SO4 3.9 0.9 - - - +
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Residues in contact with ASP 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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169B ASN* 3.1 24.2 + - - +
171B LYS* 3.2 16.3 + - - +
182B THR* 1.3 86.7 - - - +
184B LYS* 1.3 59.1 + - + +
186B ALA* 3.7 1.8 - - - +
187B GLU* 2.9 31.9 + - - +
1404B SO4 3.1 22.0 + - - +
1406B SO4 3.0 25.3 + - - -
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Residues in contact with LYS 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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181B GLY 3.4 8.3 - - - +
182B THR 3.1 0.2 - - - -
183B ASP* 1.3 75.0 - - - +
185B ASP* 1.3 63.6 + - - +
187B GLU* 3.3 7.7 + - + +
188B ALA* 2.9 31.3 + - - +
344B GLY 4.3 18.7 + - - +
345B ARG* 4.9 5.1 - - - +
346B GLY* 4.8 7.0 - - - +
1404B SO4 3.1 22.1 + - - +
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Residues in contact with ASP 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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181B GLY 3.2 10.9 + - - +
182B THR* 2.9 14.0 + - - +
184B LYS* 1.3 78.2 - - - +
186B ALA* 1.3 63.7 + - - +
188B ALA* 3.1 4.5 + - - +
189B LEU* 2.9 30.1 + - - +
235B LEU* 4.3 8.5 - - + +
283B GLN* 5.1 3.3 - - - +
346B GLY* 3.0 20.8 - - - -
347B SER* 3.0 30.1 + - - +
350B VAL* 3.6 32.7 - - + +
351B GLN* 4.9 1.2 + - - +
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Residues in contact with ALA 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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167B ILE* 4.1 9.4 - - + +
169B ASN* 3.6 32.5 - - + +
182B THR 2.7 18.1 + - - +
183B ASP 3.7 3.6 - - - +
185B ASP* 1.3 72.7 - - - +
187B GLU* 1.3 57.9 + - - +
189B LEU* 3.2 5.5 + - - +
190B PHE* 2.8 32.7 + - - +
202B VAL* 4.8 8.1 - - + -
235B LEU* 3.9 12.0 - - + +
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Residues in contact with GLU 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 ASP 2.9 18.8 + - - +
184B LYS* 3.6 9.0 - - + +
186B ALA* 1.3 75.5 - - - +
188B ALA* 1.3 62.7 + - - +
190B PHE* 3.1 35.1 - - + -
191B LYS* 3.0 54.9 + - - +
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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
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184B LYS 2.9 16.7 + - - +
185B ASP* 3.5 6.5 - - - +
187B GLU* 1.3 74.8 - - - +
189B LEU* 1.3 60.2 + - - +
191B LYS* 3.9 6.6 - - - +
192B CYS* 2.9 30.8 + - - +
350B VAL* 4.8 2.7 - - + -
351B GLN* 6.1 1.8 - - - -
354B CYS* 3.4 20.1 - - + +
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Residues in contact with LEU 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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167B ILE* 3.5 15.7 - - + -
185B ASP 2.9 24.6 + - - +
186B ALA* 3.6 2.2 - - - +
188B ALA* 1.3 74.9 - - - +
190B PHE* 1.3 60.0 + - - +
192B CYS* 3.1 1.2 + - - -
193B PHE* 2.7 41.8 + - + +
233B ILE* 3.5 39.9 - - + -
235B LEU* 3.8 24.5 - - + -
350B VAL* 3.7 16.2 - - + -
353B LEU* 4.2 21.1 - - + -
354B CYS* 3.4 21.8 - - - -
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Residues in contact with PHE 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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167B ILE* 3.5 9.8 - - + +
186B ALA 2.8 18.0 + - - +
187B GLU* 3.1 35.9 - - - -
189B LEU* 1.3 73.2 - - - +
191B LYS* 1.3 78.9 + - + +
194B ARG* 2.9 67.8 + - + +
200B VAL* 3.2 29.2 - - + +
202B VAL* 4.1 21.8 - - + -
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Residues in contact with LYS 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 GLU* 3.0 43.5 + - - +
188B ALA* 3.9 5.6 - - - +
190B PHE* 1.3 94.7 - - + +
192B CYS* 1.3 64.2 + - - +
194B ARG* 3.0 28.2 + - - +
195B SER* 2.9 25.6 + - - -
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Residues in contact with CYS 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 21.8 + - - +
189B LEU* 3.4 3.4 - - - +
191B LYS* 1.3 75.9 - - - +
193B PHE* 1.3 64.6 + - - +
195B SER* 3.1 11.5 + - - -
196B LEU* 3.0 22.4 + - - +
354B CYS* 3.8 24.0 - - + -
357B LEU* 3.4 47.1 - - - -
358B GLU* 4.6 14.4 - - + -
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Residues in contact with PHE 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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165B CYS* 3.8 27.4 - - - -
189B LEU* 2.7 28.3 + - + +
192B CYS* 1.3 82.3 - - + +
194B ARG* 1.3 58.7 + - - +
196B LEU* 3.2 17.4 - - + +
198B PHE* 3.0 57.5 + + + +
200B VAL* 3.9 6.3 - - + -
231B ALA* 4.5 3.8 - - + -
233B ILE* 4.0 16.8 - - + -
281B PHE* 3.9 38.6 - + - -
353B LEU* 4.4 12.6 - - + -
357B LEU* 3.5 28.3 - - + -
400B PHE* 5.2 3.1 - + - -
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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
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190B PHE* 2.9 64.1 + - + +
191B LYS* 3.2 30.6 + - - +
193B PHE* 1.3 73.6 - - - +
195B SER* 1.3 62.7 + - - +
196B LEU 3.0 4.0 - - - -
197B GLY* 2.8 22.2 + - - -
198B PHE 3.8 14.7 + - - +
200B VAL* 3.8 9.4 - - + +
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Residues in contact with SER 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 LYS 2.9 12.4 + - - -
192B CYS* 3.1 11.8 + - - -
194B ARG* 1.3 84.2 - - - +
196B LEU* 1.3 65.4 + - - +
197B GLY* 3.1 1.1 + - - -
358B GLU* 5.9 4.7 - - - +
362B LYS* 4.8 12.5 - - - -
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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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162B LEU* 3.3 12.9 - - - +
192B CYS* 3.0 12.8 + - - +
193B PHE* 3.2 25.6 - - + +
194B ARG 3.0 0.4 - - - -
195B SER* 1.3 79.9 - - - +
197B GLY* 1.3 56.9 + - - +
198B PHE* 3.5 29.4 - - + -
357B LEU* 4.4 17.7 - - + +
361B GLY* 4.0 21.1 - - - +
362B LYS* 3.7 31.1 - - + +
400B PHE* 3.7 36.7 - - + +
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Residues in contact with GLY 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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162B LEU* 3.5 23.9 + - - +
194B ARG 2.8 9.9 + - - -
195B SER 3.1 1.4 - - - -
196B LEU* 1.3 81.9 - - - +
198B PHE* 1.3 66.9 + - - +
199B ASP* 4.0 5.2 + - - +
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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