Contacts of the helix formed by residues 161 - 169 (chain B) in PDB entry 3V5I
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 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B SER* 3.8 2.2 - - - -
159B GLY 4.0 0.8 + - - -
160B GLN* 1.3 74.4 + - - +
162B ILE* 1.3 65.2 + - - +
163B GLU* 3.6 17.1 + - - +
164B LYS* 3.0 33.9 + - - +
165B ILE* 3.0 15.7 + - - +
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Residues in contact with ILE 162 (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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151B ASN* 4.4 13.2 + - + +
152B ARG* 4.2 28.0 - - + +
155B SER* 3.6 22.8 + - - +
161B SER* 1.3 72.1 - - - +
163B GLU* 1.3 71.5 + - - +
165B ILE* 3.3 9.3 + - - +
166B GLN* 3.0 29.3 + - + +
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Residues in contact with GLU 163 (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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161B SER* 3.8 17.7 + - - +
162B ILE* 1.3 90.2 + - + +
164B LYS* 1.3 61.1 + - - +
166B GLN* 3.5 7.7 + - - +
167B LYS* 3.2 22.2 + - - +
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Residues in contact with LYS 164 (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 GLN* 3.3 35.9 - - + +
161B SER* 3.0 21.3 + - - +
163B GLU* 1.3 76.5 - - - +
165B ILE* 1.3 59.5 + - - +
167B LYS* 3.3 5.5 + - + +
168B ASP* 2.8 65.4 + - - +
183B TYR* 3.8 11.4 - - - +
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Residues in contact with ILE 165 (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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122B ILE* 6.0 0.2 - - + -
151B ASN* 3.5 37.9 - - + +
154B LEU* 4.1 27.6 - - + -
155B SER 4.5 2.9 - - - +
158B THR* 4.0 9.4 - - - +
160B GLN* 3.8 20.0 - - + +
161B SER 3.0 18.5 + - - +
162B ILE* 3.6 8.3 - - - +
164B LYS* 1.3 75.5 - - - +
166B GLN* 1.3 63.3 + - - +
168B ASP 3.1 0.9 + - - -
169B THR* 2.9 37.6 + - + +
183B TYR* 3.7 28.3 - - + +
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Residues in contact with GLN 166 (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 ARG* 3.0 54.1 + - - +
151B ASN* 2.9 27.8 + - - +
162B ILE* 3.0 19.9 + - + +
163B GLU* 3.6 9.2 - - - +
165B ILE* 1.3 76.9 - - - +
167B LYS* 1.3 63.3 + - - +
170B ASP* 3.4 7.4 + - - +
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Residues in contact with LYS 167 (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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163B GLU 3.2 13.9 + - - +
164B LYS* 3.8 5.6 - - + +
165B ILE 3.3 0.2 - - - -
166B GLN* 1.3 80.3 - - - +
168B ASP* 1.3 69.0 + - - +
169B THR 3.4 1.0 + - - -
170B ASP* 3.4 19.0 + - - +
171B ARG 5.1 0.2 + - - -
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Residues in contact with ASP 168 (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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122B ILE* 4.5 2.9 - - + -
164B LYS* 2.8 51.5 + - - +
165B ILE 3.1 1.8 + - - +
167B LYS* 1.3 79.8 - - - +
169B THR* 1.3 58.9 + - - +
170B ASP 3.5 0.2 - - - -
171B ARG 3.9 2.8 + - - +
173B ASN* 3.1 40.0 + - - +
183B TYR* 2.7 33.5 + - + +
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Residues in contact with THR 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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122B ILE* 3.7 32.5 - - + -
123B HIS* 3.6 18.7 - - - +
124B GLN* 2.9 24.2 + - - +
147B ARG* 3.0 20.1 + - - -
151B ASN* 4.2 6.3 + - - +
154B LEU* 5.3 3.4 - - + -
165B ILE* 2.9 36.9 + - + +
166B GLN* 4.1 0.3 - - - -
167B LYS 3.3 0.2 - - - -
168B ASP* 1.3 80.6 - - - +
170B ASP* 1.3 64.0 + - - +
171B ARG* 3.2 8.5 + - - +
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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