Contacts of the helix formed by residues 165 - 180 (chain C) in PDB entry 3C6Q
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 165 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162C ASP* 2.9 20.2 + - - +
163C CYS 4.7 1.1 - - - +
164C GLU* 1.3 77.8 - - - +
166C GLY* 1.3 69.4 + - - +
167C ALA* 3.5 7.9 + - - +
168C ARG* 2.8 51.4 + - + +
169C ALA* 3.0 22.7 + - - +
192C TYR* 4.2 3.3 - - - -
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Residues in contact with GLY 166 (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 ASP* 1.3 74.5 + - - +
167C ALA* 1.3 60.0 + - - +
169C ALA* 3.1 6.0 + - - +
170C VAL* 2.9 30.0 + - - +
192C TYR* 3.7 26.6 - - - -
196C ALA* 4.8 1.4 - - - +
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Residues in contact with ALA 167 (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 ASP* 3.5 8.2 + - - +
166C GLY* 1.3 74.7 - - - +
168C ARG* 1.3 61.7 + - - +
170C VAL* 3.4 11.7 + - - +
171C SER* 3.3 22.2 + - - -
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Residues in contact with ARG 168 (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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40C LYS* 6.3 1.8 - - - +
161C ASN 5.4 1.7 + - - -
162C ASP* 3.9 22.7 + - + +
163C CYS* 4.2 26.3 + - - +
165C ASP* 2.8 38.6 + - + +
166C GLY 3.2 0.2 - - - -
167C ALA* 1.3 74.2 - - - +
169C ALA* 1.3 65.4 + - - +
171C SER* 3.0 17.4 + - - +
172C LEU* 3.2 26.4 - - + +
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Residues in contact with ALA 169 (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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162C ASP* 3.1 29.7 - - - +
165C ASP 3.0 11.2 + - - +
166C GLY* 3.3 10.3 - - - +
168C ARG* 1.3 74.9 - - - +
170C VAL* 1.3 67.2 + - - +
172C LEU* 2.9 18.1 + - - +
173C ALA* 3.0 13.6 + - - +
192C TYR* 5.0 5.6 - - + -
193C ASN* 4.6 6.1 - - - +
196C ALA* 3.9 18.2 - - + -
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Residues in contact with VAL 170 (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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166C GLY 2.9 23.3 + - - +
167C ALA* 3.7 10.3 - - - +
168C ARG 3.4 0.4 - - - -
169C ALA* 1.3 74.4 - - - +
171C SER* 1.3 56.7 + - - +
173C ALA* 4.8 0.2 - - - -
174C GLU* 3.1 33.2 + - - +
196C ALA* 4.2 19.1 - - + +
199C LEU* 4.1 26.2 - - + -
200C VAL* 3.2 27.1 - - + +
203C ASN* 6.0 1.3 - - - +
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Residues in contact with SER 171 (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 ALA 3.3 10.6 + - - -
168C ARG* 3.0 19.2 + - - +
170C VAL* 1.3 74.9 - - - +
172C LEU* 1.3 61.4 + - - +
173C ALA 3.1 1.3 - - - -
174C GLU* 3.2 19.2 - - - +
175C ALA* 2.9 32.1 + - - +
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Residues in contact with LEU 172 (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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160C LEU* 3.7 45.2 - - + +
161C ASN 4.0 13.2 - - - +
162C ASP* 3.8 24.7 - - + +
168C ARG* 3.2 23.1 - - + +
169C ALA* 2.9 8.9 + - - +
171C SER* 1.3 82.0 + - - +
173C ALA* 1.3 52.9 + - - +
175C ALA* 3.6 6.7 - - + +
176C ALA* 2.8 34.0 + - - +
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Residues in contact with ALA 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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160C LEU* 4.8 1.3 - - - +
169C ALA 3.0 10.2 + - - +
170C VAL* 3.8 3.1 - - - +
172C LEU* 1.3 75.1 - - - +
174C GLU* 1.3 57.3 + - - +
175C ALA 3.2 0.9 - - - -
176C ALA* 3.8 6.9 - - - +
177C LEU* 2.8 35.5 + - - +
186C PHE* 3.9 18.7 - - + -
196C ALA* 5.6 0.4 - - + -
197C GLN* 4.6 16.2 - - + +
200C VAL* 3.5 25.3 - - + +
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Residues in contact with GLU 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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170C VAL* 3.1 27.4 + - - +
171C SER* 3.2 25.0 - - - +
173C ALA* 1.3 76.9 - - - +
175C ALA* 1.3 59.1 + - - +
177C LEU* 3.2 3.5 + - - +
178C ASN* 2.9 39.4 + - - +
200C VAL* 3.6 21.2 - - + +
203C ASN* 5.0 10.2 + - - +
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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
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171C SER 2.9 18.2 + - - +
172C LEU* 3.6 8.7 - - + +
174C GLU* 1.3 73.3 - - - +
176C ALA* 1.3 54.9 + - - +
178C ASN* 2.7 31.5 + - - +
179C ALA* 2.7 20.9 + - - +
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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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127C VAL* 4.0 23.1 - - + +
158C ASP* 5.5 2.9 - - - +
160C LEU* 3.8 20.0 - - + -
172C LEU 2.8 22.1 + - - +
173C ALA* 3.8 7.2 - - - +
175C ALA* 1.3 71.5 - - - +
177C LEU* 1.3 58.7 + - - +
179C ALA* 4.6 2.5 - - - +
180C HIS* 3.0 42.8 + - + +
186C PHE* 4.3 3.6 - - + -
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Residues in contact with LEU 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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173C ALA 2.8 23.3 + - - +
174C GLU 3.4 4.7 - - - +
176C ALA* 1.3 72.6 - - - +
178C ASN* 1.3 64.0 + - - +
180C HIS 3.4 21.4 - - - +
181C PRO* 3.6 9.9 - - + +
183C LEU* 4.5 11.4 - - + -
186C PHE* 4.5 8.2 - - + -
200C VAL* 3.7 24.7 - - + +
201C VAL* 4.8 7.2 - - + -
204C ALA* 3.6 30.7 - - + -
206C LYS* 5.0 11.2 - - + +
210C VAL* 4.5 20.0 - - + -
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Residues in contact with ASN 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 GLU* 2.9 33.5 + - - +
175C ALA* 2.7 12.3 + - - +
177C LEU* 1.3 76.7 - - - +
179C ALA* 1.3 63.8 + - - +
180C HIS 2.9 5.5 + - - -
181C PRO* 3.0 21.6 - - - +
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Residues in contact with ALA 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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158C ASP* 6.0 0.2 - - - +
175C ALA 2.7 17.7 + - - +
176C ALA* 4.7 1.1 - - - -
178C ASN* 1.3 73.2 - - - +
180C HIS* 1.3 80.9 + - + +
181C PRO* 3.3 6.2 - - - +
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Residues in contact with HIS 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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125C LYS* 4.3 16.9 + - + +
127C VAL* 5.0 3.8 - - + -
157C VAL* 3.8 36.6 + - + +
158C ASP* 3.7 21.2 + - - -
176C ALA* 3.0 23.7 + - - +
177C LEU* 3.4 10.0 - - - +
179C ALA* 1.3 95.4 + - + +
181C PRO* 1.3 56.6 - - - +
182C ASP* 3.1 12.1 - - - +
183C LEU* 3.1 39.1 + - + +
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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