Contacts of the helix formed by residues 172 - 184 (chain B) in PDB entry 1V1A
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 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B TYR* 3.6 1.6 - - - -
168B GLN 5.2 0.4 - - - -
171B TRP* 1.3 78.3 - - - +
173B PRO* 1.3 75.1 - - - +
174B GLU* 3.6 15.1 + - - +
175B GLU* 2.9 34.6 + - - +
176B ALA* 3.2 21.0 + - - +
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Residues in contact with PRO 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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166B TYR* 3.2 15.7 - - + +
172B SER* 1.3 90.7 - - - +
174B GLU* 1.3 66.0 + - + +
176B ALA* 3.1 4.0 - - - +
177B ARG* 3.1 48.2 + - - +
199B LEU* 4.0 17.7 - - + +
200B LEU* 3.1 24.5 - - + +
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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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172B SER* 3.2 11.8 + - - +
173B PRO* 1.3 74.0 - - + +
175B GLU* 1.3 67.7 + - + +
176B ALA 2.8 4.9 + - - -
177B ARG* 2.8 27.5 + - - +
178B GLY* 2.8 21.5 + - - -
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Residues in contact with GLU 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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143B ARG* 4.2 18.0 + - - +
171B TRP* 3.9 27.4 - - + +
172B SER* 2.9 37.5 + - - +
174B GLU* 1.3 75.3 - - + +
176B ALA* 1.3 61.1 + - - +
178B GLY* 3.7 4.3 - - - +
179B PHE* 3.0 23.0 + - - +
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Residues in contact with ALA 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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166B TYR* 4.0 13.0 - - + -
171B TRP* 3.9 19.7 - - + -
172B SER 3.2 14.0 + - - +
173B PRO 3.1 13.2 - - - +
174B GLU 2.8 0.8 + - - -
175B GLU* 1.3 74.6 - - - +
177B ARG* 1.3 63.0 + - - +
179B PHE* 3.1 6.9 + - - +
180B LEU* 2.8 29.3 + - + +
200B LEU* 3.8 22.4 - - + -
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Residues in contact with ARG 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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173B PRO* 3.1 36.9 + - - +
174B GLU* 2.8 31.1 + - - +
176B ALA* 1.3 69.7 - - - +
178B GLY* 1.3 60.1 + - - +
180B LEU* 2.9 14.0 + - + +
181B GLU* 2.7 41.0 + - - +
199B LEU 4.5 1.8 + - - -
200B LEU* 2.5 35.1 + - + +
201B PHE* 4.3 19.5 - - + -
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Residues in contact with GLY 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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143B ARG* 4.3 9.3 + - - -
174B GLU 2.8 12.8 + - - -
175B GLU* 3.8 6.3 - - - -
177B ARG* 1.3 78.4 - - - +
179B PHE* 1.3 62.5 + - - +
181B GLU* 3.6 6.9 + - - +
182B ARG* 3.3 18.4 + - - +
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Residues in contact with PHE 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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133B GLY* 4.9 8.1 - - - -
136B PRO* 3.5 35.9 - - + -
143B ARG* 4.0 24.1 - - + +
146B SER* 3.8 20.0 - - - -
147B LEU* 4.2 20.6 - - + -
150B MET* 4.3 3.6 - - + -
162B LEU* 5.0 15.9 - - + -
171B TRP* 3.8 25.1 - + + -
175B GLU 3.0 13.6 + - - +
176B ALA 3.1 7.8 + - - +
178B GLY* 1.3 73.3 - - - +
180B LEU* 1.3 77.0 + - + +
182B ARG* 2.9 8.7 + - + +
183B ALA* 2.9 38.4 + - + +
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Residues in contact with LEU 180 (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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133B GLY* 6.5 1.1 - - - -
162B LEU* 5.3 10.3 - - + -
164B VAL* 5.0 23.1 - - + -
171B TRP* 6.1 2.0 - - + -
176B ALA* 2.8 19.3 + - + +
177B ARG* 2.9 23.7 + - - +
179B PHE* 1.3 90.7 - - + +
181B GLU* 1.3 63.4 + - - +
182B ARG 2.9 0.3 + - - -
183B ALA* 4.6 1.6 - - - +
184B LEU* 2.8 33.7 + - + +
190B LEU* 5.6 2.9 - - + -
200B LEU* 4.4 13.0 - - + -
201B PHE* 4.1 16.8 - - + -
211B LEU* 3.7 31.9 - - + -
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Residues in contact with GLU 181 (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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177B ARG* 2.7 23.1 + - - +
178B GLY* 3.8 7.4 - - - +
180B LEU* 1.3 73.2 - - - +
182B ARG* 1.3 60.9 + - - +
184B LEU* 4.5 3.0 - - - +
185B PRO* 3.8 13.0 - - - +
210B ALA* 5.2 12.1 - - - +
211B LEU* 5.2 1.8 - - - +
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Residues in contact with ARG 182 (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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143B ARG* 6.1 0.7 - - - +
147B LEU* 3.6 44.0 - - + +
151B GLU* 6.3 2.2 - - - +
178B GLY 3.3 10.5 + - - +
179B PHE* 2.9 12.9 + - + +
180B LEU 2.9 0.6 + - - -
181B GLU* 1.3 81.2 - - - +
183B ALA* 1.3 58.9 + - - +
185B PRO* 3.1 18.2 - - - +
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Residues in contact with ALA 183 (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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147B LEU* 3.5 26.0 - - + -
150B MET* 3.6 23.8 - - + +
162B LEU* 5.7 2.7 - - + -
179B PHE* 2.9 28.9 + - + +
180B LEU* 4.5 1.3 - - - +
182B ARG* 1.3 70.7 - - - +
184B LEU* 1.3 63.5 + - - +
185B PRO* 3.2 4.5 - - - -
186B GLY 3.4 8.0 + - - -
187B VAL* 3.2 18.8 + - + +
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Residues in contact with LEU 184 (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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180B LEU* 2.8 17.7 + - + +
181B GLU* 4.5 4.0 - - - +
183B ALA* 1.3 75.7 - - - +
185B PRO* 1.3 73.0 - - + +
187B VAL* 3.0 27.7 + - + +
190B LEU* 4.9 11.0 - - + -
210B ALA 4.3 7.6 - - - +
211B LEU* 3.8 38.1 - - + +
212B SER 3.4 33.9 - - - +
213B ALA* 4.6 10.7 - - + +
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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