Contacts of the helix formed by residues 174 - 189 (chain C) in PDB entry 6QY3
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 SER 174 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172C TYR 3.9 2.2 + - - -
173C PHE* 1.3 76.2 - - - +
175C LYS* 1.3 55.8 + - - +
176C ASP* 3.2 7.6 - - - -
177C GLU* 2.9 12.4 + - - +
178C ILE* 2.7 34.1 + - - +
25D VAL* 4.9 12.0 - - - +
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Residues in contact with LYS 175 (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 SER* 1.3 72.7 - - - +
176C ASP* 1.3 58.6 + - - +
178C ILE* 3.1 10.1 + - - +
179C TYR* 2.9 27.2 + - - +
201C GLU 5.0 11.2 - - - +
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Residues in contact with ASP 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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174C SER* 3.2 5.2 - - - -
175C LYS* 1.3 79.1 - - - +
177C GLU* 1.3 58.0 + - - +
179C TYR* 3.1 9.5 + - - +
180C GLN* 2.9 27.8 + - - +
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Residues in contact with GLU 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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145C PHE* 5.1 14.4 - - + -
173C PHE* 3.9 12.9 - - + +
174C SER* 2.9 25.7 + - - +
176C ASP* 1.3 78.4 - - - +
178C ILE* 1.3 57.7 + - - +
180C GLN* 3.4 8.0 + - - +
181C ILE* 2.9 28.6 + - - +
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Residues in contact with ILE 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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170C LEU* 6.0 6.1 - - + +
173C PHE* 4.5 9.3 - - + +
174C SER 2.7 15.2 + - - +
175C LYS* 3.1 13.7 + - - +
177C GLU* 1.3 70.5 - - - +
179C TYR* 1.3 60.9 + - - +
181C ILE* 3.3 6.8 + - - +
182C LEU* 2.9 29.6 + - - +
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Residues in contact with TYR 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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175C LYS 2.9 12.9 + - - +
176C ASP* 3.4 11.7 - - - +
178C ILE* 1.3 76.4 - - - +
180C GLN* 1.3 57.8 + - - +
182C LEU* 3.3 6.3 + - - +
183C GLU* 2.9 30.4 + - - +
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Residues in contact with GLN 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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176C ASP 2.9 15.6 + - - +
177C GLU* 3.7 8.5 - - - +
179C TYR* 1.3 76.5 - - - +
181C ILE* 1.3 58.5 + - - +
183C GLU* 3.9 5.2 - - - +
184C TYR* 2.9 30.3 + - - +
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Residues in contact with ILE 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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148C ILE* 6.5 0.7 - - + -
177C GLU 2.9 18.9 + - - +
178C ILE* 3.7 7.4 - - - +
180C GLN* 1.3 73.0 - - - +
182C LEU* 1.3 61.0 + - - +
184C TYR* 3.5 5.8 + - - +
185C THR* 2.9 28.9 + - - -
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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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17C GLY* 5.6 5.9 + - - -
178C ILE 2.9 17.4 + - - +
179C TYR* 3.8 6.1 - - - +
181C ILE* 1.3 73.9 - - - +
183C GLU* 1.3 60.2 + - - +
185C THR* 3.3 7.4 + - - -
186C LYS* 2.9 28.8 + - - +
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Residues in contact with GLU 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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179C TYR 2.9 17.9 + - - +
180C GLN* 3.9 5.8 - - - +
182C LEU* 1.3 76.5 - - - +
184C TYR* 1.3 59.2 + - - +
186C LYS* 3.3 7.1 + - - +
187C LEU* 2.9 28.8 + - - +
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Residues in contact with TYR 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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180C GLN 2.9 19.0 + - - +
181C ILE* 3.8 6.1 - - - +
183C GLU* 1.3 75.7 - - - +
185C THR* 1.3 58.6 + - - +
187C LEU* 3.4 6.9 + - - +
188C SER* 2.9 30.5 + - - -
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Residues in contact with THR 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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16C LEU* 4.7 3.1 - - - +
17C GLY* 4.3 21.5 - - - -
152C LEU* 6.6 0.2 - - - -
181C ILE 2.9 18.5 + - - -
182C LEU* 3.6 7.9 - - - -
183C GLU 3.2 0.2 - - - -
184C TYR* 1.3 74.3 - - - +
186C LYS* 1.3 59.1 + - - +
188C SER* 3.4 4.5 + - - +
189C GLN* 3.0 27.5 + - - -
190C ALA* 3.8 12.6 + - - +
192C VAL* 5.1 9.6 - - - -
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Residues in contact with LYS 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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16C LEU* 4.6 16.3 - - + +
17C GLY 5.2 0.2 - - - +
182C LEU 2.9 16.3 + - - +
183C GLU* 3.3 6.9 + - - +
185C THR* 1.3 76.9 - - - +
187C LEU* 1.3 61.0 + - - +
189C GLN* 3.7 8.8 + - - +
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Residues in contact with LEU 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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183C GLU 2.9 17.3 + - - +
184C TYR* 3.8 7.6 - - - +
185C THR 3.2 0.2 - - - -
186C LYS* 1.3 79.6 - - - +
188C SER* 1.3 59.0 + - - +
189C GLN* 3.4 1.8 - - - +
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Residues in contact with SER 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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152C LEU* 5.7 7.4 - - - -
156C LYS* 5.1 15.9 - - - +
184C TYR 2.9 18.0 + - - -
185C THR* 4.1 4.7 - - - -
187C LEU* 1.3 75.7 - - - +
189C GLN* 1.3 62.2 + - - +
190C ALA* 3.0 19.9 + - - +
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Residues in contact with GLN 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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16C LEU* 4.7 9.4 + - - -
185C THR 3.0 9.3 + - - -
186C LYS* 3.7 8.0 + - - +
187C LEU 3.4 4.7 - - - +
188C SER* 1.3 76.7 - - - +
190C ALA* 1.3 65.6 + - - +
191C ASP* 3.8 0.5 + - - +
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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