Contacts of the helix formed by residues 164 - 176 (chain L) in PDB entry 3D1N
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 THR 164 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D T 3.9 34.4 + - - +
9D T 3.0 20.0 - - - +
158L ARG* 3.9 0.7 - - - -
162L GLY 5.6 0.7 - - - +
163L LEU* 1.3 75.0 - - - +
165L GLN* 1.3 65.8 + - - +
166L THR* 3.7 7.8 + - - -
167L GLN* 2.6 49.4 + - - +
168L VAL* 3.2 16.2 + - - +
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Residues in contact with GLN 165 (chain L).
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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9D T 2.8 63.5 + - - +
10D A 3.8 1.4 + - - -
158L ARG* 3.6 12.8 - - - +
164L THR* 1.3 71.4 - - - +
166L THR* 1.3 52.8 + - - +
168L VAL* 3.3 4.5 + - - +
169L GLY* 2.6 35.2 + - - -
182L GLN* 3.0 28.1 + - + +
185L ILE* 3.9 25.9 - - + +
186L SER* 3.4 21.0 - - - +
189L GLU* 3.1 23.8 + - - +
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Residues in contact with THR 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D T 3.8 20.1 + - - +
9D T 3.1 24.3 + - + +
164L THR* 3.0 7.1 - - - -
165L GLN* 1.3 78.3 - - - +
167L GLN* 1.3 56.5 + - - +
169L GLY* 3.3 2.1 + - - -
170L GLN* 2.9 45.9 + - + +
182L GLN* 3.7 15.1 - - + +
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Residues in contact with GLN 167 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162L GLY 3.9 3.5 + - - +
163L LEU* 3.2 26.1 - - + +
164L THR* 2.6 53.7 + - - +
166L THR* 1.3 72.8 - - - +
168L VAL* 1.3 67.6 + - + +
170L GLN* 3.0 9.4 + - - +
171L ALA* 2.9 23.0 + - - +
224L MSE 4.3 21.6 - - - +
227L VAL* 3.8 22.5 - - + +
229L GLY 5.2 5.0 + - - +
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Residues in contact with VAL 168 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154L PHE* 4.4 7.4 - - + -
158L ARG* 4.1 26.9 - - + -
163L LEU* 4.3 15.9 - - + +
164L THR 3.2 15.3 - - - +
165L GLN* 3.6 5.8 - - - +
167L GLN* 1.3 70.3 - - - +
169L GLY* 1.3 69.3 + - - +
170L GLN 3.0 0.5 + - - -
171L ALA* 3.1 6.5 + - - -
172L MSE 2.7 66.0 + - + +
185L ILE* 4.2 11.7 - - + -
208L TRP* 4.2 14.1 - - + -
227L VAL* 5.6 0.2 - - - -
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Residues in contact with GLY 169 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165L GLN 2.6 22.0 + - - -
166L THR 3.4 3.4 - - - -
168L VAL* 1.3 72.3 - - - +
170L GLN* 1.3 57.0 + - - +
173L THR* 2.8 39.2 + - - +
180L TYR 3.4 16.4 - - - -
181L SER* 4.2 0.9 - - - -
182L GLN* 4.0 14.1 - - - -
185L ILE* 4.3 2.1 - - - +
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Residues in contact with GLN 170 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166L THR* 2.9 32.6 + - + +
167L GLN* 3.0 8.5 + - - +
169L GLY* 1.3 74.3 - - - +
171L ALA* 1.3 65.9 + - - +
173L THR* 3.1 21.5 + - - +
174L ALA* 3.2 14.2 + - - +
227L VAL* 4.8 4.9 - - + +
231L PRO* 4.5 40.9 - - + +
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Residues in contact with ALA 171 (chain L).
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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167L GLN 2.9 12.9 + - - +
168L VAL 3.7 3.4 - - - +
170L GLN* 1.3 76.7 - - - +
172L MSE 1.3 64.4 + - - +
174L ALA* 3.3 15.2 - - - +
175L THR* 3.4 13.2 + - - +
208L TRP* 3.5 32.7 + - + +
226L PHE 4.3 4.5 - - - +
227L VAL* 3.5 33.5 + - + +
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Residues in contact with MSE 172 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154L PHE* 3.8 11.4 - - + -
168L VAL* 2.7 53.9 + - + +
171L ALA* 1.3 68.3 - - - +
173L THR* 1.3 59.8 + - - +
174L ALA 2.9 2.5 + - - -
175L THR* 3.0 5.4 + - - -
176L GLU* 2.7 42.7 + - - +
180L TYR* 3.4 40.2 - - + +
185L ILE* 4.8 2.0 - - + -
204L VAL 4.8 2.2 - - - +
205L LEU* 3.6 25.1 - - + -
208L TRP* 3.6 45.3 - - + +
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Residues in contact with THR 173 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169L GLY 2.8 32.0 + - - +
170L GLN* 3.1 17.5 + - - -
172L MSE 1.3 72.9 - - - +
174L ALA* 1.3 65.3 + - - +
177L GLY* 3.3 33.2 + - - +
178L PRO* 4.4 7.6 - - + -
180L TYR 3.3 23.8 - - - +
181L SER* 3.6 11.0 - - - +
269L LYS* 5.7 6.5 - - - +
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Residues in contact with ALA 174 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170L GLN 3.2 9.6 + - - +
171L ALA* 3.3 13.0 - - - +
172L MSE 2.9 0.8 + - - -
173L THR* 1.3 86.4 + - - +
175L THR* 1.3 66.5 + - + +
176L GLU 3.6 1.0 + - - -
227L VAL 6.0 0.2 - - - +
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Residues in contact with THR 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171L ALA 3.4 14.2 + - - +
172L MSE 3.0 1.8 + - - -
174L ALA* 1.3 82.5 - - + +
176L GLU* 1.3 82.6 + - - +
208L TRP* 4.2 13.2 + - - -
226L PHE* 5.8 9.3 - - + -
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Residues in contact with GLU 176 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172L MSE 2.7 23.3 + - - +
173L THR 4.1 0.9 - - - -
174L ALA 3.4 1.1 - - - -
175L THR* 1.3 108.9 + - - +
177L GLY* 1.3 59.1 + - - +
180L TYR* 3.5 25.1 - - + -
204L VAL* 3.3 35.9 - - + +
208L TRP* 4.9 10.1 - - - +
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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