Contacts of the helix formed by residues 161 - 169 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A SER* 3.8 1.6 - - - -
159A GLY 4.1 0.6 + - - -
160A GLN* 1.3 74.5 + - - +
162A ILE* 1.3 65.3 + - - +
163A GLU* 3.7 16.6 + - - +
164A LYS* 3.1 30.4 + - - +
165A ILE* 3.1 15.0 + - - +
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Residues in contact with ILE 162 (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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151A ASN* 4.3 13.5 + - + +
152A ARG* 4.3 27.6 - - + +
155A SER* 3.5 22.8 + - - +
161A SER* 1.3 72.5 - - - +
163A GLU* 1.3 71.1 + - - +
165A ILE* 3.2 9.7 + - - +
166A GLN* 2.9 30.6 + - + +
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Residues in contact with GLU 163 (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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161A SER* 3.1 18.4 + - - +
162A ILE* 1.3 87.6 + - - +
164A LYS* 1.3 62.6 + - - +
166A GLN* 3.5 7.0 + - - +
167A LYS* 3.1 23.0 + - - +
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Residues in contact with LYS 164 (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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160A GLN* 3.3 36.3 - - + +
161A SER* 3.1 22.3 + - - +
163A GLU* 1.3 76.1 - - - +
165A ILE* 1.3 59.1 + - - +
167A LYS* 3.2 6.6 + - + +
168A ASP* 2.8 56.2 + - - +
183A TYR* 3.9 12.3 - - - +
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Residues in contact with ILE 165 (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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122A ILE* 6.0 0.2 - - + -
151A ASN* 3.5 38.4 - - + +
154A LEU* 4.1 28.5 - - + -
155A SER 4.5 1.8 - - - +
158A THR* 4.1 9.0 - - - +
160A GLN* 3.8 21.5 - - + +
161A SER 3.1 18.7 + - - +
162A ILE* 3.2 8.9 + - - +
164A LYS* 1.3 71.4 - - - +
166A GLN* 1.3 67.2 + - - +
168A ASP 3.0 1.4 + - - -
169A THR* 2.8 36.7 + - + +
183A TYR* 3.7 28.7 - - + +
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Residues in contact with GLN 166 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A ARG* 3.0 54.8 + - - +
151A ASN* 2.9 26.6 + - - +
162A ILE* 2.9 18.6 + - + +
163A GLU* 3.6 8.5 - - - +
165A ILE* 1.3 77.8 - - - +
167A LYS* 1.3 64.1 + - - +
170A ASP* 3.4 7.1 + - - +
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Residues in contact with LYS 167 (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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163A GLU 3.1 13.9 + - - +
164A LYS* 3.7 6.5 - - - +
165A ILE 3.2 0.2 - - - -
166A GLN* 1.3 82.6 - - - +
168A ASP* 1.3 66.9 + - - +
169A THR 3.4 0.7 + - - -
170A ASP* 3.5 17.1 + - - +
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Residues in contact with ASP 168 (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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122A ILE* 4.5 3.1 - - + -
164A LYS* 2.8 50.7 + - - +
165A ILE 3.8 1.6 - - - +
167A LYS* 1.3 80.5 - - - +
169A THR* 1.3 60.7 + - - +
170A ASP 3.5 0.4 - - - -
171A ARG 3.9 2.6 + - - +
173A ASN* 3.1 41.8 + - - +
183A TYR* 2.7 34.0 + - + +
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Residues in contact with THR 169 (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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122A ILE* 3.7 33.9 - - + -
123A HIS* 3.6 19.0 - - - +
124A GLN* 2.9 28.5 + - - +
147A ARG* 3.0 24.0 + - - -
151A ASN* 4.3 6.8 + - - +
154A LEU* 5.3 3.8 - - + -
165A ILE* 2.8 34.4 + - + +
166A GLN* 4.1 0.5 - - - -
168A ASP* 1.3 81.2 - - - +
170A ASP* 1.3 62.8 + - - +
171A ARG 3.3 7.3 + - - -
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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