Contacts of the helix formed by residues 168 - 179 (chain B) in PDB entry 4ADV
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 GLU 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B VAL* 3.1 34.4 - - + +
70B GLY* 3.6 1.8 - - - +
71B THR* 2.6 52.9 + - - -
72B LYS* 3.8 0.3 + - - +
95B TRP* 4.3 8.3 - - - +
162B VAL* 3.4 29.4 - - + -
163B ILE* 4.4 3.4 - - + +
164B ASP 3.8 5.5 + - - +
165B ALA 4.5 2.0 - - - -
166B ASP 3.4 1.5 - - - -
167B HIS* 1.3 87.6 - - + +
169B HIS* 1.3 66.0 + - - +
170B ILE 3.6 1.6 - - - -
171B ALA* 3.3 6.0 - - + +
172B ILE* 3.3 21.5 + - - +
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Residues in contact with HIS 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B ALA 4.2 8.2 + - - +
166B ASP 3.0 17.6 + - - +
167B HIS 2.6 12.6 + - - +
168B GLU* 1.3 74.6 - - - +
170B ILE* 1.3 90.1 + - + +
172B ILE* 3.0 12.7 + - - +
173B LYS* 3.1 25.4 + - + +
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Residues in contact with ILE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101A A 3.2 80.5 - - + +
95B TRP* 4.3 10.8 - - + +
96B LEU 5.2 2.5 - - - +
97B GLY* 5.5 0.9 - - - -
167B HIS 4.8 0.6 + - - +
168B GLU 3.6 0.2 - - - -
169B HIS* 1.3 99.6 - - + +
171B ALA* 1.3 65.0 + - - +
173B LYS* 3.0 21.5 + - - +
174B GLU* 3.2 19.9 + - - +
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B VAL* 3.9 22.4 - - + -
95B TRP* 3.3 55.3 - - + +
100B LEU* 3.8 3.8 - - - +
160B LEU* 4.6 3.0 - - + +
168B GLU* 3.3 16.9 + - + +
169B HIS 3.1 0.2 - - - -
170B ILE* 1.3 80.2 - - - +
172B ILE* 1.3 63.3 + - + +
174B GLU 3.7 0.2 + - - -
175B ALA* 3.5 13.2 + - - +
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Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LEU* 5.5 1.8 - - - -
162B VAL* 3.6 29.4 - - + -
165B ALA* 3.6 43.1 - - + +
168B GLU 3.3 11.7 - - - +
169B HIS* 3.0 5.7 + - - +
171B ALA* 1.3 72.4 - - - +
173B LYS* 1.3 61.6 + - - +
175B ALA* 3.0 18.3 - - - +
176B ASN* 2.7 25.0 + - - +
182B VAL* 4.0 15.7 - - + -
184B ALA* 4.5 3.4 - - + -
194B GLY* 3.6 30.1 - - - +
195B VAL* 4.7 3.1 - - + -
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Residues in contact with LYS 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075A U 4.0 7.0 - - - +
1076A U 3.1 28.1 + - - -
1101A A 3.2 24.5 - - - +
169B HIS* 3.1 22.9 + - + +
170B ILE* 3.0 17.8 + - + +
172B ILE* 1.3 76.0 - - - +
174B GLU* 1.3 69.0 + - - +
175B ALA 2.9 0.2 + - - -
176B ASN* 2.5 42.0 + - - +
177B ASN* 3.5 18.8 + - + +
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Residues in contact with GLU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075A U 5.5 1.8 - - - -
1101A A 3.5 20.2 - - - +
95B TRP* 3.0 25.2 - - - -
96B LEU 3.9 0.7 - - - +
98B GLY* 3.2 25.0 + - - -
100B LEU* 3.2 28.9 + - + +
101B THR* 3.1 31.5 - - + +
170B ILE* 3.2 18.8 + - - +
171B ALA 4.1 2.5 - - - +
173B LYS* 1.3 81.9 - - + +
175B ALA* 1.3 64.4 + - - +
177B ASN* 3.0 16.7 + - - +
178B LEU* 3.1 18.9 - - - +
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU* 3.4 23.6 - - + +
160B LEU* 4.5 4.7 - - + -
171B ALA 3.5 3.0 + - - +
172B ILE* 3.0 15.5 + - - +
173B LYS 2.9 1.2 + - - -
174B GLU* 1.3 73.5 - - - +
176B ASN* 1.3 54.5 + - - +
177B ASN 2.6 15.4 + - - -
178B LEU* 2.7 15.4 + - - -
179B GLY 3.0 9.7 + - - -
180B ILE* 3.4 18.6 + - + +
182B VAL* 3.5 25.1 - - + -
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Residues in contact with ASN 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ILE* 2.7 39.4 + - - +
173B LYS* 2.5 35.5 + - - +
175B ALA* 1.3 72.9 - - - +
177B ASN* 1.3 56.1 + - - +
178B LEU 3.5 0.2 - - - -
179B GLY* 4.3 6.8 + - - +
180B ILE 4.5 3.1 + - - +
182B VAL* 4.8 3.1 - - + +
194B GLY* 4.0 15.5 + - - +
196B ASP* 6.0 1.6 - - - +
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Residues in contact with ASN 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075A U 3.7 24.8 + - - -
1076A U 5.1 8.3 + - - -
101B THR* 6.0 0.2 - - - -
173B LYS* 3.5 23.0 + - - +
174B GLU* 3.0 18.6 + - - +
175B ALA 2.6 3.4 + - - -
176B ASN* 1.3 77.6 - - - +
178B LEU* 1.3 65.4 + - + +
179B GLY 3.6 0.4 - - - -
69E ASN* 3.3 12.6 - - - +
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075A U 5.4 0.2 - - - +
100B LEU* 3.0 24.7 - - + +
101B THR* 3.8 25.6 - - - +
156B LEU* 3.5 18.2 - - + -
174B GLU 3.1 20.4 - - - +
175B ALA* 2.7 7.6 + - - +
177B ASN* 1.3 91.4 - - + +
179B GLY* 1.3 58.4 + - - +
180B ILE* 4.0 19.2 - - + +
68E ARG* 4.6 5.8 - - + +
69E ASN* 2.6 55.9 + - - +
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Residues in contact with GLY 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ALA 3.0 3.4 + - - -
176B ASN* 4.3 5.0 - - - -
177B ASN 3.6 2.4 - - - +
178B LEU* 1.3 80.2 - - - +
180B ILE* 1.3 63.5 + - - +
181B PRO* 3.2 13.6 - - - +
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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