Contacts of the helix formed by residues 177 - 185 (chain A) in PDB entry 2V5I
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 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A LEU* 4.1 4.3 - - - +
175A TYR* 3.7 5.2 - - - +
176A SER* 1.3 90.9 - - - +
178A LEU* 1.3 65.1 + - - +
179A GLN* 3.7 8.6 + - - +
180A ASP* 2.9 47.1 + - - +
181A ALA* 3.2 10.4 + - - +
195A TYR* 3.7 14.6 - - - +
201A GLU* 5.3 1.3 - - - -
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Residues in contact with LEU 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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172A LEU* 3.9 15.0 - - + -
177A THR* 1.3 70.5 - - - +
179A GLN* 1.3 63.3 + - - +
181A ALA* 3.1 4.7 + - + +
182A VAL* 2.9 33.1 + - + +
189A LEU* 4.6 4.7 - - + -
191A ILE* 4.2 25.4 - - + -
195A TYR* 3.1 31.7 + - + +
201A GLU* 4.3 3.1 - - - +
203A VAL* 4.0 25.8 - - + -
205A PHE* 6.2 0.2 - - + -
218A PHE* 4.0 23.6 - - + -
224A LEU* 4.3 10.5 - - + -
226A PHE* 4.0 19.3 - - + -
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Residues in contact with GLN 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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177A THR* 3.2 8.8 + - - +
178A LEU* 1.3 78.1 - - - +
180A ASP* 1.3 60.1 + - - +
182A VAL* 3.2 2.9 + - - +
183A THR* 2.8 61.6 + - - +
201A GLU* 5.2 1.8 + - - +
202A SER 3.8 9.9 - - - +
203A VAL* 3.3 17.0 - - + +
204A ASP* 2.7 52.9 + - - +
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Residues in contact with ASP 180 (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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175A TYR* 3.8 24.6 - - + -
176A SER* 4.0 9.0 + - - -
177A THR* 2.9 43.9 + - - +
179A GLN* 1.3 77.0 - - - +
181A ALA* 1.3 62.4 + - - +
183A THR* 3.5 7.3 + - - -
184A ASP* 3.3 17.8 + - - +
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL* 3.6 11.0 - - - +
172A LEU* 4.1 15.3 - - + -
175A TYR* 3.6 31.7 - - + -
177A THR 3.2 8.8 + - - +
178A LEU* 3.1 9.9 + - + +
180A ASP* 1.3 77.3 - - - +
182A VAL* 1.3 62.6 + - - +
184A ASP* 3.1 3.6 + - - +
185A ALA 3.1 17.5 + - - -
189A LEU* 4.0 20.9 - - + -
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 2.9 24.6 + - + +
179A GLN* 3.8 3.8 - - - +
181A ALA* 1.3 75.9 - - - +
183A THR* 1.3 57.9 + - - +
185A ALA* 3.2 14.0 + - - +
189A LEU* 3.8 24.9 - - + -
203A VAL* 3.8 19.5 - - + -
204A ASP 3.6 22.9 - - - +
205A PHE* 3.6 39.3 - - + +
208A LYS* 2.8 21.9 + - - -
210A LEU* 4.5 3.1 - - + -
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Residues in contact with THR 183 (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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179A GLN* 2.8 37.8 + - - +
180A ASP* 3.7 8.2 + - - -
181A ALA 3.3 0.2 - - - -
182A VAL* 1.3 75.9 - - - +
184A ASP* 1.3 59.1 + - + +
185A ALA 4.0 0.3 - - - +
204A ASP 5.5 0.7 - - - -
208A LYS* 2.9 18.9 + - - +
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Residues in contact with ASP 184 (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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170A VAL* 3.9 10.9 - - - +
175A TYR* 2.7 35.5 + - + +
180A ASP 3.3 8.9 + - - +
181A ALA 3.1 6.7 + - - +
183A THR* 1.3 79.6 - - + +
185A ALA* 1.3 62.2 + - - +
186A VAL* 3.7 11.1 + - - +
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Residues in contact with ALA 185 (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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170A VAL* 4.0 19.7 - - + -
181A ALA 3.1 11.4 + - - +
182A VAL* 3.2 15.1 + - - +
183A THR 4.0 0.2 - - - +
184A ASP* 1.3 79.3 - - - +
186A VAL* 1.3 60.6 + - - +
188A GLY 4.1 7.9 - - - +
189A LEU* 4.7 3.6 - - + -
208A LYS* 2.8 27.3 + - - +
210A LEU* 3.7 26.7 - - + -
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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