Contacts of the helix formed by residues 144 - 156 (chain A) in PDB entry 1I4A
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 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A GLU* 5.5 0.4 + - - -
143A THR* 1.3 78.9 - - - +
145A PHE* 1.3 77.5 + - - +
147A PHE* 3.6 9.8 + - - +
148A GLN* 3.2 19.0 + - - +
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Residues in contact with PHE 145 (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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144A SER* 1.3 81.9 - - - +
146A MET* 1.3 94.1 + - + +
147A PHE 4.7 0.2 - - - +
148A GLN* 3.3 8.6 + - - +
149A ARG* 3.2 26.2 + - - +
189A GLU* 4.7 6.3 - - - -
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Residues in contact with MET 146 (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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145A PHE* 1.3 103.9 - - + +
147A PHE* 1.3 64.7 + - - +
149A ARG* 3.2 28.7 + - - +
150A VAL* 3.1 25.6 + - - +
189A GLU* 3.2 27.8 - - + +
190A VAL* 4.1 26.9 - - + +
193A LEU* 3.9 27.1 - - + -
231A PHE* 3.7 30.7 - - + -
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Residues in contact with PHE 147 (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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105A GLU* 3.5 46.0 - - + -
109A ILE* 3.5 37.7 - - + -
143A THR* 3.8 15.3 - - + -
144A SER 3.6 8.2 + - - +
145A PHE* 3.3 0.6 - - - +
146A MET* 1.3 77.3 - - - +
148A GLN* 1.3 63.3 + - - +
150A VAL* 3.2 3.1 + - - +
151A LEU* 3.1 52.7 + - + +
230A SER* 3.4 27.6 - - - -
231A PHE* 3.9 21.7 - - + +
234A ALA* 4.1 7.6 - - + -
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Residues in contact with GLN 148 (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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139A ILE* 4.3 0.7 - - + +
140A ARG* 3.1 47.6 + - - +
143A THR* 2.9 44.3 + - - +
144A SER* 3.2 18.8 + - - +
145A PHE 3.4 10.9 - - - +
146A MET 3.2 0.2 - - - -
147A PHE* 1.3 80.2 - - - +
149A ARG* 1.3 63.3 + - - +
151A LEU* 3.2 4.9 + - - +
152A VAL* 2.8 41.8 + - + +
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Residues in contact with ARG 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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145A PHE* 3.2 14.4 + - - +
146A MET* 3.4 27.6 - - - +
148A GLN* 1.3 81.9 - - - +
150A VAL* 1.3 64.9 + - - +
152A VAL* 3.3 8.2 + - - +
153A SER* 3.0 24.8 + - - -
190A VAL* 3.9 27.3 - - - +
193A LEU* 3.4 23.4 - - + +
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Residues in contact with VAL 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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146A MET 3.1 13.7 + - - +
147A PHE* 3.2 7.2 + - - +
149A ARG* 1.3 75.2 - - - +
151A LEU* 1.3 58.5 + - + +
153A SER* 3.3 2.6 + - - -
154A LEU* 2.9 43.3 + - + +
193A LEU* 3.2 24.2 - - + -
197A CYS* 3.8 14.8 - - - -
231A PHE* 3.5 26.9 - - + -
234A ALA* 3.9 23.1 - - + -
235A LEU* 4.1 7.0 - - + -
238A ILE* 4.3 5.4 - - + -
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Residues in contact with LEU 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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108A LEU* 3.7 35.2 - - + +
109A ILE* 4.6 4.9 - - + +
112A LEU* 3.7 28.2 - - + +
139A ILE* 3.7 15.7 - - + -
143A THR* 4.1 9.4 - - + +
147A PHE* 3.1 54.1 + - + +
148A GLN 3.6 6.3 - - - +
150A VAL* 1.3 78.3 - - + +
152A VAL* 1.3 56.2 + - - +
154A LEU* 3.8 8.4 - - + +
155A SER* 2.8 39.4 + - - -
234A ALA* 5.3 0.7 - - + -
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Residues in contact with VAL 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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136A GLU* 4.0 17.8 - - + +
139A ILE* 4.3 7.6 - - + -
140A ARG* 3.9 41.1 - - + +
148A GLN* 2.8 37.2 + - + +
149A ARG* 3.6 8.1 - - - +
151A LEU* 1.3 75.1 - - - +
153A SER* 1.3 67.2 + - - +
155A SER* 2.9 18.6 + - - -
156A ALA* 3.3 11.3 + - - +
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Residues in contact with SER 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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149A ARG 3.0 16.4 + - - -
150A VAL* 3.5 4.7 - - - -
152A VAL* 1.3 81.4 - - - +
154A LEU* 1.3 63.1 + - - +
156A ALA* 3.3 14.6 + - - +
157A GLY 3.8 3.3 + - - -
158A GLY 4.5 4.3 + - - -
193A LEU* 4.6 4.7 - - - -
197A CYS* 3.2 33.8 + - - +
198A SER* 5.2 1.7 + - - -
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Residues in contact with LEU 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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109A ILE* 5.6 1.1 - - - +
112A LEU* 3.8 43.5 - - + +
113A ALA* 4.2 7.4 - - + +
120A ILE* 3.4 20.3 - - + +
150A VAL* 2.9 38.0 + - + +
151A LEU* 3.8 8.1 - - + +
153A SER* 1.3 76.0 - - - +
155A SER* 1.3 58.5 + - - +
157A GLY* 3.0 18.9 + - - -
159A ARG* 3.8 28.5 - - + +
197A CYS* 4.3 11.7 - - + +
234A ALA* 5.6 2.0 - - + -
238A ILE* 4.2 16.2 - - + -
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Residues in contact with SER 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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112A LEU* 4.0 8.0 - - - +
120A ILE* 3.2 8.8 - - - +
124A ASN* 2.7 40.7 + - - +
135A LEU* 4.1 14.6 - - - -
136A GLU* 4.5 12.7 + - - +
139A ILE* 3.7 23.6 - - - +
151A LEU 2.8 20.0 + - - -
152A VAL* 2.9 20.8 + - - -
154A LEU* 1.3 73.6 - - - +
156A ALA* 1.3 50.5 + - - +
157A GLY 3.3 0.4 - - - -
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Residues in contact with ALA 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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121A ARG* 4.2 10.2 - - - +
124A ASN* 4.3 6.5 + - - +
136A GLU* 5.1 9.0 - - - +
152A VAL* 3.3 8.7 + - + +
153A SER* 3.3 11.6 + - - +
154A LEU 3.1 1.2 + - - -
155A SER* 1.3 80.2 + - - +
157A GLY* 1.3 63.9 + - - +
158A GLY* 3.3 5.5 + - - +
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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