Contacts of the helix formed by residues 169 - 179 (chain A) in PDB entry 2FDR
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 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ASP* 4.9 1.2 + - - -
48A GLY* 5.9 6.7 - - - -
143A LYS* 5.5 1.4 + - - +
167A GLU* 3.4 8.9 + - - +
168A ASP* 1.3 91.3 + - - +
170A VAL* 1.3 58.5 + - - +
171A HIS* 3.6 6.7 + - - +
172A GLY* 3.0 18.5 + - - -
173A ILE* 3.0 27.9 + - - +
200A LEU* 3.9 5.2 - - - -
1001A MG 4.4 4.3 - - - -
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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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47A ALA 5.6 2.2 - - - +
48A GLY* 5.3 10.4 - - - -
169A SER* 1.3 73.0 - - - +
171A HIS* 1.3 78.9 + - + +
173A ILE* 3.3 1.8 + - - +
174A HIS* 3.0 44.2 + - + +
199A ARG* 3.8 22.4 - - + +
200A LEU* 3.9 7.8 - - + +
203A ALA* 3.2 32.1 - - + -
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Residues in contact with HIS 171 (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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48A GLY* 3.9 34.0 + - - -
49A MSE 5.4 1.8 - - - -
50A THR* 6.4 1.8 - - + -
108A ASN* 5.4 2.5 - - - +
143A LYS* 3.7 11.3 + - + +
144A PRO* 3.4 49.6 - - + +
169A SER* 3.3 6.1 + - - +
170A VAL* 1.3 92.9 - - + +
172A GLY* 1.3 56.5 + - - +
174A HIS* 3.5 4.8 + + - -
175A GLY 3.0 23.2 + - - -
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Residues in contact with GLY 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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143A LYS* 3.6 16.2 - - - +
149A PHE* 3.3 10.4 - - - -
167A GLU* 3.3 32.4 - - - +
169A SER* 3.0 11.1 + - - -
171A HIS* 1.3 75.1 - - - +
173A ILE* 1.3 59.8 + - - +
176A ALA* 3.0 25.6 + - - +
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Residues in contact with ILE 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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167A GLU* 3.7 15.0 - - + +
169A SER 3.0 15.5 + - - +
170A VAL 3.8 4.5 - - - +
171A HIS 3.3 0.2 - - - -
172A GLY* 1.3 73.2 - - - +
174A HIS* 1.3 60.8 + - - +
176A ALA* 3.2 3.2 + - - +
177A ARG* 2.9 33.0 + - + +
183A VAL* 3.8 21.5 - - + +
185A GLY* 4.3 7.2 - - - -
200A LEU* 3.6 38.6 - - + +
203A ALA* 3.5 30.5 - - + +
204A GLY 3.7 3.6 - - - +
205A ALA* 3.6 26.0 - - + +
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Residues in contact with HIS 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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144A PRO* 4.0 15.7 - - + +
170A VAL* 3.0 39.9 + - + +
171A HIS* 3.9 8.5 - + - +
173A ILE* 1.3 72.3 - - - +
175A GLY* 1.3 56.6 - - - +
177A ARG* 3.2 4.4 + - - +
178A ALA* 2.8 37.0 + - - +
202A ASP 4.8 2.2 - - - -
203A ALA* 3.4 37.4 + - + +
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Residues in contact with GLY 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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144A PRO* 3.1 21.4 + - - -
145A LYS 3.7 10.3 - - - -
146A PRO* 3.5 11.8 - - - +
149A PHE* 3.5 15.3 - - - -
171A HIS 3.0 14.1 + - - -
173A ILE 3.3 0.2 - - - -
174A HIS* 1.3 76.4 - - - +
176A ALA* 1.3 61.1 + - - +
178A ALA* 3.3 0.9 + - - +
179A ALA* 3.1 18.2 + - - +
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Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A PHE* 3.3 11.3 - - + -
165A VAL* 3.8 29.4 - - + -
172A GLY 3.0 17.9 + - - +
173A ILE* 3.2 0.6 + - - +
175A GLY* 1.3 75.1 - - - +
177A ARG* 1.3 62.6 + - - +
179A ALA* 3.2 10.5 + - - +
180A GLY 3.3 0.2 + - - -
181A MSE 3.1 26.5 + - + +
183A VAL* 3.6 23.3 - - + -
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Residues in contact with ARG 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 ILE 2.9 20.5 + - - +
174A HIS* 3.8 5.6 - - - +
176A ALA* 1.3 75.7 - - - +
178A ALA* 1.3 58.7 + - - +
180A GLY* 2.9 20.8 + - - -
181A MSE 3.8 13.5 + - - -
182A ARG* 5.5 1.1 - - - +
183A VAL* 3.7 17.0 - - + +
203A ALA 3.9 16.8 - - - +
204A GLY* 2.9 37.5 + - - +
206A GLU* 5.4 2.4 - - - +
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Residues in contact with ALA 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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144A PRO 4.5 2.9 - - - +
146A PRO* 3.9 26.2 - - + +
150A LEU* 5.7 0.2 - - - +
174A HIS 2.8 18.9 + - - +
175A GLY* 3.5 6.5 - - - +
177A ARG* 1.3 76.4 - - - +
179A ALA* 1.3 58.2 + - - +
180A GLY 3.3 0.6 + - - -
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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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146A PRO* 3.8 14.8 - - + -
149A PHE* 4.1 16.6 - - + -
150A LEU* 3.8 22.8 - - + +
160A PRO* 3.1 25.6 - - - +
175A GLY 3.1 12.4 + - - +
176A ALA 3.4 10.1 - - - +
177A ARG 3.1 1.0 - - - -
178A ALA* 1.3 75.9 - - - +
180A GLY* 1.3 58.0 + - - +
181A MSE 4.1 7.9 - - + -
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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