Contacts of the helix formed by residues 181 - 191 (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 SER 181 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C G 3.8 22.6 - - - +
3C C 5.8 1.3 - - - -
169L GLY* 4.2 1.3 - - - -
173L THR* 3.6 11.4 - - - +
178L PRO 3.4 14.1 + - - -
179L ALA 3.6 0.8 - - - -
180L TYR* 1.3 79.9 - - - +
182L GLN* 1.3 65.4 + - - +
183L SER* 3.6 15.9 + - - -
184L ALA* 3.1 15.1 + - - +
185L ILE* 3.0 21.4 + - - +
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Residues in contact with GLN 182 (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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9D T 3.4 20.5 - - + +
10D A 2.9 48.6 + - - -
165L GLN* 3.0 38.3 + - + +
166L THR* 3.7 30.5 - - + +
169L GLY* 4.0 5.2 - - - -
181L SER* 1.3 70.5 - - - +
183L SER* 1.3 69.3 + - - +
185L ILE* 3.2 12.3 + - - +
186L SER* 2.9 18.2 + - - -
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Residues in contact with SER 183 (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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2C G 4.3 4.4 - - - -
3C C 3.6 25.3 + - - -
4C A 4.4 3.1 + - - -
11D T 3.2 35.5 - - - +
181L SER* 3.6 12.3 + - - -
182L GLN* 1.3 89.7 + - - +
184L ALA* 1.3 58.0 + - - +
186L SER* 3.1 3.6 + - - -
187L ARG* 2.9 35.0 + - - +
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Residues in contact with ALA 184 (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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2C G 5.7 5.3 - - + +
179L ALA 3.5 24.0 - - - +
180L TYR* 4.3 0.9 - - - -
181L SER* 3.1 24.8 + - - +
183L SER* 1.3 78.6 + - - +
185L ILE* 1.3 55.0 + - + +
187L ARG* 3.1 7.9 + - - +
188L PHE* 2.7 38.1 + - - +
193L ILE* 5.7 0.7 - - - +
201L LEU* 5.4 7.6 - - + +
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Residues in contact with ILE 185 (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* 4.1 16.2 - - + -
158L ARG* 4.8 1.8 - - - -
165L GLN* 3.9 27.4 - - + +
168L VAL* 4.2 18.6 - - + -
169L GLY 4.3 2.5 - - - +
172L MSE 4.8 4.7 - - + -
180L TYR* 4.0 17.5 - - + +
181L SER 3.0 17.4 + - - +
182L GLN* 3.4 12.3 - - - +
184L ALA* 1.3 76.2 - - + +
186L SER* 1.3 64.2 + - - +
188L PHE* 3.7 5.9 - - - +
189L GLU* 2.9 47.9 + - - +
205L LEU* 4.9 16.8 - - + -
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Residues in contact with SER 186 (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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9D T 3.2 4.7 + - - -
10D A 3.1 44.7 + - - -
11D T 4.5 2.0 - - - -
165L GLN* 3.4 25.5 - - - +
182L GLN* 2.9 10.5 + - - -
183L SER 3.1 8.5 + - - -
185L ILE* 1.3 76.2 - - - +
187L ARG* 1.3 53.6 + - - +
189L GLU* 3.6 1.2 - - - +
190L LYS* 2.8 45.4 + - - +
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Residues in contact with ARG 187 (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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2C G 3.0 24.2 + - - -
3C C 3.8 6.5 - - - +
11D T 3.4 30.1 - - + +
12D G 2.9 49.9 + - - -
13D C 3.5 9.1 - - - +
183L SER* 2.9 20.0 + - - +
184L ALA* 3.6 6.7 - - - +
186L SER* 1.3 74.1 - - - +
188L PHE* 1.3 59.8 + - - +
190L LYS* 3.4 10.5 + - - +
191L LEU 2.7 7.6 + - - -
192L ASP* 2.6 70.3 + - + +
193L ILE* 4.4 10.1 - - + -
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Residues in contact with PHE 188 (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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147L ILE* 5.2 4.7 - - + -
150L PHE* 3.6 30.3 - + - -
151L ALA* 4.0 17.8 - - + +
154L PHE* 5.3 3.6 - + + -
184L ALA 2.7 20.7 + - - +
185L ILE* 3.7 7.4 - - + +
187L ARG* 1.3 73.3 - - - +
189L GLU* 1.3 62.0 + - + +
191L LEU* 2.6 35.5 + - + +
193L ILE* 3.6 15.6 - - + +
198L ALA* 3.9 21.1 - - + -
201L LEU* 3.4 44.4 - - + -
202L LYS* 3.9 7.9 - - + -
205L LEU* 3.6 26.7 - - + -
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Residues in contact with GLU 189 (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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10D A 4.6 2.3 + - - +
151L ALA* 4.1 19.7 - - - +
154L PHE* 4.0 18.0 - - + -
155L LYS* 3.6 34.0 - - + +
158L ARG* 2.8 42.2 + - - -
165L GLN* 3.1 23.0 + - - +
185L ILE* 2.9 29.0 + - + +
186L SER 3.6 2.9 - - - +
188L PHE* 1.3 78.1 - - + +
190L LYS* 1.3 63.4 + - + +
191L LEU* 3.3 1.4 + - - +
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Residues in contact with LYS 190 (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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10D A 3.5 47.5 - - - +
11D T 2.8 31.1 + - - +
186L SER* 2.8 27.6 + - - +
187L ARG* 4.0 16.6 - - - +
189L GLU* 1.3 73.0 - - + +
191L LEU* 1.3 69.0 + - - +
192L ASP* 4.2 14.7 + - + +
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Residues in contact with LEU 191 (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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144L MSE 4.7 8.1 - - + -
147L ILE* 4.0 20.6 - - + -
148L ARG* 3.5 38.1 - - + +
151L ALA* 3.9 14.4 - - + -
187L ARG 2.7 3.3 + - - -
188L PHE* 2.6 26.4 + - + +
189L GLU 3.0 1.1 - - - +
190L LYS* 1.3 81.6 - - - +
192L ASP* 1.3 53.9 - - - +
193L ILE* 3.1 20.6 + - + +
198L ALA* 4.7 11.9 - - + -
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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