Contacts of the helix formed by residues 148 - 156 (chain A) in PDB entry 4IQJ
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 ALA 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A PHE* 3.6 2.2 - - - -
95A HIS* 3.1 24.9 - - - +
143A SER 3.1 26.5 - - - +
144A GLY* 3.7 8.7 - - - -
145A CYS 3.0 16.3 + - - +
146A LEU 3.7 0.2 - - - +
147A GLY* 1.3 79.4 - - - +
149A GLU* 1.3 66.9 + - - +
150A ILE 3.7 0.2 - - - -
151A PRO* 3.7 4.1 - - + +
152A GLN* 3.2 25.3 + - - +
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Residues in contact with GLU 149 (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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75A VAL* 3.8 26.5 - - - +
76A ALA 4.9 1.0 - - - +
94A PHE* 3.5 34.0 - - + -
95A HIS 4.8 1.6 - - - +
96A LEU* 4.2 15.6 - - + +
129A ARG* 3.0 23.9 + - - +
143A SER 4.7 0.4 + - - -
148A ALA* 1.3 76.7 - - - +
150A ILE* 1.3 64.9 + - + +
152A GLN* 3.1 13.0 + - - +
153A PHE* 3.1 23.0 + - + -
165A ARG* 2.6 48.9 + - + +
169A ASP* 4.5 7.6 - - - +
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Residues in contact with ILE 150 (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 SER* 5.1 8.2 + - - +
149A GLU* 1.3 78.5 - - + +
151A PRO* 1.3 69.7 - - + +
152A GLN 3.3 0.5 + - - -
153A PHE* 3.4 6.8 + - - -
154A ILE* 3.3 24.7 + - + +
162A ALA* 3.6 28.1 - - + +
165A ARG* 4.2 10.3 - - + -
166A LEU* 3.5 49.1 - - + +
169A ASP* 4.4 5.6 - - - +
177A PHE* 4.4 14.6 - - + -
179A ILE* 5.8 0.4 - - + -
196A LEU* 3.8 24.5 - - + -
199A PHE* 4.6 7.2 - - + -
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Residues in contact with PRO 151 (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 SER* 4.0 13.2 - - - +
144A GLY 4.2 5.6 - - - +
145A CYS 3.0 29.6 - - - +
146A LEU* 4.2 11.2 - - - -
148A ALA* 3.7 11.7 - - + +
149A GLU 3.8 0.4 - - - -
150A ILE* 1.3 97.1 - - + +
152A GLN* 1.3 57.6 + - - +
154A ILE* 3.5 5.9 + - + +
155A LEU* 3.3 26.4 + - - +
192A VAL* 3.6 31.7 - - + +
196A LEU* 4.8 8.5 - - + -
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Residues in contact with GLN 152 (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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94A PHE* 3.6 24.0 - - + -
146A LEU 2.9 21.7 + - - +
147A GLY* 4.2 6.2 - - - +
148A ALA 3.2 16.3 + - - +
149A GLU 3.1 5.6 + - - +
151A PRO* 1.3 76.0 - - - +
153A PHE* 1.3 61.5 + - + +
155A LEU* 3.3 19.7 + - - +
156A GLN* 3.1 46.4 + - + +
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Residues in contact with PHE 153 (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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94A PHE* 4.9 14.8 - + - -
149A GLU* 3.1 29.7 + - + -
150A ILE* 3.4 1.5 + - - +
152A GLN* 1.3 74.3 - - + +
154A ILE* 1.3 63.0 + - - +
156A GLN* 3.4 12.9 + - + +
158A ARG* 3.0 44.2 + - + +
161A LEU* 3.8 36.3 - - + -
162A ALA* 3.7 24.9 - - + +
165A ARG* 3.7 44.0 - - + -
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Residues in contact with ILE 154 (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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150A ILE* 3.3 17.9 + - + +
151A PRO* 3.7 7.6 - - + +
152A GLN 3.2 0.6 - - - -
153A PHE* 1.3 76.0 - - - +
155A LEU* 1.3 63.4 + - - +
157A ASP* 3.3 11.3 + - - +
158A ARG 5.0 2.5 - - - +
159A LEU* 5.0 9.4 - - + +
162A ALA* 4.1 11.4 - - + -
191A LYS* 3.6 27.6 - - + +
192A VAL* 4.1 22.9 - - + +
195A VAL* 3.5 52.5 - - + -
196A LEU* 4.2 16.2 - - + -
199A PHE* 4.3 7.6 - - + -
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Residues in contact with LEU 155 (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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146A LEU* 4.4 22.2 - - + +
151A PRO 3.3 15.4 + - - +
152A GLN* 3.3 29.0 + - - +
154A ILE* 1.3 78.7 - - - +
156A GLN* 1.3 58.5 + - + +
157A ASP* 3.2 9.3 + - - +
188A GLU* 3.8 32.5 - - + +
191A LYS* 4.5 15.3 + - + +
192A VAL* 3.7 18.8 - - + -
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Residues in contact with GLN 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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152A GLN* 3.1 33.3 + - + +
153A PHE* 3.7 14.4 - - + +
154A ILE 3.2 0.8 - - - -
155A LEU* 1.3 75.8 - - + +
157A ASP* 1.3 70.0 + - - +
158A ARG* 3.3 20.3 + - + +
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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