Contacts of the helix formed by residues 138 - 154 (chain A) in PDB entry 1M4U
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 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A GLN* 3.3 18.0 - - - +
137A LEU* 1.3 82.3 - - - +
139A LYS* 1.3 67.8 + - - +
140A LYS* 2.5 47.4 + - - +
141A LEU* 3.2 5.3 + - - +
142A ARG* 3.0 19.3 + - - +
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Residues in contact with LYS 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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135A GLN* 3.2 14.4 + - - +
138A SER* 1.3 68.2 + - - +
140A LYS* 1.3 90.2 + - - +
142A ARG* 2.5 36.5 + - + +
143A ARG* 3.7 21.8 - - - +
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Residues in contact with LYS 140 (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 LEU 4.6 0.6 + - - -
138A SER* 2.5 34.2 + - - +
139A LYS* 1.3 95.6 + - - +
141A LEU* 1.3 99.1 + - + +
142A ARG 2.4 14.9 + - - -
143A ARG* 2.9 11.4 + - - +
144A LYS* 3.5 26.0 + - - +
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Residues in contact with LEU 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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137A LEU* 3.7 54.1 - - + +
138A SER 3.2 4.8 + - - +
140A LYS* 1.3 107.1 - - + +
142A ARG* 1.3 65.6 + - - +
144A LYS* 3.8 10.5 - - + +
145A LEU* 3.0 32.1 + - + +
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Residues in contact with ARG 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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121A LYS 3.2 12.7 + - - -
122A GLY 5.7 0.2 - - - -
123A LEU 2.9 17.3 + - - +
124A GLU* 2.7 49.5 + - - +
125A PHE* 3.7 13.3 - - + +
137A LEU* 6.0 1.6 - - - -
138A SER 3.0 7.6 + - - +
139A LYS* 2.5 32.6 + - + +
140A LYS 2.4 11.5 + - - -
141A LEU* 1.3 73.0 - - - +
143A ARG* 1.3 64.1 + - - +
145A LEU* 3.1 2.8 + - - +
146A GLN* 2.6 65.9 + - - +
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Residues in contact with ARG 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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116A MET* 5.4 3.9 - - + +
139A LYS* 3.7 21.1 - - - +
140A LYS 2.9 2.9 + - - +
142A ARG* 1.3 81.0 - - + +
144A LYS* 1.3 65.7 + - + +
146A GLN* 3.3 18.6 + - + +
147A MET* 3.0 67.5 + - + +
150A TRP* 6.0 1.2 - - - -
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Residues in contact with LYS 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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140A LYS* 3.5 25.8 + - - +
141A LEU* 3.5 9.8 + - + +
142A ARG 3.0 1.0 - - - -
143A ARG* 1.3 83.7 - - + +
145A LEU* 1.3 65.1 + - - +
147A MET* 4.0 6.2 - - + +
148A TRP* 3.1 23.0 + - - +
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Residues in contact with LEU 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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125A PHE* 2.9 39.0 - - + -
137A LEU* 5.2 2.5 - - + -
141A LEU* 3.0 34.4 + - + +
142A ARG 3.6 3.4 - - - +
144A LYS* 1.3 77.3 - - - +
146A GLN* 1.3 62.4 + - - +
148A TRP* 3.3 10.9 + - + +
149A LEU* 2.8 49.8 + - + +
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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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116A MET* 3.8 20.8 - - + +
120A ILE* 3.3 31.0 + - + +
121A LYS* 3.1 15.3 + - - +
123A LEU 2.8 10.5 + - - -
125A PHE* 3.6 14.4 - - + -
142A ARG* 2.6 60.9 + - - +
143A ARG* 3.6 17.6 - - - +
144A LYS 3.0 0.2 - - - -
145A LEU* 1.3 85.2 - - - +
147A MET* 1.3 57.5 + - - +
149A LEU 3.0 0.9 + - - -
150A TRP* 2.9 27.9 + - - +
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Residues in contact with MET 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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112A PRO* 5.5 7.0 - - + -
116A MET* 3.7 24.7 - - - -
143A ARG* 3.0 57.1 + - - +
144A LYS* 4.0 6.7 - - + +
145A LEU 3.4 0.2 - - - -
146A GLN* 1.3 74.9 - - - +
148A TRP* 1.3 63.4 + - - +
150A TRP* 3.2 27.9 + - + +
151A SER* 3.1 25.9 + - - +
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Residues in contact with TRP 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 LYS 3.1 18.4 + - - +
145A LEU* 3.7 10.8 - - + +
146A GLN 3.1 0.2 - - - -
147A MET* 1.3 76.7 - - - +
149A LEU* 1.3 102.2 + - + +
151A SER* 3.9 5.3 - - - +
152A GLN* 3.0 45.3 + - + +
186A VAL* 3.7 27.8 - - + -
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Residues in contact with LEU 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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120A ILE* 3.8 15.7 - - + -
123A LEU* 4.0 22.9 - - + -
125A PHE* 4.2 2.5 - - + -
145A LEU* 2.8 39.5 + - + +
146A GLN* 3.0 7.8 + - - +
148A TRP* 1.3 112.0 - - + +
150A TRP* 1.3 55.6 - - - +
152A GLN* 3.3 3.1 + - + +
153A THR* 2.7 44.5 + - + +
186A VAL* 5.1 7.0 - - + -
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Residues in contact with TRP 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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112A PRO* 3.6 34.5 - - + +
113A SER 3.8 17.4 + - - -
114A GLY 4.3 5.4 - - - -
115A ALA* 3.5 8.0 + - - -
116A MET* 3.3 59.9 - - + -
117A PRO* 3.6 23.3 - - + +
120A ILE* 3.8 9.8 - - + +
143A ARG* 6.0 0.9 - - - -
146A GLN 2.9 11.3 + - - +
147A MET* 3.3 32.8 - - + +
149A LEU* 1.3 77.4 - - - +
151A SER* 1.3 56.1 + - - +
153A THR* 3.4 1.4 + - - -
154A PHE* 2.8 42.7 + + + +
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Residues in contact with SER 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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109A ARG* 2.5 61.8 + - - +
110A GLN* 3.7 29.2 + - - -
112A PRO* 4.2 5.4 - - - +
147A MET* 3.1 14.2 + - - +
148A TRP* 4.1 5.6 - - - -
150A TRP* 1.3 76.7 - - - +
152A GLN* 1.3 61.4 + - - +
153A THR 3.5 0.2 + - - -
154A PHE* 3.9 1.6 + - - -
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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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109A ARG* 4.3 4.1 + - - +
148A TRP* 3.0 41.4 + - + +
149A LEU* 3.6 5.2 - - - +
150A TRP 3.1 0.2 - - - -
151A SER* 1.3 79.3 - - - +
153A THR* 1.3 66.1 + - + +
182A ARG* 2.9 44.7 + - - +
183A SER 3.5 14.5 + - - -
184A CYS* 3.4 8.4 - - - +
185A SER 3.8 16.0 + - - -
186A VAL* 4.3 18.6 - - + +
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Residues in contact with THR 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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117A PRO* 5.9 0.5 - - - +
120A ILE* 3.7 14.6 - - + +
149A LEU* 2.7 28.9 + - + +
150A TRP* 3.5 4.2 + - - -
152A GLN* 1.3 83.5 - - + +
154A PHE* 1.3 67.7 + - - +
155A CYS* 3.5 12.8 + - - -
184A CYS* 3.1 24.2 - - - +
185A SER* 4.8 3.8 - - - -
186A VAL* 5.4 2.5 - - + +
230A CYS* 3.9 15.2 + - - +
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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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108A LEU 4.3 5.4 - - - -
109A ARG* 3.2 35.1 - - + -
111A ARG 5.0 0.4 - - - -
112A PRO* 3.8 31.6 - - + -
113A SER* 3.4 38.4 - - - -
150A TRP* 2.8 27.4 + + + +
151A SER* 3.9 6.2 + - - +
152A GLN 3.6 1.1 - - - +
153A THR* 1.3 80.9 - - - +
155A CYS* 1.3 74.1 + - - +
156A PRO* 3.8 29.4 - - + -
184A CYS* 5.2 0.7 - - - +
192A CYS* 4.4 1.7 - - - -
228A CYS 5.9 1.1 - - - -
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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