Contacts of the helix formed by residues 170 - 184 (chain C) in PDB entry 3QEL
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 ASP 170 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168C SER* 2.6 35.4 + - - -
169C ASP* 1.3 73.7 - - - +
171C HIS* 1.3 72.5 + - - +
172C GLU* 3.3 12.6 + - - +
173C GLY 2.9 26.0 + - - -
174C ARG* 3.1 30.5 + - - +
220C PRO* 3.5 18.4 - - + +
248C ASP* 5.4 0.5 - - - +
273C ARG* 5.4 2.5 + - - -
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Residues in contact with HIS 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C MET* 6.4 0.9 - - + -
126C SER* 4.4 4.4 + - - -
127C ILE* 3.7 42.2 + - + -
130C ASP* 4.6 14.8 + - + +
133C ILE* 6.2 1.8 - - + -
170C ASP* 1.3 78.0 - - - +
172C GLU* 1.3 53.4 + - - +
174C ARG* 3.0 21.0 + - - +
175C ALA* 2.8 44.9 + - + +
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Residues in contact with GLU 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C MET* 3.5 26.8 - - + +
126C SER* 2.8 45.9 + - - -
144C TYR* 3.5 24.7 - - + +
145C SER* 3.5 6.8 + - - -
168C SER* 5.5 0.2 - - - +
170C ASP* 3.3 8.6 + - - +
171C HIS* 1.3 79.9 - - - +
173C GLY* 1.3 63.2 + - - +
175C ALA* 3.1 13.1 + - - +
176C ALA* 3.2 13.7 + - - +
243C SER* 5.0 3.6 - - - +
273C ARG* 4.0 29.8 - - - +
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Residues in contact with GLY 173 (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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167C VAL* 3.3 21.0 - - - +
168C SER* 3.2 28.7 + - - -
170C ASP* 2.9 11.1 + - - -
171C HIS 3.3 0.2 - - - -
172C GLU* 1.3 76.3 - - - +
174C ARG* 1.3 57.0 + - - +
176C ALA* 3.6 2.1 + - - +
177C GLN 3.2 18.5 + - - -
243C SER* 3.8 13.5 - - - -
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Residues in contact with ARG 174 (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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167C VAL* 5.3 0.4 - - + -
168C SER 4.6 3.8 - - - +
169C ASP* 3.0 34.2 + - - +
170C ASP* 3.1 25.5 + - - +
171C HIS* 3.0 30.1 + - - +
173C GLY* 1.3 75.0 - - - +
175C ALA* 1.3 59.4 + - - +
177C GLN* 3.4 19.3 - - - +
178C LYS* 2.9 30.5 + - - +
217C GLN* 4.8 7.4 - - - +
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Residues in contact with ALA 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C SER* 3.6 32.1 - - - +
145C SER* 3.6 9.3 - - - +
171C HIS* 2.8 20.9 + - + +
172C GLU 3.1 9.6 + - - +
174C ARG* 1.3 77.5 - - - +
176C ALA* 1.3 56.2 + - - +
178C LYS* 3.6 5.4 + - - +
179C LYS* 3.0 28.4 + - - +
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Residues in contact with ALA 176 (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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144C TYR 5.5 0.9 - - - +
145C SER* 3.8 20.1 - - - +
148C ALA* 4.6 1.9 - - - +
151C TRP* 4.4 18.1 - - + -
165C LEU* 5.1 1.6 - - + -
167C VAL* 5.1 1.3 - - + -
172C GLU* 3.2 6.4 + - - +
173C GLY 3.7 8.3 - - - +
175C ALA* 1.3 76.5 - - - +
177C GLN* 1.3 68.0 + - - +
179C LYS* 3.2 2.1 + - - +
180C LEU* 2.9 26.7 + - - +
243C SER* 3.8 26.0 - - - +
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Residues in contact with GLN 177 (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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165C LEU* 4.0 13.4 - - + +
167C VAL* 4.0 13.2 - - + +
173C GLY 3.2 11.0 + - - +
174C ARG* 3.4 16.9 - - - +
176C ALA* 1.3 78.8 - - - +
178C LYS* 1.3 66.1 + - - +
180C LEU* 3.9 1.2 - - - +
181C GLU* 3.1 43.7 + - - +
215C VAL* 3.5 29.8 - - + +
217C GLN* 2.8 30.0 + - - +
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Residues in contact with LYS 178 (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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174C ARG 2.9 16.0 + - - +
175C ALA* 3.9 5.2 - - - +
177C GLN* 1.3 76.4 - - - +
179C LYS* 1.3 65.1 + - - +
181C GLU* 3.0 9.3 + - - +
182C THR* 2.8 31.2 + - - +
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Residues in contact with LYS 179 (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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145C SER* 3.6 27.6 - - - +
146C HIS* 5.4 5.4 - - + -
148C ALA* 4.1 6.5 - - + -
175C ALA 3.0 19.4 + - - +
176C ALA 3.2 2.2 + - - +
178C LYS* 1.3 76.6 - - - +
180C LEU* 1.3 65.5 + - - +
182C THR* 3.5 7.6 + - - +
183C LEU* 3.1 23.2 + - + +
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Residues in contact with LEU 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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148C ALA* 3.8 30.2 - - + +
151C TRP* 4.7 10.1 - - + -
152C PHE* 4.7 9.6 - - + +
155C MET* 4.7 9.6 - - - -
163C VAL* 5.3 4.3 - - + -
165C LEU* 3.8 27.1 - - + -
176C ALA 2.9 16.0 + - - +
177C GLN 3.9 3.1 - - - +
179C LYS* 1.3 76.7 - - - +
181C GLU* 1.3 60.7 + - + +
183C LEU* 2.8 26.2 + - + +
184C LEU* 2.9 36.1 + - + +
212C ALA* 5.4 1.8 - - + -
241C ILE* 4.2 22.2 - - + -
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Residues in contact with GLU 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C LEU* 5.7 2.7 - - + -
177C GLN* 3.1 39.3 + - + +
178C LYS* 3.0 7.2 + - - +
180C LEU* 1.3 77.2 - - + +
182C THR* 1.3 67.7 + - - +
184C LEU* 2.8 24.5 + - + +
185C GLU* 3.0 17.2 + - - +
212C ALA* 5.6 5.7 - - + +
215C VAL* 4.0 22.8 - - + +
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Residues in contact with THR 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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178C LYS* 2.8 24.5 + - - +
179C LYS* 3.6 8.1 - - - +
181C GLU* 1.3 71.9 - - - +
183C LEU* 1.3 66.7 + - + +
185C GLU* 3.4 18.7 + - - +
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Residues in contact with LEU 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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148C ALA* 3.4 38.8 - - + +
149C LEU* 3.7 29.2 - - + +
152C PHE* 3.9 42.2 - - + -
179C LYS* 3.1 18.7 + - + +
180C LEU* 2.8 13.2 + - + +
182C THR* 1.3 81.6 - - + +
184C LEU* 1.3 56.8 + - - +
185C GLU 3.1 9.2 + - - +
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Residues in contact with LEU 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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152C PHE* 3.5 32.3 - - + -
155C MET* 3.9 16.8 - - + -
180C LEU* 2.9 35.6 + - + +
181C GLU* 2.8 16.2 + - + +
183C LEU* 1.3 73.5 - - - +
185C GLU* 1.3 57.5 + - - +
210C PRO 3.3 25.6 - - - +
211C LYS* 4.2 4.5 - - - +
212C ALA* 3.9 35.0 - - + +
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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