Contacts of the helix formed by residues 143 - 158 (chain A) in PDB entry 4WMI
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 GLU 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A THR* 3.4 8.5 - - - -
106A LYS* 2.9 37.5 + - + +
107A ALA 4.4 0.3 + - - -
108A GLU* 5.2 0.9 + - - +
142A SER* 1.3 75.9 - - - +
144A GLU* 1.3 78.5 + - + +
145A ALA* 3.9 11.6 - - + +
146A SER* 2.7 34.8 + - - -
147A ARG* 3.0 18.9 + - - +
172A ASP* 4.6 3.1 - - - +
173A VAL* 3.6 20.1 - - + +
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Residues in contact with GLU 144 (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 GLU* 1.3 85.0 - - + +
145A ALA* 1.3 63.8 + - - +
147A ARG* 3.1 41.4 + - - +
148A GLU* 3.2 18.3 + - + +
172A ASP* 4.5 14.3 - - - +
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Residues in contact with ALA 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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108A GLU* 3.7 34.1 - - + +
143A GLU* 3.4 12.2 + - + +
144A GLU* 1.3 79.4 - - - +
146A SER* 1.3 61.2 + - - +
148A GLU* 3.2 10.4 + - - +
149A VAL* 3.2 25.2 + - - +
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Residues in contact with SER 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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104A PHE* 3.1 28.3 - - - -
106A LYS 3.1 5.2 + - - -
107A ALA* 2.8 32.8 + - - +
108A GLU 5.1 0.4 - - - +
142A SER* 4.0 2.0 - - - -
143A GLU* 2.7 31.4 + - - -
144A GLU 3.3 0.4 - - - -
145A ALA* 1.3 72.1 - - - +
147A ARG* 1.3 61.5 + - - +
149A VAL* 3.2 7.6 + - - -
150A ALA* 2.9 31.2 + - - +
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Residues in contact with ARG 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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142A SER* 3.8 4.8 - - - +
143A GLU 3.0 12.9 + - - +
144A GLU* 3.1 31.3 + - - +
146A SER* 1.3 75.3 - - - +
148A GLU* 1.3 73.5 + - - +
150A ALA* 3.3 2.6 + - - +
151A LYS* 3.0 44.6 + - - +
170A PHE* 3.7 52.7 - - + +
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Residues in contact with GLU 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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144A GLU* 3.2 13.0 + - + +
145A ALA* 3.5 9.6 - - - +
146A SER 3.2 0.2 - - - -
147A ARG* 1.3 104.5 + - - +
149A VAL* 1.3 64.9 + - + +
151A LYS* 3.3 22.0 + - - +
152A ALA* 3.1 21.8 + - - +
155A ARG* 5.2 0.5 + - - -
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Residues in contact with VAL 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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104A PHE* 4.0 13.2 - - + -
107A ALA* 4.4 1.1 - - + -
108A GLU* 4.2 29.8 - - + +
114A GLN* 3.6 39.0 - - + +
145A ALA 3.2 14.6 + - - +
146A SER* 3.6 7.4 - - - +
148A GLU* 1.3 78.4 - - + +
150A ALA* 1.3 62.4 + - - +
152A ALA* 3.3 7.5 + - - +
153A LEU* 3.2 22.3 + - + +
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Residues in contact with ALA 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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104A PHE* 3.7 21.7 - - + -
121A LEU* 6.3 0.7 - - + -
140A PHE* 5.0 6.3 - - + -
146A SER 2.9 17.2 + - - +
147A ARG 3.7 4.3 - - - +
149A VAL* 1.3 77.3 - - - +
151A LYS* 1.3 57.9 + - - +
153A LEU* 3.3 8.0 + - + +
154A LEU* 2.8 45.1 + - + +
170A PHE* 3.7 20.6 - - + -
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Residues in contact with LYS 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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147A ARG* 3.0 40.0 + - + +
148A GLU* 3.6 23.3 + - - +
149A VAL 3.3 0.2 - - - -
150A ALA* 1.3 77.2 - - - +
152A ALA* 1.3 61.9 + - - +
154A LEU* 3.5 6.5 + - + +
155A ARG* 3.1 49.5 + - - +
168A VAL* 6.1 0.2 - - + -
170A PHE* 3.9 27.4 - - + -
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Residues in contact with ALA 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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148A GLU 3.1 13.1 + - - +
149A VAL* 3.6 10.3 - - - +
150A ALA 3.3 0.2 - - - -
151A LYS* 1.3 76.1 - - - +
153A LEU* 1.3 62.1 + - - +
155A ARG* 3.3 32.5 - - - +
156A GLU* 3.8 8.8 + - - +
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Residues in contact with LEU 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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104A PHE* 5.4 4.7 - - + -
114A GLN* 4.5 4.5 - - + +
117A ALA* 3.8 22.0 - - + -
118A ARG* 3.4 48.9 - - + +
121A LEU* 3.8 26.5 - - + -
149A VAL* 3.2 12.4 + - + +
150A ALA* 3.3 10.5 + - - +
152A ALA* 1.3 79.6 - - - +
154A LEU* 1.3 62.6 + - - +
156A GLU* 3.3 21.3 + - - +
157A LEU* 3.5 24.4 + - + +
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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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121A LEU* 3.9 31.0 - - + -
125A LEU* 4.8 8.1 - - + -
138A LEU* 4.7 8.1 - - + -
140A PHE* 3.9 28.9 - - + -
150A ALA* 2.8 44.1 + - + +
151A LYS* 3.9 6.3 - - - +
153A LEU* 1.3 74.3 - - - +
155A ARG* 1.3 57.0 + - - +
157A LEU* 2.8 20.0 + - + +
158A LEU* 2.8 43.5 + - + +
168A VAL* 4.3 16.8 - - + -
170A PHE* 4.6 1.1 - - + -
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Residues in contact with ARG 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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148A GLU 5.2 0.6 + - - -
151A LYS* 3.1 44.1 + - - +
152A ALA* 3.3 31.8 - - - +
154A LEU* 1.3 74.8 - - - +
156A GLU* 1.3 57.7 + - + +
158A LEU* 3.2 23.1 - - - +
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Residues in contact with GLU 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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118A ARG* 2.8 42.0 + - - +
152A ALA 4.1 8.5 - - - +
153A LEU* 3.3 11.7 + - - +
154A LEU 3.2 0.4 - - - -
155A ARG* 1.3 81.0 - - + +
157A LEU* 1.3 66.4 + - + +
158A LEU 3.8 0.4 - - - -
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Residues in contact with LEU 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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118A ARG* 4.7 5.6 - - + +
121A LEU* 3.8 31.4 - - + -
122A SER* 3.8 31.4 - - - +
125A LEU* 3.7 24.5 - - + +
153A LEU* 3.5 31.6 + - + +
154A LEU* 2.8 10.7 + - + +
156A GLU* 1.3 88.7 - - + +
158A LEU* 1.3 59.4 + - - +
159A PRO 3.6 10.7 - - - +
160A PRO* 4.1 5.2 - - - +
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Residues in contact with LEU 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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125A LEU* 4.0 22.7 - - + -
138A LEU* 5.1 0.9 - - + -
154A LEU* 2.8 31.2 + - + +
155A ARG* 3.2 18.9 - - - +
156A GLU 4.7 0.7 - - - -
157A LEU* 1.3 76.8 - - - +
159A PRO* 1.4 67.8 - - + +
160A PRO* 3.9 17.7 - - + -
166A CYS* 3.8 30.1 - - + +
168A VAL* 3.8 29.4 - - + -
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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