Contacts of the helix formed by residues 157 - 168 (chain A) in PDB entry 1DZF
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 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A LYS* 3.4 40.5 - - - +
72A PHE* 3.6 13.2 - - - -
156A LEU* 1.3 76.5 - - - +
158A SER* 1.3 65.5 + - - +
159A ASP* 3.6 8.8 + - - +
160A GLU* 2.7 37.3 + - - +
161A LYS* 2.9 22.2 + - - +
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Residues in contact with SER 158 (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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71A LYS 4.7 5.8 + - - -
72A PHE* 5.1 1.8 - - - -
73A PRO* 5.8 2.3 - - - +
157A SER* 1.3 73.0 - - - +
159A ASP* 1.3 71.2 + - - +
161A LYS* 3.6 11.0 - - - +
162A ARG* 3.0 24.7 + - - +
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Residues in contact with ASP 159 (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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71A LYS 6.1 0.2 - - - -
157A SER* 3.1 9.1 + - - +
158A SER* 1.3 89.6 + - - +
160A GLU* 1.3 57.6 + - - +
162A ARG* 3.2 14.8 + - - +
163A GLU* 2.9 30.2 + - - +
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Residues in contact with GLU 160 (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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71A LYS* 3.4 27.3 + - - -
156A LEU* 3.4 28.1 - - + +
157A SER* 2.7 39.2 + - - +
159A ASP* 1.3 78.9 - - - +
161A LYS* 1.3 56.7 + - - +
163A GLU* 3.3 8.1 + - - +
164A LEU* 2.9 28.2 + - - +
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Residues in contact with LYS 161 (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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156A LEU* 4.3 10.9 - - + +
157A SER 2.9 15.5 + - - +
158A SER* 3.6 10.1 - - - +
160A GLU* 1.3 74.7 - - - +
162A ARG* 1.3 66.2 + - - +
164A LEU* 3.1 8.3 + - + +
165A LEU* 3.0 48.9 + - + +
172A GLU* 2.8 30.5 + - - -
175A LEU* 5.8 0.2 - - - -
193A GLY* 2.8 30.5 + - - +
194A GLU* 5.6 0.4 - - - -
195A VAL* 3.9 20.0 - - + +
213A ILE* 4.0 9.6 - - - +
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Residues in contact with ARG 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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158A SER 3.0 14.1 + - - +
159A ASP* 3.5 17.3 + - - +
161A LYS* 1.3 75.7 - - - +
163A GLU* 1.3 58.2 + - - +
164A LEU 3.2 0.2 + - - -
165A LEU* 3.2 10.5 + - - +
166A LYS* 2.9 33.1 + - + +
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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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159A ASP 2.9 13.6 + - - +
160A GLU* 3.5 12.1 - - - +
162A ARG* 1.3 77.2 - - - +
164A LEU* 1.3 57.5 + - - +
166A LYS* 4.0 12.7 - - - +
167A ARG* 3.1 31.7 + - + +
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Residues in contact with LEU 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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156A LEU* 4.1 11.4 - - + -
160A GLU 2.9 13.3 + - - +
161A LYS* 3.1 10.7 + - + +
163A GLU* 1.3 74.7 - - - +
165A LEU* 1.3 67.5 + - + +
167A ARG* 3.4 3.8 + - - +
168A TYR* 3.2 52.2 + - + +
170A LEU* 5.8 0.2 - - - +
175A LEU* 4.2 26.0 - - + -
195A VAL* 4.2 4.0 - - + -
211A TYR* 3.8 57.9 - - + -
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Residues in contact with LEU 165 (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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161A LYS* 3.0 47.9 + - + +
162A ARG* 3.7 7.4 - - - +
164A LEU* 1.3 79.3 - - + +
166A LYS* 1.3 61.0 + - - +
168A TYR 3.8 0.2 + - - -
169A ARG* 3.4 3.5 + - - -
170A LEU* 3.1 51.2 + - + +
171A LYS* 3.7 5.8 - - - +
172A GLU* 3.7 28.3 - - + +
175A LEU* 3.8 21.3 - - + -
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Residues in contact with LYS 166 (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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162A ARG* 2.9 20.0 + - + +
163A GLU* 4.0 14.4 - - - +
165A LEU* 1.3 78.2 - - - +
167A ARG* 1.3 65.3 + - - +
168A TYR 3.2 1.2 + - - -
169A ARG* 3.4 10.1 + - - +
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Residues in contact with ARG 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 25.3 + - + +
164A LEU* 3.4 5.1 + - - +
166A LYS* 1.3 79.3 - - - +
168A TYR* 1.3 97.9 + - + +
169A ARG 3.6 0.4 - - - -
208A TYR* 6.1 2.8 - - - -
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Residues in contact with TYR 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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164A LEU* 3.2 47.3 + - + +
166A LYS 3.2 0.4 - - - -
167A ARG* 1.3 122.7 + - + +
169A ARG* 1.3 73.0 + - - +
170A LEU* 3.0 31.9 - - + +
208A TYR* 5.8 4.9 - - - -
211A TYR* 5.6 4.4 - + - -
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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