Contacts of the helix formed by residues 137 - 155 (chain A) in PDB entry 3MEK
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 THR 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LYS 4.5 5.8 - - - +
136A LEU* 1.3 75.6 - - - +
138A GLU* 1.3 64.2 + - - +
139A ASP* 3.6 9.7 + - - +
140A ARG* 3.1 23.9 + - - +
141A LYS* 3.0 22.8 + - - +
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Residues in contact with GLU 138 (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 4.1 0.2 + - - -
137A THR* 1.3 72.2 - - - +
139A ASP* 1.3 62.3 + - - +
141A LYS* 3.4 12.6 + - - +
142A GLU* 3.0 24.3 + - - +
145A ARG* 4.6 3.4 + - - +
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Residues in contact with ASP 139 (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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137A THR* 3.1 8.6 + - - +
138A GLU* 1.3 78.6 - - - +
140A ARG* 1.3 63.4 + - - +
142A GLU* 3.4 9.0 + - - +
143A GLY* 3.2 17.7 + - - -
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 3.9 28.5 - - + +
137A THR* 3.1 23.1 + - - +
139A ASP* 1.3 81.8 + - - +
141A LYS* 1.3 55.5 + - - +
143A GLY* 3.1 5.7 + - - +
144A LEU* 2.9 43.5 + - + +
147A LEU* 6.3 0.2 - - - +
179A ILE* 3.8 39.3 - - - +
255A ASP* 2.9 35.3 + - - +
256A GLN* 4.1 3.0 - - - +
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Residues in contact with LYS 141 (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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133A ILE* 4.2 21.1 + - - +
134A ASN* 6.0 0.4 - - - +
136A LEU* 3.7 27.5 + - + +
137A THR 3.0 14.8 + - - +
138A GLU* 3.6 13.9 - - - +
140A ARG* 1.3 74.3 - - - +
142A GLU* 1.3 56.9 + - - +
144A LEU* 3.1 4.7 + - - +
145A ARG* 2.9 52.6 + - - +
172A PHE* 3.7 25.8 - - + -
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Residues in contact with GLU 142 (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 GLU 3.0 16.9 + - - +
139A ASP* 3.7 7.9 - - - +
140A ARG 3.3 0.2 - - - -
141A LYS* 1.3 76.3 - - - +
143A GLY* 1.3 60.8 + - - +
145A ARG* 3.3 31.3 + - - +
146A GLN* 2.8 56.8 + - + +
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Residues in contact with GLY 143 (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 ASP 3.2 10.0 + - - -
140A ARG* 3.1 10.3 + - - -
142A GLU* 1.3 76.3 - - - +
144A LEU* 1.3 62.0 + - - +
146A GLN* 3.3 9.1 + - - +
147A LEU* 3.2 27.9 + - - +
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Residues in contact with LEU 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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136A LEU* 3.7 30.5 - - + -
140A ARG* 2.9 27.3 + - + +
141A LYS* 3.1 1.7 + - - +
143A GLY* 1.3 73.3 - - - +
145A ARG* 1.3 61.0 + - - +
147A LEU* 3.2 13.6 + - + +
148A VAL* 2.9 33.6 + - - +
172A PHE* 3.6 30.3 - - + +
175A PHE* 3.9 21.8 - - + +
176A ALA* 3.8 18.8 - - + +
179A ILE* 3.8 27.1 - - + -
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Residues in contact with ARG 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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138A GLU* 4.6 2.6 + - - +
141A LYS* 2.9 35.1 + - - +
142A GLU* 3.3 47.5 + - - +
144A LEU* 1.3 76.6 - - - +
146A GLN* 1.3 63.9 + - - +
148A VAL* 3.3 9.0 + - + +
149A MSE 3.1 30.8 + - - +
172A PHE* 4.1 17.2 - - + -
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Residues in contact with GLN 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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142A GLU* 2.8 39.4 + - + +
143A GLY* 3.6 9.0 - - - +
144A LEU 3.3 0.4 - - - -
145A ARG* 1.3 78.4 - - - +
147A LEU* 1.3 54.4 + - + +
149A MSE 3.4 22.1 + - - +
150A THR* 2.8 37.6 + - - +
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Residues in contact with LEU 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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99A PRO* 4.3 14.8 - - + -
101A SER* 3.7 25.1 - - - +
102A VAL* 4.0 13.5 - - + +
143A GLY 3.2 19.3 + - - +
144A LEU* 3.2 24.0 + - + +
146A GLN* 1.3 75.2 - - + +
148A VAL* 1.3 58.0 + - - +
150A THR* 3.6 4.8 - - - +
151A PHE* 2.9 30.5 + - - +
175A PHE* 3.4 28.3 - - + -
179A ILE* 4.6 12.1 - - + -
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Residues in contact with VAL 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 LEU 2.9 20.0 + - - +
145A ARG* 3.3 10.7 + - - +
147A LEU* 1.3 74.5 - - - +
149A MSE 1.3 60.3 + - + +
151A PHE* 3.3 4.7 + - - +
152A GLN* 2.9 52.7 + - - +
171A LEU* 3.7 22.7 - - + +
172A PHE* 3.6 37.2 - - + +
175A PHE* 3.9 9.6 - - + -
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Residues in contact with MSE 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 ARG* 3.1 22.0 + - - +
146A GLN* 3.8 23.6 - - - +
148A VAL* 1.3 73.7 - - + +
150A THR* 1.3 65.5 + - - +
152A GLN* 3.4 18.1 + - - +
153A HIS* 3.1 23.7 + - - +
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Residues in contact with THR 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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98A PRO* 5.0 3.1 - - + -
99A PRO* 3.8 30.7 - - + +
102A VAL* 3.9 13.0 - - + -
146A GLN* 2.8 23.3 + - - +
147A LEU* 3.3 9.0 + - - +
149A MSE 1.3 76.0 - - - +
151A PHE* 1.3 55.5 + - - +
153A HIS* 3.2 8.9 + - + +
154A PHE* 2.8 28.9 + - + +
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Residues in contact with PHE 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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102A VAL* 3.9 21.5 - - + +
105A LEU* 3.8 9.6 - - + -
106A GLY* 3.6 24.7 - - - -
109A VAL* 3.9 24.7 - - + -
147A LEU 2.9 16.0 + - - +
148A VAL 3.5 4.0 - - - +
150A THR* 1.3 76.1 - - - +
152A GLN* 1.3 61.8 + - - +
155A MSE 2.8 65.9 + - + +
159A ILE* 5.6 4.5 - - + -
165A LEU* 4.7 9.2 - - + -
171A LEU* 3.7 35.0 - - + -
175A PHE* 3.7 26.7 - + + -
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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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148A VAL* 2.9 36.2 + - - +
149A MSE 3.7 21.1 - - - +
150A THR 3.3 0.2 - - - -
151A PHE* 1.3 77.6 - - - +
153A HIS* 1.3 61.1 + - - +
155A MSE 4.1 2.4 - - - +
156A ARG* 3.4 24.3 + - - +
159A ILE 5.0 2.3 - - - +
171A LEU* 4.0 21.8 - - + +
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Residues in contact with HIS 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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93A CYS* 4.3 13.1 - - + +
149A MSE 3.1 12.9 + - - +
150A THR* 3.5 10.3 - - + +
152A GLN* 1.3 73.9 - - - +
154A PHE* 1.3 67.0 + - - +
155A MSE 3.2 0.7 + - - -
156A ARG* 2.8 66.8 + - - +
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Residues in contact with PHE 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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86A GLU* 4.6 7.6 - - + -
89A CYS* 3.2 47.0 - - + +
90A LEU* 3.6 37.9 - - + -
92A SER* 4.8 1.2 + - - -
93A CYS* 3.9 20.1 - - + -
98A PRO* 3.7 21.5 - - + -
102A VAL* 3.7 25.6 - - + -
103A ARG* 4.3 21.5 - - + -
106A GLY* 5.1 1.3 - - - -
150A THR* 2.8 21.7 + - + +
151A PHE 3.3 2.9 + - - +
153A HIS* 1.3 75.3 - - + +
155A MSE 1.3 96.3 + - + +
156A ARG* 3.6 0.7 + - - -
157A GLU 4.9 1.0 + - - -
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Residues in contact with MSE 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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86A GLU* 5.1 0.7 - - - -
89A CYS* 3.7 23.8 - - + -
106A GLY* 3.9 17.9 - - - +
109A VAL* 5.9 0.9 - - - -
110A PHE* 3.5 33.9 - - + -
151A PHE* 2.8 48.3 + - + +
152A GLN* 4.1 2.9 - - - +
154A PHE* 1.3 127.9 - - + +
156A ARG* 1.3 64.1 + - - +
157A GLU 3.2 2.9 - - - -
158A GLU* 2.9 6.3 + - - -
159A ILE* 2.8 41.8 + - + +
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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