Contacts of the helix formed by residues 142 - 156 (chain A) in PDB entry 5E1M
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 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A THR* 3.8 12.6 - - - +
6A ILE* 3.9 21.5 - - + -
9A GLU* 3.8 22.0 - - + +
12A PHE* 4.2 2.2 - - + -
13A TYR* 3.1 15.1 + - + +
141A LEU* 1.3 75.7 - - - +
143A ASP* 1.3 58.9 + - - +
144A GLN* 3.6 1.9 + - - -
145A HIS* 3.0 18.5 + - - -
146A LEU* 2.8 26.9 + - - +
185A ARG* 3.4 0.9 - - - +
310A UNX 2.7 28.2 - - - -
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Residues in contact with ASP 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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1A SER* 3.2 18.4 - - - -
2A THR* 2.9 43.7 + - - +
142A THR* 1.3 71.4 - - - +
144A GLN* 1.3 64.3 + - - +
146A LEU* 3.8 1.1 - - - +
147A ALA* 2.9 26.3 + - - +
174A VAL* 5.7 0.3 - - - +
185A ARG* 2.9 34.2 + - - +
189A VAL* 4.8 1.5 - - - +
192A ARG* 3.4 7.1 + - - -
193A ILE* 3.4 17.4 - - + +
311A UNX 4.0 13.9 - - - -
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Residues in contact with GLN 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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142A THR* 3.2 1.6 + - - -
143A ASP* 1.3 81.8 - - - +
145A HIS* 1.3 60.2 + - + +
147A ALA* 3.8 5.0 - - - +
148A GLU* 2.8 68.0 + - - +
151A ARG* 4.5 8.3 - - - +
310A UNX 3.8 15.7 - - - -
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Residues in contact with HIS 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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9A GLU* 3.2 27.5 + - - -
13A TYR* 2.5 38.1 + + - +
120A GLN* 3.8 22.9 - - + +
141A LEU* 3.8 6.3 - - + +
142A THR* 3.0 17.1 + - - +
144A GLN* 1.3 83.1 - - + +
146A LEU* 1.3 57.9 + - - +
148A GLU* 3.5 11.9 + - + +
149A PHE* 2.8 31.0 + - - +
152A ARG* 5.1 1.6 + - - -
310A UNX 3.7 10.6 - - - -
323A UNX 3.6 21.7 - - - -
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Residues in contact with LEU 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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134A ILE* 5.8 1.1 - - + -
138A ILE* 3.9 39.9 - - + +
141A LEU* 3.8 22.8 - - + +
142A THR 2.8 17.2 + - - +
143A ASP 3.8 2.9 - - - +
145A HIS* 1.3 74.9 - - - +
147A ALA* 1.3 66.8 + - - +
149A PHE* 3.3 6.5 + - + +
150A LEU* 2.9 46.6 + - + +
165A ILE* 5.6 1.1 - - + -
185A ARG* 3.8 30.5 - - - +
190A VAL* 6.1 2.0 - - + -
193A ILE* 4.0 22.4 - - + -
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Residues in contact with ALA 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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143A ASP 2.9 17.4 + - - +
144A GLN* 3.8 6.5 - - - +
146A LEU* 1.3 77.0 - - - +
148A GLU* 1.3 64.6 + - - +
150A LEU* 3.3 2.8 + - - +
151A ARG* 3.0 42.6 + - - +
193A ILE* 4.0 12.5 - - + +
196A SER* 3.8 22.4 - - - +
197A ALA* 3.6 6.1 - - + +
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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 GLN* 2.8 52.8 + - - +
145A HIS* 3.9 12.5 - - + +
147A ALA* 1.3 73.9 - - - +
149A PHE* 1.3 65.3 + - - +
151A ARG* 3.1 19.7 + - - +
152A ARG* 3.0 39.9 + - - +
313A UNX 2.8 25.0 - - - -
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Residues in contact with PHE 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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66A LEU* 5.3 0.7 - - + -
68A CYS* 3.8 18.6 - - - -
119A LEU* 3.4 55.0 - - + +
122A PHE* 3.9 24.9 - + - -
124A PRO* 4.5 3.4 - - + -
134A ILE* 3.9 21.1 - - + -
141A LEU* 4.0 11.4 - - + -
145A HIS 2.8 21.9 + - - +
146A LEU* 3.3 8.3 + - + +
148A GLU* 1.3 73.2 - - - +
150A LEU* 1.3 61.5 + - + +
152A ARG* 3.1 19.3 + - + +
153A CYS* 2.8 55.8 + - - -
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Residues in contact with LEU 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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134A ILE* 3.9 28.0 - - + -
146A LEU* 2.9 42.9 + - + +
149A PHE* 1.3 77.3 - - + +
151A ARG* 1.4 57.2 + - - +
153A CYS* 3.3 4.9 + - + +
154A LYS* 2.9 28.2 + - - +
163A ILE* 4.2 12.6 - - + -
165A ILE* 4.1 23.8 - - + -
193A ILE* 4.4 13.7 - - + -
194A ILE* 4.6 12.6 - - + -
197A ALA* 3.6 21.3 - - + -
199A LEU* 3.9 15.7 - - + +
222A LEU* 4.9 0.2 - - + -
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Residues in contact with ARG 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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144A GLN* 4.5 7.5 - - - +
147A ALA* 3.0 27.6 + - - +
148A GLU* 3.1 40.6 + - - +
150A LEU* 1.4 76.0 - - - +
152A ARG* 1.3 64.5 + - + +
154A LYS* 3.3 1.9 + - - +
155A GLY* 3.2 11.1 + - - -
196A SER* 2.8 37.0 + - - -
197A ALA* 3.7 21.4 - - - +
322A UNX 2.7 29.1 - - - -
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Residues in contact with ARG 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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119A LEU 3.0 20.0 + - - -
120A GLN* 3.6 19.2 + - - +
121A ASP 5.4 0.4 - - - -
122A PHE 2.8 29.6 + - - +
123A THR* 3.5 27.7 + - + +
124A PRO* 4.0 18.3 - - + +
145A HIS 5.1 0.8 + - - -
148A GLU* 3.0 31.2 + - - +
149A PHE* 3.6 19.1 - - - +
151A ARG* 1.3 77.2 - - + +
153A CYS* 1.3 62.3 + - - +
155A GLY* 3.2 12.4 + - - -
156A SER* 3.3 12.8 + - - -
313A UNX 3.0 29.0 - - - -
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Residues in contact with CYS 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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66A LEU* 5.2 0.7 - - - -
68A CYS* 5.1 0.2 - - - -
124A PRO* 4.3 5.4 - - - -
132A ILE* 3.4 28.6 - - + +
134A ILE* 4.5 3.8 - - - -
149A PHE* 2.8 54.9 + - - +
150A LEU* 3.5 11.2 - - + +
152A ARG* 1.3 73.0 - - - +
154A LYS* 1.3 65.5 + - - +
156A SER* 2.9 24.2 + - - -
157A LEU* 3.3 6.2 + - - +
163A ILE* 3.7 18.2 - - + -
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Residues in contact with LYS 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 LEU 2.9 14.1 + - - +
151A ARG* 3.4 10.3 - - - +
152A ARG 3.3 0.2 - - - -
153A CYS* 1.3 75.0 - - - +
155A GLY* 1.3 60.0 + - - +
156A SER 3.3 1.2 + - - -
157A LEU* 3.3 23.8 + - + +
163A ILE* 3.8 8.9 - - - +
197A ALA 4.3 7.9 - - - +
198A GLY* 2.9 31.8 + - - +
199A LEU* 3.9 18.4 - - + -
223A ARG* 4.2 13.0 - - - +
322A UNX 3.8 13.0 - - - -
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Residues in contact with GLY 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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124A PRO 5.6 0.7 - - - -
126A PRO* 3.4 12.8 - - - +
127A ASP 3.3 14.0 + - - -
151A ARG 3.2 9.6 + - - -
152A ARG* 3.2 6.0 + - - -
153A CYS 3.2 1.0 - - - -
154A LYS* 1.3 78.1 - - - +
156A SER* 1.3 56.2 + - - +
157A LEU 3.5 2.4 - - - +
322A UNX 4.2 4.4 - - - -
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Residues in contact with SER 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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124A PRO* 3.6 30.1 - - - +
125A GLU 3.1 25.6 - - - -
126A PRO* 3.9 0.2 - - - -
127A ASP 3.5 2.9 - - - +
128A SER 2.8 22.5 + - - -
129A TYR* 3.0 13.2 + - - -
132A ILE* 3.1 17.3 - - - +
152A ARG 3.3 3.4 + - - -
153A CYS 2.9 15.7 + - - -
155A GLY* 1.3 76.7 - - - +
157A LEU* 1.3 59.8 + - - +
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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