Contacts of the helix formed by residues 158 - 167 (chain A) in PDB entry 1CX4
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 PRO 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A LEU 3.9 1.1 - - - +
157A ASP* 1.3 88.4 - - + +
159A GLU* 1.3 66.3 + - + +
161A MET* 4.0 8.2 - - + +
162A SER* 3.3 24.1 + - - -
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Residues in contact with GLU 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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157A ASP* 2.7 22.4 + - - +
158A PRO* 1.3 81.6 - - + +
160A GLN* 1.3 60.5 + - + +
161A MET 3.2 1.1 - - - -
162A SER* 2.7 22.8 + - - -
163A GLN* 3.4 13.1 + - - +
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Residues in contact with GLN 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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155A ASN 4.6 2.4 + - - -
156A LEU* 3.8 23.8 - - + +
157A ASP* 2.7 54.9 + - - +
159A GLU* 1.3 73.5 - - + +
161A MET* 1.3 62.2 + - - +
163A GLN* 3.2 11.9 + - - +
164A VAL* 3.1 27.4 + - - +
253A ILE* 3.8 26.2 - - + +
256A LYS* 4.3 22.6 + - - +
257A ASN* 4.7 2.4 - - - +
260A LYS* 4.6 12.9 + - - +
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Residues in contact with MET 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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147A CYS* 5.6 4.3 - - + +
153A PHE* 3.2 56.8 - - + +
156A LEU* 4.3 15.2 - - + +
157A ASP 3.1 15.8 + - - +
158A PRO* 4.0 8.7 - - + +
160A GLN* 1.3 76.0 - - - +
162A SER* 1.3 59.0 + - - +
164A VAL* 3.3 10.3 + - - +
165A LEU* 2.9 51.3 + - + +
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Residues in contact with SER 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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130A ARG* 5.5 1.0 + - - -
140A ARG* 5.6 0.6 + - - +
158A PRO 3.3 14.2 + - - -
159A GLU* 2.7 23.2 + - - -
161A MET* 1.3 78.7 - - - +
163A GLN* 1.3 61.3 + - - +
165A LEU* 3.3 12.1 + - - +
166A ASP* 3.0 37.0 + - - +
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Residues in contact with GLN 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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130A ARG* 3.2 50.1 + - - +
131A ILE 4.8 1.4 - - - +
159A GLU 3.5 14.8 - - - +
160A GLN* 3.2 10.6 + - - +
162A SER* 1.3 81.6 + - - +
164A VAL* 1.3 64.5 + - - +
166A ASP* 3.3 2.9 + - - +
167A ALA* 3.1 24.4 + - - +
249A THR* 4.7 2.2 - - - +
252A ARG* 2.7 31.1 + - - +
253A ILE* 3.6 15.5 - - + +
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Residues in contact with VAL 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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153A PHE* 4.0 24.2 - - + -
156A LEU* 4.4 10.8 - - + -
160A GLN 3.1 17.5 + - - +
161A MET* 3.5 11.9 - - - +
162A SER 3.3 0.2 - - - -
163A GLN* 1.3 77.4 - - - +
165A LEU* 1.3 63.5 + - + +
167A ALA* 3.1 8.0 + - - +
168A MET* 3.0 35.4 + - + +
245A LEU* 4.0 24.6 - - + +
249A THR* 4.8 4.7 - - + +
253A ILE* 3.9 26.7 - - + -
254A ILE* 4.8 5.4 - - + -
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Residues in contact with LEU 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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135A LYS* 3.1 22.5 + - - -
140A ARG* 3.7 28.7 - - - +
143A LEU* 3.8 13.7 - - + +
144A GLN* 4.5 17.3 - - + -
147A CYS* 4.5 22.9 - - + -
153A PHE* 5.7 0.2 - - + -
161A MET* 2.9 44.7 + - + +
162A SER* 3.5 9.2 - - - +
164A VAL* 1.3 83.4 - - + +
166A ASP* 1.3 60.2 + - - +
168A MET* 3.4 12.4 + - + +
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Residues in contact with ASP 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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130A ARG* 2.9 31.1 + - - +
131A ILE 4.1 2.5 - - - +
132A ILE* 4.4 19.7 - - + +
133A HIS 3.0 27.5 + - - -
135A LYS* 3.3 12.3 + - - +
140A ARG* 3.7 15.0 + - - +
162A SER* 3.0 23.8 + - - +
163A GLN 3.8 2.7 - - - +
164A VAL 3.3 0.2 - - - -
165A LEU* 1.3 76.2 - - - +
167A ALA* 1.3 57.2 + - - +
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Residues in contact with ALA 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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131A ILE* 3.7 20.5 + - + +
133A HIS* 3.3 17.1 - - - -
163A GLN 3.1 16.5 + - - +
164A VAL 3.1 4.9 + - - +
166A ASP* 1.3 78.1 - - - +
168A MET* 1.3 62.4 + - - +
169A PHE* 3.6 7.3 + - - -
244A GLY 4.0 1.4 - - - +
245A LEU* 3.7 22.5 - - + +
246A ASP* 4.4 4.9 - - - +
249A THR* 3.9 18.4 - - + +
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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