Contacts of the helix formed by residues 165 - 180 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A ASP* 3.1 28.3 + - - +
163A CYS 4.0 2.9 - - - +
164A GLU* 1.3 79.4 - - - +
166A GLY* 1.3 58.3 + - - +
167A ALA* 2.9 20.4 + - - +
168A ARG* 2.7 44.8 + - - +
169A ALA* 2.9 23.3 + - - +
192A TYR* 5.1 3.0 - - - -
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Residues in contact with GLY 166 (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* 1.3 70.4 + - - +
167A ALA* 1.3 67.2 + - - +
169A ALA* 3.3 9.4 - - - +
170A VAL* 2.9 30.8 + - - +
192A TYR* 4.2 28.0 - - - -
196A ALA* 4.8 2.9 - - - +
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Residues in contact with ALA 167 (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* 2.9 11.8 + - - +
166A GLY* 1.3 78.2 - - - +
168A ARG* 1.3 66.3 + - + +
170A VAL* 3.2 8.8 + - - +
171A SER* 3.2 19.9 + - - -
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Residues in contact with ARG 168 (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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161A ASN 4.0 9.9 + - - -
162A ASP* 3.5 32.5 + - + +
163A CYS* 4.0 15.9 - - - +
165A ASP* 2.7 34.0 + - - +
167A ALA* 1.3 72.8 - - + +
169A ALA* 1.3 51.3 + - - +
171A SER* 2.7 31.6 + - - -
172A LEU* 2.7 38.3 + - - +
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Residues in contact with ALA 169 (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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162A ASP* 3.3 28.6 - - - +
165A ASP 2.9 12.9 + - - +
166A GLY* 3.3 15.3 - - - +
168A ARG* 1.3 73.2 - - - +
170A VAL* 1.3 55.7 + - - +
172A LEU* 3.4 4.3 + - - +
173A ALA* 2.9 31.5 + - - +
192A TYR* 5.3 3.4 - - + +
193A ASN* 4.2 9.2 - - - +
196A ALA* 3.9 18.5 - - + +
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Residues in contact with VAL 170 (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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166A GLY 2.9 23.0 + - - +
167A ALA* 3.4 9.2 - - - +
169A ALA* 1.3 72.0 - - - +
171A SER* 1.3 63.4 + - - +
173A ALA 3.4 0.5 + - - -
174A GLU* 3.1 40.3 + - - +
196A ALA* 4.2 16.8 - - + +
199A LEU* 4.1 27.8 - - + -
200A VAL* 3.4 22.6 - - + +
203A ASN* 6.2 0.9 - - - +
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Residues in contact with SER 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ALA 3.2 10.0 + - - -
168A ARG* 2.7 17.5 + - - -
170A VAL* 1.3 73.2 - - - +
172A LEU* 1.3 63.0 - - - -
174A GLU* 3.1 15.0 + - - +
175A ALA* 2.9 28.6 + - - +
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Residues in contact with LEU 172 (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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160A LEU* 3.3 39.8 - - + +
161A ASN 3.7 8.7 - - - +
162A ASP* 3.5 43.1 - - + +
168A ARG* 2.7 33.8 + - - +
169A ALA* 3.6 5.4 - - - +
171A SER* 1.3 75.0 - - - +
173A ALA* 1.3 63.2 + - - +
175A ALA* 3.1 10.3 + - + +
176A ALA 3.1 18.2 + - - -
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Residues in contact with ALA 173 (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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160A LEU* 4.2 3.5 - - - +
169A ALA 2.9 20.7 + - - +
170A VAL* 4.6 0.2 - - - -
171A SER 3.3 0.2 - - - -
172A LEU* 1.3 73.3 - - - +
174A GLU* 1.3 55.7 + - - +
176A ALA* 3.4 3.5 + - - +
177A LEU* 3.0 28.1 + - - +
186A PHE* 3.7 26.5 - - + -
196A ALA 5.1 0.2 - - - -
197A GLN* 4.5 16.6 - - + -
200A VAL* 3.7 26.0 - - + -
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Residues in contact with GLU 174 (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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170A VAL* 3.1 30.3 + - - +
171A SER* 3.1 13.3 + - - +
173A ALA* 1.3 72.7 - - - +
175A ALA* 1.3 61.1 + - - +
177A LEU* 3.1 4.8 + - - +
178A ASN* 2.8 41.9 + - - +
200A VAL* 3.7 22.9 - - + +
203A ASN* 5.4 6.2 + - - +
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Residues in contact with ALA 175 (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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160A LEU* 5.7 1.6 - - + -
171A SER 2.9 14.2 + - - +
172A LEU* 3.3 16.6 - - + +
174A GLU* 1.3 75.6 - - - +
176A ALA* 1.3 51.9 + - - +
178A ASN* 2.9 8.9 + - - +
179A ALA* 2.7 38.0 + - - +
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Residues in contact with ALA 176 (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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127A VAL* 3.9 25.8 - - + -
158A ASP* 5.6 1.8 - - - +
160A LEU* 3.9 18.6 - - + +
172A LEU 3.1 8.9 + - - +
173A ALA 3.5 8.5 - - - +
175A ALA* 1.3 78.5 - - - +
177A LEU* 1.3 55.6 + - - +
179A ALA* 4.4 2.2 - - - +
180A HIS* 2.7 47.6 + - + +
183A LEU* 5.0 1.2 - - - +
186A PHE* 4.3 5.8 - - + -
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Residues in contact with LEU 177 (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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173A ALA 3.0 9.5 + - - +
174A GLU* 3.1 10.0 + - - +
176A ALA* 1.3 75.8 - - - +
178A ASN* 1.3 63.1 + - - +
180A HIS 3.0 21.5 - - - +
181A PRO* 3.9 4.9 - - - +
183A LEU* 3.7 14.6 - - + -
186A PHE* 3.4 35.9 - - + -
200A VAL* 3.4 27.8 - - + +
201A VAL* 4.6 4.9 - - + -
204A ALA* 3.6 28.9 - - + -
206A LYS* 4.6 12.8 - - + +
210A VAL* 4.9 10.1 - - + -
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Residues in contact with ASN 178 (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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174A GLU* 2.8 29.8 + - - +
175A ALA* 3.6 5.9 - - - +
177A LEU* 1.3 78.9 - - - +
179A ALA* 1.3 63.2 + - - +
181A PRO* 4.5 9.0 - - - +
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Residues in contact with ALA 179 (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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175A ALA 2.7 19.4 + - - +
176A ALA* 4.0 4.0 - - - +
178A ASN* 1.3 74.6 - - - +
180A HIS* 1.3 78.8 + - + +
181A PRO* 3.3 9.2 - - - +
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Residues in contact with HIS 180 (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 LYS* 5.6 7.4 + - + -
127A VAL* 4.0 15.9 - - + -
157A VAL* 4.1 22.1 - - + +
158A ASP* 2.7 29.0 + - - -
176A ALA* 2.7 39.2 + - - +
177A LEU* 3.0 15.8 - - - +
179A ALA* 1.3 89.3 + - + +
181A PRO* 1.3 65.4 - - - +
182A ASP* 3.2 10.5 + - - +
183A LEU* 3.5 26.2 + - + +
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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