Contacts of the helix formed by residues 185 - 199 (chain A) in PDB entry 3QFR
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 ASN 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A MET 4.3 0.4 + - - -
142A THR* 3.4 9.4 + - - -
175A GLY* 2.9 37.7 - - - -
176A LEU 2.9 17.0 + - - +
177A GLY* 3.5 4.0 - - - -
183A HIS 3.2 0.8 + - - -
184A PHE* 1.3 87.2 - - + +
186A ALA* 1.3 65.0 + - - +
187A MET 3.1 4.3 + - - -
188A GLY* 3.3 2.4 + - - +
189A LYS* 3.1 20.9 + - - +
208A LEU* 3.8 21.5 - - + -
209A GLY 2.8 28.4 + - - +
751A FMN 2.8 15.2 + - - -
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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
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142A THR* 3.5 2.0 + - - -
146A GLY* 3.8 20.4 - - - +
183A HIS* 3.5 30.7 + - + -
184A PHE 3.0 5.7 + - - -
185A ASN* 1.3 76.3 - - - +
187A MET* 1.3 57.2 + - - +
189A LYS* 3.5 7.5 + - - +
190A TYR* 2.9 30.7 + - - +
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Residues in contact with MET 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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140A MET* 3.6 41.7 - - + -
141A ALA 3.9 14.8 - - - +
142A THR* 3.0 20.6 + - - +
146A GLY 4.9 2.4 + - - -
147A ASP 4.4 6.7 - - - +
148A PRO* 3.5 33.0 - - + -
149A THR 5.4 0.2 - - - +
152A ALA* 4.2 9.9 - - + +
155A PHE* 4.5 4.9 - - + -
156A TYR* 3.7 28.0 - - + -
159A LEU* 5.5 0.2 - - + -
186A ALA* 1.3 73.9 - - - +
188A GLY* 1.3 67.5 + - - +
190A TYR* 3.1 5.1 + - - +
191A VAL* 2.9 41.8 + - + +
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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
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140A MET* 4.4 10.1 + - - +
142A THR* 4.2 1.2 + - - -
173A VAL* 3.6 17.3 - - - +
175A GLY* 4.3 16.8 - - - -
185A ASN* 3.3 6.8 + - - +
187A MET* 1.3 79.1 - - - +
189A LYS* 1.3 62.0 + - - +
191A VAL* 3.5 1.3 + - - -
192A ASP* 3.1 26.0 + - - +
206A LEU* 3.6 9.7 - - - +
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Residues in contact with LYS 189 (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 PHE* 3.3 37.7 + - - +
185A ASN* 3.1 15.6 + - - +
186A ALA* 3.8 7.0 - - - +
188A GLY* 1.3 76.7 - - - +
190A TYR* 1.3 56.3 + - - +
192A ASP* 3.9 1.6 - - - +
193A LYS* 3.0 32.0 + - - +
206A LEU* 3.8 24.7 - - + +
208A LEU* 4.0 23.1 - - + +
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Residues in contact with TYR 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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156A TYR* 3.6 35.4 - + + -
159A LEU* 3.5 30.0 + - + -
160A GLN* 2.8 45.4 + - + +
186A ALA 2.9 19.4 + - - +
187A MET* 3.6 4.9 - - - +
189A LYS* 1.3 74.3 - - - +
191A VAL* 1.3 64.6 + - + +
193A LYS* 3.3 13.7 + - + +
194A ARG* 2.8 54.3 + - + +
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Residues in contact with VAL 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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138A PHE* 4.1 22.4 - - + -
140A MET* 4.4 6.7 - - + -
155A PHE* 4.1 15.9 - - + -
159A LEU* 4.0 18.4 - - + -
173A VAL* 4.2 6.7 - - + -
187A MET* 2.9 47.1 + - + +
188A GLY* 3.9 5.4 - - - +
190A TYR* 1.3 76.8 - - + +
192A ASP* 1.3 62.7 + - - +
194A ARG* 3.7 0.9 - - - +
195A LEU* 3.0 47.6 + - + +
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Residues in contact with ASP 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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171A PHE* 3.5 21.3 - - - -
173A VAL* 4.1 11.3 + - + +
188A GLY 3.1 17.1 + - - +
189A LYS 3.9 2.6 - - - +
191A VAL* 1.3 77.4 - - - +
193A LYS* 1.3 65.1 + - - +
195A LEU 3.6 0.2 + - - -
196A GLU 3.5 10.9 + - - -
202A ARG* 2.6 58.1 + - - +
204A PHE 4.8 0.7 - - - +
206A LEU* 3.9 33.7 - - + +
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Residues in contact with LYS 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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189A LYS 3.0 18.4 + - - +
190A TYR* 3.8 13.5 - - + +
192A ASP* 1.3 82.6 + - - +
194A ARG* 1.3 61.6 + - - +
196A GLU* 3.5 5.5 + - - +
197A GLN* 3.1 55.2 + - + +
202A ARG* 4.6 3.6 - - - +
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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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159A LEU* 2.7 45.6 + - + +
160A GLN* 4.5 6.3 + - - +
162A THR 3.0 27.3 + - - -
163A ASP* 4.9 3.2 + - - +
190A TYR* 2.8 48.6 + - + +
191A VAL* 3.7 4.7 - - - +
193A LYS* 1.3 73.0 - - - +
195A LEU* 1.3 64.5 + - - +
197A GLN* 2.7 52.5 + - - +
198A LEU* 3.1 46.1 + - + +
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Residues in contact with LEU 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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125A LEU* 4.4 12.1 - - + -
136A VAL* 5.9 0.2 - - + -
138A PHE* 3.4 31.4 - - + -
155A PHE* 5.3 1.1 - - + -
159A LEU* 4.3 18.6 - - + -
166A LEU* 3.9 23.3 - - + -
169A VAL* 6.4 0.9 - - + -
171A PHE* 3.5 41.7 - - + -
191A VAL* 3.0 29.6 + - + +
193A LYS 3.4 0.2 - - - -
194A ARG* 1.3 76.7 - - - +
196A GLU* 1.3 61.6 + - - +
198A LEU* 3.2 6.0 + - + +
199A GLY 3.1 5.2 + - - -
200A ALA* 2.9 28.7 + - + +
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Residues in contact with GLU 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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171A PHE* 4.0 3.9 - - + -
192A ASP 3.5 2.4 + - - -
193A LYS* 3.5 7.7 + - - +
194A ARG 3.3 0.4 - - - -
195A LEU* 1.3 76.2 - - - +
197A GLN* 1.3 69.8 + - + +
199A GLY* 2.9 15.2 + - - -
200A ALA 3.9 13.4 - - - +
202A ARG* 2.8 45.6 + - + +
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Residues in contact with GLN 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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163A ASP* 5.7 0.3 - - - +
193A LYS* 3.1 48.5 + - + +
194A ARG* 2.7 46.0 + - - +
195A LEU 3.4 0.2 - - - -
196A GLU* 1.3 79.9 - - + +
198A LEU* 1.3 62.5 + - - +
199A GLY* 3.5 0.5 + - - -
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Residues in contact with LEU 198 (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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158A TRP* 4.5 3.1 - - + -
159A LEU* 4.1 18.4 - - + -
162A THR* 4.0 19.5 - - + +
163A ASP* 4.0 21.8 - - - +
164A VAL* 3.4 24.8 - - + +
165A ASP* 3.5 8.1 - - - +
166A LEU* 2.9 48.3 + - + -
194A ARG* 3.1 50.0 + - + +
195A LEU* 3.5 6.3 - - - +
196A GLU 3.1 0.4 - - - -
197A GLN* 1.3 76.6 - - - +
199A GLY* 1.3 57.9 + - - +
200A ALA 3.7 0.7 - - - -
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Residues in contact with GLY 199 (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 ASP* 4.7 3.4 - - - -
166A LEU 3.7 10.6 - - - +
167A SER* 4.0 12.8 + - - -
168A GLY 4.9 0.5 + - - -
196A GLU 2.9 12.8 + - - -
197A GLN 3.2 1.2 - - - -
198A LEU* 1.3 80.2 - - - +
200A ALA* 1.3 69.6 + - - +
201A GLN* 4.5 1.9 - - - +
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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