Contacts of the helix formed by residues 145 - 158 (chain A) in PDB entry 3E2C
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 GLY 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A ILE 2.8 16.6 + - - -
142A GLN 4.1 2.7 + - - -
143A LYS 3.6 1.4 - - - -
144A MET* 1.3 79.1 - - - +
146A LEU* 1.3 66.6 + - - -
147A GLN 3.3 3.1 + - - -
148A ASN* 3.4 2.1 + - - -
149A TYR* 3.0 22.6 + - - +
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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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82A ASP* 3.9 33.9 - - + +
83A VAL* 4.1 6.3 - - + +
84A GLU* 3.9 39.2 + - + +
141A ILE* 4.0 13.7 + - + +
145A GLY* 1.3 71.0 - - - -
147A GLN* 1.3 71.9 + - + +
149A TYR* 3.2 14.0 + - + +
150A LEU* 2.8 52.7 + - + +
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Residues in contact with GLN 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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145A GLY 3.3 0.6 - - - -
146A LEU* 1.3 93.9 - - + +
148A ASN* 1.3 58.4 + - - +
150A LEU* 3.2 19.1 + - - +
151A GLN* 2.9 44.6 + - - +
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Residues in contact with ASN 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 MET* 2.9 40.4 + - + +
145A GLY* 3.4 2.0 + - - -
146A LEU 3.4 0.2 - - - -
147A GLN* 1.3 74.7 - - - +
149A TYR* 1.3 65.1 + - - +
151A GLN* 3.2 23.0 + - - +
152A ALA* 3.0 24.8 + - - +
155A ARG* 5.1 0.9 + - - -
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Residues in contact with TYR 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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40A LEU* 3.7 20.1 - - + +
83A VAL* 4.2 14.6 - - + -
87A LEU* 4.0 3.1 - - - +
137A GLU* 2.6 42.5 + - - +
140A LEU* 4.4 11.9 - - + -
141A ILE* 3.5 48.5 - - + -
144A MET* 3.9 19.1 - - - +
145A GLY 3.0 18.7 + - - +
146A LEU* 3.4 8.1 - - + +
148A ASN* 1.3 76.0 - - - +
150A LEU* 1.3 69.5 + - + +
152A ALA* 3.3 3.9 + - + +
153A GLN* 2.9 52.1 + - + +
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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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37A LEU* 3.8 23.3 - - + +
40A LEU* 4.9 0.9 - - + -
83A VAL* 3.7 35.7 - - + -
146A LEU* 2.8 40.9 + - + +
147A GLN* 3.2 23.5 + - - +
149A TYR* 1.3 85.0 - - + +
151A GLN* 1.3 66.0 + - - +
153A GLN* 3.2 13.9 + - + +
154A ILE* 3.2 21.9 + - + +
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Residues in contact with GLN 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 GLN* 2.9 28.4 + - - +
148A ASN* 3.2 26.1 + - - +
150A LEU* 1.3 74.4 - - - +
152A ALA* 1.3 57.4 + - - +
154A ILE* 3.3 10.0 + - - +
155A ARG* 2.9 54.5 + - - +
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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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144A MET* 4.0 17.9 - - + -
148A ASN 3.0 17.9 + - - +
149A TYR* 3.6 4.5 - - - +
151A GLN* 1.3 73.9 - - - +
153A GLN* 1.3 60.7 + - - +
155A ARG* 3.8 16.3 - - - +
156A GLU* 2.8 59.2 + - - +
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Residues in contact with GLN 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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37A LEU* 4.1 16.1 - - + +
39A ARG* 3.0 52.8 + - + +
40A LEU* 3.7 19.9 + - + +
137A GLU* 4.0 1.6 + - - -
149A TYR* 2.9 52.0 + - + +
150A LEU* 3.2 10.7 + - - +
152A ALA* 1.3 77.4 - - - +
154A ILE* 1.3 62.1 + - - +
156A GLU* 4.5 7.6 + - - +
157A GLU* 3.3 24.8 + - - +
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Residues in contact with ILE 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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35A TRP 5.4 4.7 - - - +
36A GLY 4.4 12.3 - - - +
37A LEU* 3.9 22.7 - - + +
150A LEU* 3.2 19.0 + - + +
151A GLN* 3.7 8.5 - - - +
152A ALA 3.2 0.4 - - - -
153A GLN* 1.3 73.5 - - - +
155A ARG* 1.3 66.4 + - - +
157A GLU* 4.0 2.8 - - - +
158A GLY* 3.0 23.0 + - - +
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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 ASN 5.1 1.0 + - - -
151A GLN* 2.9 41.3 + - - +
152A ALA* 3.8 25.6 - - - +
154A ILE* 1.3 79.5 - - - +
156A GLU* 1.3 64.9 + - + +
158A GLY* 3.4 12.5 + - - -
201A SO4 2.9 45.8 + - - +
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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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152A ALA* 2.8 45.1 + - - +
153A GLN* 4.5 9.0 + - - +
155A ARG* 1.3 76.6 + - + +
157A GLU* 1.3 63.6 + - - +
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Residues in contact with GLU 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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38A LYS* 3.9 38.3 - - + +
39A ARG* 4.1 24.6 - - + +
153A GLN 3.3 19.7 + - - +
154A ILE* 4.0 3.1 - - - +
156A GLU* 1.3 77.8 - - - +
158A GLY* 1.3 72.1 + - - +
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Residues in contact with GLY 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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38A LYS* 4.9 10.9 + - - +
154A ILE 3.0 17.5 + - - +
155A ARG 3.8 8.5 - - - -
156A GLU 3.3 1.6 - - - -
157A GLU* 1.3 93.6 - - - +
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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