Contacts of the helix formed by residues 155 - 167 (chain A) in PDB entry 4IXA
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 ARG 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A MET* 1.3 79.2 - - - +
156A ILE* 1.3 66.4 + - + +
157A LYS* 3.4 12.2 - - - +
158A GLU* 2.7 40.3 + - - +
159A PHE* 3.1 19.0 + - - +
197A HIS* 3.4 22.2 + - - -
200A ARG* 2.8 42.0 - - - +
204A LYS* 5.3 0.2 - - - +
151B GLU* 5.9 0.8 + - - -
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Residues in contact with ILE 156 (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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143A LYS* 4.1 29.2 - - + -
154A MET 3.9 0.8 + - - -
155A ARG* 1.3 73.5 - - + +
157A LYS* 1.3 66.4 + - + +
159A PHE* 3.2 5.6 + - - +
160A GLU* 2.9 53.6 + - + +
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Residues in contact with LYS 157 (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 ARG* 3.4 8.3 - - - +
156A ILE* 1.3 85.2 - - + +
158A GLU* 1.3 61.1 + - - +
160A GLU* 3.0 25.9 + - - +
161A LEU* 2.9 29.5 + - - +
182A VAL* 2.4 37.6 + - + +
183A TRP* 3.9 29.8 - - + +
186A ASP* 2.8 39.9 + - + +
197A HIS* 4.0 21.0 - - + +
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Residues in contact with GLU 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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154A MET* 3.4 28.6 - - + +
155A ARG* 2.7 46.5 + - - +
157A LYS* 1.3 74.9 - - - +
159A PHE* 1.3 67.1 + - - +
161A LEU* 3.4 3.5 + - - -
162A LEU* 3.0 19.4 + - - +
197A HIS* 3.8 13.2 - - + +
200A ARG* 3.5 23.1 - - + +
201A ILE* 3.4 19.3 + - + +
204A LYS* 2.6 37.4 + - - -
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Residues in contact with PHE 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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138A LEU* 4.0 16.4 - - + -
139A LYS 3.5 27.6 - - - -
140A ASN* 3.4 22.7 - - - -
143A LYS* 3.7 42.6 - - + +
144A THR* 3.3 26.5 - - - -
145A LEU* 4.4 7.6 - - + -
154A MET* 3.6 16.3 - - + -
155A ARG 3.1 10.2 + - - +
156A ILE* 3.2 9.1 + - - +
158A GLU* 1.3 80.4 - - - +
160A GLU* 1.3 56.4 + - - +
162A LEU* 3.1 4.5 + - + +
163A TRP* 2.7 54.6 + + + -
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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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140A ASN* 5.7 0.9 - - - +
143A LYS* 3.8 27.0 - - + -
156A ILE* 2.9 42.6 + - - +
157A LYS* 3.0 38.9 + - - +
159A PHE* 1.3 80.6 - - - +
161A LEU* 1.3 62.6 + - - +
163A TRP* 3.7 5.9 - - - +
164A TYR* 3.0 24.9 + - - +
182A VAL* 4.2 13.0 - - + +
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Residues in contact with LEU 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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157A LYS 2.9 17.0 + - - +
158A GLU 3.7 3.6 - - - +
159A PHE 3.2 0.2 - - - -
160A GLU* 1.3 77.4 - - - +
162A LEU* 1.3 62.4 + - - +
164A TYR* 3.2 4.3 + - - +
165A LEU* 3.1 29.2 + - + +
178A LEU* 3.8 38.4 - - + -
182A VAL* 4.0 13.2 - - + +
183A TRP* 4.3 17.9 - - + -
194A VAL* 4.3 3.4 - - + +
197A HIS* 3.5 29.6 - - + -
198A ILE* 3.5 25.8 - - + +
201A ILE* 3.8 12.3 - - + -
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Residues in contact with LEU 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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136A LEU* 4.8 6.3 - - + -
138A LEU* 3.6 20.9 - - + -
145A LEU* 3.5 32.5 - - + -
154A MET* 4.6 3.1 - - - -
158A GLU 3.0 18.0 + - - +
159A PHE* 3.6 5.4 - - + +
161A LEU* 1.3 77.3 - - - +
163A TRP* 1.3 58.5 + - - +
165A LEU* 3.3 4.1 + - + -
166A ALA* 2.9 30.2 + - + +
201A ILE* 3.9 33.4 - - + +
205A LEU* 5.3 3.4 - - + -
215A ILE* 4.2 7.9 - - + -
225A PHE* 3.9 32.1 - - + -
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Residues in contact with TRP 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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128A MET* 3.3 28.5 - - + -
129A GLU 3.6 17.7 - - - -
130A GLN 3.8 0.2 - - - -
131A LEU* 3.6 27.6 - - + -
138A LEU* 3.6 43.5 - - + +
140A ASN* 3.6 41.3 - - + +
159A PHE* 2.7 36.2 + + + +
160A GLU* 3.7 7.6 - - - +
162A LEU* 1.3 74.0 - - - +
164A TYR* 1.3 58.3 + + + +
167A SER* 2.7 55.6 + - - -
168A ARG* 6.1 0.2 - - - -
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Residues in contact with TYR 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 GLU 3.0 17.7 + - - +
161A LEU 3.6 4.5 - - - +
163A TRP* 1.3 81.2 - + + +
165A LEU* 1.3 62.0 + - - +
167A SER* 4.5 0.7 - - - -
168A ARG* 2.9 71.6 + - - +
173A ILE* 4.0 15.0 - - + -
177A GLU* 2.5 36.3 + - + +
178A LEU* 3.9 18.2 - - + -
181A LYS* 3.7 32.8 + - + +
182A VAL* 3.8 20.0 - - + -
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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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161A LEU* 3.1 21.8 + - + +
162A LEU* 3.9 3.8 - - - +
164A TYR* 1.3 75.0 - - - +
166A ALA* 1.3 58.7 + - - +
168A ARG* 2.8 31.7 + - - +
169A GLU 3.4 0.7 + - - -
171A GLU 4.9 0.8 - - - +
173A ILE* 3.6 33.0 - - + -
178A LEU* 4.1 12.1 - - + -
198A ILE* 4.0 28.0 - - + -
215A ILE* 4.1 25.1 - - + -
223A TYR* 3.6 21.5 - - + +
224A LYS* 4.6 2.0 - - - -
225A PHE* 3.7 20.1 + - + +
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Residues in contact with ALA 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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131A LEU* 3.9 5.8 - - + +
133A PHE* 3.6 24.9 - - + -
138A LEU* 3.6 25.8 - - + -
162A LEU* 2.9 21.1 + - + +
163A TRP 4.2 0.2 - - - +
165A LEU* 1.3 69.3 - - - +
167A SER* 1.3 59.7 + - - +
168A ARG 3.0 6.4 + - - -
169A GLU* 3.5 9.5 + - - +
225A PHE* 3.6 32.2 - - + +
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Residues in contact with SER 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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128A MET* 5.9 0.5 - - - +
131A LEU* 3.8 12.5 - - - +
163A TRP* 2.7 50.4 + - - -
164A TYR* 3.7 6.7 - - - -
166A ALA* 1.3 76.0 - - - +
168A ARG* 1.3 73.5 + - - +
169A GLU 3.6 1.3 + - - -
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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