Contacts of the helix formed by residues 181 - 197 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LYS* 4.7 3.4 - - - +
179A ARG 3.9 0.2 + - - -
180A ASN* 1.3 72.8 - - - +
182A THR* 1.3 57.1 + - - +
183A ASP* 3.0 4.9 - - - +
184A LYS* 3.0 18.5 + - - +
185A ASP* 2.9 33.6 + - - +
343A PRO 5.2 0.2 + - - -
344A GLY* 3.7 24.4 - - - -
346A GLY* 4.3 6.6 - - - -
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Residues in contact with THR 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ASN* 2.7 36.1 + - - +
170A ASN 4.0 1.0 + - - -
171A LYS* 3.2 29.4 - - + +
179A ARG* 2.9 57.7 + - - +
180A ASN 2.8 5.8 + - - -
181A GLY* 1.3 77.2 - - - +
183A ASP* 1.3 66.0 + - - +
185A ASP* 3.4 11.9 - - - +
186A ALA 2.9 23.2 + - - -
235A LEU* 3.9 1.9 - - - +
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Residues in contact with ASP 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ASN* 3.1 20.5 - - - +
171A LYS* 3.4 36.4 + - - +
181A GLY* 3.0 1.5 - - - +
182A THR* 1.3 81.7 - - - +
184A LYS* 1.3 72.8 + - + +
186A ALA* 3.3 1.7 + - - +
187A GLU* 2.8 31.6 + - - +
204A ASN* 4.7 2.5 + - - -
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Residues in contact with LYS 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLY* 3.3 17.7 - - - +
183A ASP* 1.3 80.7 - - + +
185A ASP* 1.3 67.3 + - - +
187A GLU* 3.6 12.4 - - - +
188A ALA* 2.9 22.1 + - - +
343A PRO 4.0 10.5 + - - -
344A GLY* 3.8 26.5 - - - +
345A ARG 5.0 2.0 - - - -
346A GLY* 4.5 11.0 - - - +
351A GLN* 4.8 3.1 - - - +
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Residues in contact with ASP 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 4.5 8.7 + - - -
181A GLY 2.9 14.7 + - - +
182A THR* 3.4 15.8 - - - +
184A LYS* 1.3 75.3 - - - +
186A ALA* 1.3 57.0 + - - +
188A ALA* 2.7 26.3 + - - +
189A LEU* 2.8 14.4 + - - +
235A LEU* 4.3 7.3 - - + +
283A GLN* 5.0 2.3 - - - +
346A GLY* 3.1 3.1 - - - -
347A SER* 2.9 41.3 + - - -
350A VAL* 3.7 27.2 - - + +
351A GLN* 2.9 14.9 + - - +
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Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 4.3 9.6 - - + +
169A ASN* 3.4 32.5 - - + +
182A THR 2.9 16.7 + - - +
183A ASP 3.7 2.7 - - - +
185A ASP* 1.3 76.1 - - - +
187A GLU* 1.3 52.0 - - - +
189A LEU* 3.0 7.2 + - - +
190A PHE* 2.7 36.7 + - - +
202A VAL* 4.8 7.8 - - + +
235A LEU* 3.8 12.0 - - + +
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Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ASP* 2.8 22.7 + - - +
184A LYS* 3.6 13.5 - - - +
186A ALA* 1.3 73.3 - - - +
188A ALA* 1.3 63.6 + - - +
190A PHE* 3.2 8.7 + - + +
191A LYS* 3.1 52.4 + - + +
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LYS 2.9 13.1 + - - +
185A ASP* 2.7 19.1 + - - +
187A GLU* 1.3 74.1 - - - +
189A LEU* 1.3 53.5 + - - +
191A LYS* 3.5 7.1 + - - +
192A CYS* 3.0 30.7 + - - +
350A VAL* 4.6 1.1 - - + -
351A GLN* 4.5 14.1 - - - +
354A CYS* 3.6 18.8 - - + +
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 3.9 13.0 - - + +
185A ASP 2.8 12.2 + - - +
186A ALA* 3.3 7.0 - - - +
188A ALA* 1.3 74.7 - - - +
190A PHE* 1.3 60.8 + - - +
192A CYS* 4.3 0.4 - - - -
193A PHE* 2.8 47.7 + - + +
233A ILE* 3.6 41.5 - - + -
235A LEU* 3.7 29.4 - - + -
281A PHE* 6.1 0.2 - - + -
350A VAL* 3.9 19.3 - - + -
353A LEU* 4.6 13.9 - - + -
354A CYS* 3.8 17.0 - - - -
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Residues in contact with PHE 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 3.8 5.8 - - - +
186A ALA 2.7 12.3 + - - +
187A GLU* 3.4 12.1 - - - +
188A ALA 3.2 0.2 - - - -
189A LEU* 1.3 75.1 - - - +
191A LYS* 1.3 76.9 + - + +
193A PHE 3.9 0.2 - - - -
194A ARG* 2.9 42.4 + - + +
200A VAL* 3.3 53.9 - - + +
201A ILE* 4.6 1.6 - - - -
202A VAL* 3.5 24.2 - - + -
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Residues in contact with LYS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLU* 3.1 47.7 + - + +
188A ALA* 4.0 5.6 - - - +
190A PHE* 1.3 88.2 - - + +
192A CYS* 1.3 57.5 + - - +
194A ARG* 3.5 5.1 - - - +
195A SER* 2.6 35.1 + - - +
358A GLU* 4.7 6.7 - - - +
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Residues in contact with CYS 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ALA 3.0 19.8 + - - +
189A LEU* 3.7 3.4 - - - +
191A LYS* 1.3 75.5 - - - +
193A PHE* 1.3 68.7 + - - +
195A SER* 3.0 17.7 + - - -
196A LEU* 3.1 12.5 + - - +
354A CYS* 3.9 26.9 - - + -
357A LEU* 3.6 44.2 - - - -
358A GLU* 4.4 18.2 + - + +
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Residues in contact with PHE 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A CYS* 3.6 28.3 - - + -
189A LEU* 2.8 35.9 + - + +
190A PHE* 4.4 0.9 - - - +
192A CYS* 1.3 82.5 - - - +
194A ARG* 1.3 60.3 + - - +
196A LEU* 3.3 13.9 + - + +
197A GLY 3.3 4.9 + - - -
198A PHE* 2.9 50.6 + + + +
200A VAL* 4.7 3.4 - - + -
231A ALA* 4.4 7.9 - - + -
233A ILE* 3.8 22.0 - - + -
279A LEU* 5.7 0.9 - - + -
281A PHE* 3.7 42.6 - + - -
353A LEU* 4.7 4.0 - - + -
357A LEU* 3.7 23.6 - - + -
400A PHE* 5.7 1.3 - + - -
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Residues in contact with ARG 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PHE* 2.9 37.0 + - + +
191A LYS* 3.5 6.1 - - - +
193A PHE* 1.3 76.2 - - - +
195A SER* 1.3 55.2 + - - +
197A GLY* 2.7 35.4 + - - -
198A PHE 3.1 27.9 + - - -
199A ASP* 4.6 10.5 + - - +
200A VAL* 3.9 15.6 - - + +
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Residues in contact with SER 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A LYS* 2.6 20.8 + - - +
192A CYS* 3.0 8.7 + - - -
194A ARG* 1.3 78.3 - - - +
196A LEU* 1.3 61.6 + - - +
197A GLY* 2.9 1.6 + - - -
358A GLU* 3.7 22.7 + - - -
362A LYS* 4.1 21.9 + - - -
402A HIS* 5.4 4.9 - - - +
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A LEU* 3.4 15.3 - - - +
192A CYS* 3.1 11.4 + - - +
193A PHE* 3.5 20.4 - - + +
194A ARG 3.2 0.4 - - - -
195A SER* 1.3 76.5 - - - +
197A GLY* 1.3 57.1 + - - +
198A PHE* 4.0 18.6 - - + -
357A LEU* 3.8 34.5 - - + +
361A GLY* 3.4 37.5 - - - +
362A LYS* 4.9 11.7 - - + +
400A PHE* 3.5 38.3 - - + +
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Residues in contact with GLY 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A LEU* 3.2 27.9 + - - +
163A GLY 4.4 0.5 - - - +
194A ARG* 2.7 23.1 + - - -
195A SER 2.9 2.2 - - - -
196A LEU* 1.3 81.7 - - - +
198A PHE* 1.3 60.5 + - - +
199A ASP* 4.0 4.5 + - - +
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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