Contacts of the helix formed by residues 179 - 190 (chain C) in PDB entry 2QPA
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 LYS 179 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171C LEU* 3.3 24.9 - - + +
172C TYR 3.8 1.6 - - - -
173C GLY* 3.2 27.1 + - - +
174C PRO 2.6 29.5 + - - -
175C PRO* 4.4 0.4 - - - +
177C THR* 3.1 15.6 + - - +
178C GLY* 1.3 71.3 - - - -
180C SER* 1.3 55.7 + - - +
181C TYR 3.3 0.2 - - - -
182C LEU* 2.9 11.3 + - - +
183C ALA* 2.7 35.7 + - - +
230C PHE* 3.9 14.6 - - + -
275C ALA* 4.1 8.1 - - + -
276C THR 3.3 16.6 - - - +
277C ASN* 3.1 8.7 + - - -
296C ILE* 4.3 16.1 + - + -
800C PO4 3.2 22.9 + - - +
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Residues in contact with SER 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C GLY* 3.9 8.7 - - - -
179C LYS* 1.3 77.4 - - - +
181C TYR* 1.3 61.2 + - - +
182C LEU 2.9 9.4 + - - -
183C ALA* 3.4 1.7 + - - +
184C LYS* 3.3 22.3 + - - +
194C PHE* 4.2 4.3 - - - -
230C PHE* 3.3 28.3 - - - -
232C ASP* 5.3 1.1 - - - -
800C PO4 3.2 17.3 + - - -
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Residues in contact with TYR 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C VAL* 4.3 22.3 - - + +
134C ASP* 3.3 49.9 + - + +
135C VAL* 3.8 23.9 - - + +
178C GLY* 3.6 13.1 + - - +
179C LYS 3.3 0.2 - - - -
180C SER* 1.3 79.9 + - - +
182C LEU* 1.3 57.7 + - - +
184C LYS* 4.4 6.9 - - + +
185C ALA* 3.9 10.2 + - - +
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Residues in contact with LEU 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C TRP* 5.1 3.6 - - + -
135C VAL* 4.7 8.5 - - + -
138C LEU* 3.7 33.4 - - + -
141C ALA* 4.9 0.7 - - + -
142C LYS* 5.5 4.9 - - + -
145C LEU* 3.4 35.4 - - + -
171C LEU* 3.6 17.5 - - + -
178C GLY 3.8 4.0 + - - +
179C LYS* 2.9 15.0 + - - +
180C SER 2.9 1.0 - - - -
181C TYR* 1.3 79.9 - - - +
183C ALA* 1.3 69.4 + - - +
184C LYS 3.0 1.8 - - - -
185C ALA* 2.9 22.7 + - + +
186C VAL* 3.4 5.9 + - + +
296C ILE* 3.7 26.5 - - + -
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Residues in contact with ALA 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C LEU* 4.4 1.3 - - + -
179C LYS 2.7 16.1 + - - +
182C LEU* 1.3 78.8 - - - +
184C LYS* 1.3 61.5 + - - +
186C VAL* 3.2 10.1 + - - +
187C ALA* 3.1 16.6 + - - +
194C PHE* 3.2 22.2 - - + -
228C ILE* 4.4 3.5 - - - +
230C PHE* 3.4 14.1 - - + -
273C LEU* 3.2 35.5 - - + +
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Residues in contact with LYS 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C PRO* 4.2 14.1 - - + +
130C VAL* 4.0 14.6 - - + -
180C SER 3.3 13.8 + - - +
181C TYR* 4.6 6.5 - - + +
182C LEU 3.0 0.2 - - - -
183C ALA* 1.3 73.7 - - - +
185C ALA* 1.3 52.8 - - - +
186C VAL 2.9 5.5 + - - -
187C ALA* 3.1 2.5 + - - +
188C THR* 2.7 40.3 + - - -
194C PHE* 3.1 26.9 - - + -
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Residues in contact with ALA 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C VAL* 3.2 17.9 - - + +
131C LYS 3.2 20.9 - - - +
132C TRP* 3.4 19.6 - - + -
135C VAL* 4.7 6.3 - - + -
181C TYR 3.9 12.0 + - - +
182C LEU* 2.9 15.7 + - + +
184C LYS* 1.3 78.7 - - - +
186C VAL* 1.3 55.1 + - - +
188C THR 3.9 0.2 - - - -
189C GLU* 3.2 31.4 + - - +
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Residues in contact with VAL 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C TRP* 3.5 19.1 - - + -
145C LEU* 3.4 32.5 - - + -
149C VAL* 4.3 20.0 - - + -
150C ILE* 4.3 22.9 - - + -
182C LEU 3.5 13.9 - - - +
183C ALA* 3.4 8.7 - - - +
184C LYS 3.0 0.6 - - - -
185C ALA* 1.3 74.8 - - - +
187C ALA* 1.3 68.8 + - - +
188C THR 2.8 1.5 + - - -
189C GLU 3.1 0.9 + - - -
190C ALA* 2.8 29.3 + - + +
228C ILE* 4.0 13.9 - - + -
273C LEU* 5.6 4.0 - - + -
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Residues in contact with ALA 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C LYS* 5.8 0.9 - - - -
128C PRO* 5.7 1.6 - - + -
183C ALA 3.1 2.4 + - - -
184C LYS* 3.1 8.0 + - - +
186C VAL* 1.3 79.7 - - - +
188C THR* 1.3 59.9 + - - +
190C ALA 3.4 0.7 - - - -
192C SER* 2.6 40.8 + - - +
194C PHE* 3.4 44.6 - - + +
228C ILE* 3.2 24.5 - - + +
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Residues in contact with THR 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C LYS* 5.9 1.8 - - - +
128C PRO* 2.8 30.6 + - - +
129C ASN* 4.2 2.5 - - - -
130C VAL* 3.0 49.3 + - - +
131C LYS* 4.3 2.0 - - + +
184C LYS 2.7 16.3 + - - -
186C VAL 2.8 0.6 + - - -
187C ALA* 1.3 71.8 - - - +
189C GLU* 1.3 58.4 + - - +
190C ALA 2.6 15.4 + - - -
191C ASN* 2.7 17.5 + - - +
192C SER 5.2 1.1 - - - -
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Residues in contact with GLU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C LYS* 3.3 32.7 - - - +
132C TRP* 3.0 50.1 + - + +
150C ILE* 4.8 9.8 - - + +
185C ALA 3.2 14.3 + - - +
186C VAL 3.1 2.2 + - - +
188C THR* 1.3 78.6 - - - +
190C ALA* 1.3 57.2 + - - +
191C ASN 3.5 0.4 - - - -
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Residues in contact with ALA 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C VAL* 5.3 6.1 - - + -
150C ILE* 4.8 11.9 - - + -
153C VAL* 5.6 9.2 - - + -
186C VAL* 2.8 25.7 + - + +
187C ALA* 4.6 0.2 - - - -
188C THR 2.6 5.7 + - - -
189C GLU* 1.3 76.2 - - - +
191C ASN* 1.3 60.9 + - - +
192C SER* 2.4 34.9 + - - +
226C PRO* 3.8 5.4 - - - +
228C ILE* 5.2 1.3 - - + -
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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