Contacts of the helix formed by residues 181 - 196 (chain A) in PDB entry 2FQQ
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
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Residue Dist Surf HB Arom Phob DC
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171A GLU* 5.6 0.6 + - - -
180A THR* 1.3 74.1 - - - +
182A ALA* 1.3 62.9 + - - +
183A GLU* 3.3 4.6 + - - +
184A VAL* 3.6 17.9 + - - +
185A ASP* 3.9 10.4 - - - +
343B PRO 3.8 0.6 + - - -
344B THR* 3.7 30.4 - - - +
345B MET 3.7 15.4 - - - +
347B SER 4.7 0.2 + - - -
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Residues in contact with ALA 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 CYS* 4.0 22.4 - - - -
171A GLU* 4.0 12.7 + - + -
179A ARG* 3.3 33.0 + - + +
180A THR 3.3 1.4 - - - -
181A GLY* 1.3 76.4 - - - +
183A GLU* 1.3 60.3 + - - +
184A VAL 3.2 0.7 - - - -
185A ASP* 3.0 15.1 + - - +
186A ILE* 3.0 31.9 + - + +
235A MET* 6.1 0.2 - - - -
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Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLU* 3.6 13.8 + - - +
181A GLY* 3.3 2.4 - - - +
182A ALA* 1.3 78.6 - - - +
184A VAL* 1.3 54.8 + - + +
186A ILE* 3.4 14.6 + - - +
187A THR* 2.7 45.4 + - - +
204A LYS* 3.2 27.4 + - - -
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Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLY* 3.7 12.1 - - - +
182A ALA 3.2 0.4 - - - -
183A GLU* 1.3 77.8 - - + +
185A ASP* 1.3 58.8 + - - +
187A THR* 3.6 6.1 + - - -
188A GLY* 3.0 26.0 + - - -
344B THR* 3.4 25.8 - - - +
346B GLY* 3.9 20.0 - - - +
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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
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179A ARG* 4.6 4.2 + - - -
181A GLY 3.9 10.5 - - - +
182A ALA* 3.0 14.1 + - - +
184A VAL* 1.3 75.1 - - - +
186A ILE* 1.3 63.5 + - - +
189A MET* 3.2 31.0 + - - +
235A MET* 3.6 19.7 - - - +
283A GLN* 3.9 9.5 + - - +
346B GLY* 3.6 4.3 - - - -
347B SER* 2.8 45.9 + - - +
350B ILE* 4.0 17.8 - - + +
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Residues in contact with ILE 186 (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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167A ILE* 5.1 4.0 - - + -
169A CYS* 3.7 30.7 - - + -
171A GLU* 4.9 0.4 - - - +
182A ALA* 3.0 18.2 + - + +
183A GLU* 3.7 23.1 - - - +
184A VAL 3.3 0.4 - - - -
185A ASP* 1.3 74.5 - - - +
187A THR* 1.3 58.7 + - - +
189A MET* 3.4 2.2 + - - +
190A THR* 2.7 45.6 + - - +
202A VAL* 3.9 25.8 - - + -
204A LYS* 3.8 30.3 - - + +
235A MET* 3.8 10.3 - - + -
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Residues in contact with THR 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 GLU* 2.7 32.0 + - - +
184A VAL* 4.0 6.2 - - - -
186A ILE* 1.3 77.2 - - - +
188A GLY* 1.3 62.1 + - - +
190A THR* 4.8 2.9 - - - -
191A MET* 3.3 39.3 + - + +
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Residues in contact with GLY 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A VAL 3.0 17.3 + - - -
185A ASP 4.1 0.7 - - - -
187A THR* 1.3 79.4 - - - +
189A MET* 1.3 56.1 + - - +
191A MET* 4.0 3.0 - - - +
192A LEU* 3.2 27.5 + - - +
354B ILE* 3.6 23.7 - - - +
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Residues in contact with MET 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 3.8 17.3 - - + -
185A ASP 3.2 19.7 + - - +
186A ILE* 4.1 0.4 - - - +
188A GLY* 1.3 72.8 - - - +
190A THR* 1.3 61.0 + - - +
192A LEU* 3.4 13.5 + - + +
193A LEU* 3.0 45.6 + - + +
233A VAL* 3.8 34.8 - - + -
235A MET* 5.2 2.2 - - + -
281A ILE* 4.0 22.2 - - + -
350B ILE* 3.8 19.5 - - + -
353B LEU* 4.3 13.2 - - + -
354B ILE* 3.8 23.1 - - - +
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Residues in contact with THR 190 (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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167A ILE* 3.7 16.2 - - - +
186A ILE* 2.7 26.2 + - - +
187A THR* 4.3 3.6 - - - -
189A MET* 1.3 77.4 - - - +
191A MET* 1.3 67.5 + - + +
194A GLN* 3.0 37.9 + - - +
200A VAL* 3.8 27.1 - - + +
202A VAL* 3.8 17.0 - - + +
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Residues in contact with MET 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 THR* 3.3 32.4 + - + +
188A GLY* 4.0 3.4 - - - +
190A THR* 1.3 88.6 - - + +
192A LEU* 1.3 57.9 + - - +
194A GLN* 3.4 28.4 - - + +
195A ASN* 2.8 40.8 + - - +
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Residues in contact with LEU 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 GLY 3.2 18.6 + - - +
189A MET* 3.6 19.3 - - + +
190A THR 3.3 0.2 - - - -
191A MET* 1.3 77.4 - - - +
193A LEU* 1.3 66.8 + - + +
195A ASN* 3.1 18.7 + - + +
196A LEU* 3.1 31.2 + - + +
353B LEU* 5.6 0.9 - - + -
354B ILE* 3.8 27.1 - - + +
357B MET* 3.8 42.2 - - + +
358B GLN* 3.8 25.4 - - + -
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Residues in contact with LEU 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 ALA* 4.0 20.0 - - + -
167A ILE* 4.1 20.9 - - + -
189A MET* 3.0 30.8 + - + +
192A LEU* 1.3 80.5 - - + +
194A GLN* 1.3 59.3 + - - +
196A LEU* 3.2 25.1 + - + -
197A GLY 3.2 0.5 + - - -
198A TYR* 2.9 34.6 + - + -
200A VAL* 3.8 12.6 - - + -
231A PHE* 3.6 41.5 - - + -
233A VAL* 4.4 13.0 - - + -
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Residues in contact with GLN 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 THR* 3.0 26.1 + - - +
191A MET* 3.4 28.3 - - + +
193A LEU* 1.3 77.7 - - - +
195A ASN* 1.3 61.9 + - - +
197A GLY* 3.2 13.3 + - - -
198A TYR 3.4 16.7 + - - +
199A SER* 5.5 2.0 - - - +
200A VAL* 4.2 9.5 + - + +
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Residues in contact with ASN 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 MET* 2.8 24.9 + - - +
192A LEU* 3.1 13.1 + - + +
194A GLN* 1.3 77.8 - - - +
196A LEU* 1.3 62.7 + - + +
197A GLY 3.3 0.8 + - - -
402B PRO* 5.5 3.8 - - - +
403B GLY 5.2 6.8 + - - -
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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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161A ARG* 4.3 1.8 + - - -
163A ARG* 2.8 26.0 + - - -
192A LEU* 3.1 32.7 + - + +
193A LEU* 3.2 29.8 + - + +
195A ASN* 1.3 80.7 - - + +
197A GLY* 1.3 57.5 + - - +
198A TYR* 3.6 15.2 - - + -
231A PHE* 5.0 3.4 - - + -
357B MET* 4.8 13.7 - - - +
361B ALA* 4.7 15.5 - - + -
400B LEU* 3.7 35.0 - - + +
401B PHE 5.2 2.1 - - - +
402B PRO* 5.4 12.4 - - + +
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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