Contacts of the helix formed by residues 144 - 154 (chain A) in PDB entry 1EEJ
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 ASP 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ALA* 3.1 4.0 - - - +
143A LYS* 1.3 80.7 - - + +
145A LYS* 1.3 63.6 + - - +
146A ASN* 3.1 13.0 + - - +
147A LYS* 2.9 38.3 + - + +
148A ALA* 3.1 21.8 + - - +
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Residues in contact with LYS 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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76A LYS 4.3 12.0 + - - +
77A GLU* 4.5 2.2 - - - +
78A MET 3.1 29.7 + - - -
79A ILE* 3.8 25.6 - - + +
80A VAL 5.3 0.4 - - - +
139A ILE* 3.9 14.8 - - - +
140A TRP* 4.0 31.9 - - + +
142A ALA 3.8 9.1 + - - +
143A LYS 3.9 1.9 + - - +
144A ASP* 1.3 71.9 + - - +
146A ASN* 1.3 65.4 + - - +
148A ALA* 3.3 2.1 + - - +
149A PHE* 2.9 31.4 + - - +
165A VAL* 6.4 0.2 - - + -
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Residues in contact with ASN 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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79A ILE* 3.8 11.2 - - - +
80A VAL 2.7 33.2 + - - +
81A TYR* 3.1 38.6 + - + +
144A ASP* 3.1 8.2 + - - +
145A LYS* 1.3 84.5 + - - +
147A LYS* 1.3 63.0 + - - +
149A PHE 3.3 0.9 + - - -
150A ASP* 3.0 29.8 + - - +
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Residues in contact with LYS 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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144A ASP* 2.9 33.0 + - + +
146A ASN* 1.3 74.1 - - - +
148A ALA* 1.3 58.8 + - - +
150A ASP* 3.3 10.3 + - + +
151A ASP* 2.9 54.8 + - - +
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Residues in contact with ALA 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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139A ILE* 4.0 14.6 - - + +
142A ALA* 3.5 24.7 - - + -
144A ASP 3.1 17.8 + - - +
145A LYS 3.6 4.0 - - - +
147A LYS* 1.3 78.8 - - - +
149A PHE* 1.3 61.6 + - - +
151A ASP* 3.7 7.5 - - - +
152A VAL* 3.1 29.7 + - - +
158A VAL* 4.5 10.9 - - + +
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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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79A ILE* 3.7 20.9 - - + -
81A TYR* 3.7 6.7 - - - +
94A THR* 3.7 27.4 - - + -
96A ILE* 3.8 17.7 - - + -
105A HIS* 3.5 33.0 - + - -
120A TYR* 3.4 30.7 - + - -
139A ILE* 3.7 17.0 - - + +
140A TRP* 4.1 9.2 - + - -
145A LYS 2.9 17.1 + - - +
146A ASN 3.7 4.3 - - - +
147A LYS 3.3 0.2 - - - -
148A ALA* 1.3 73.0 - - - +
150A ASP* 1.3 66.3 + - - +
152A VAL* 3.3 2.9 + - - +
153A MET* 3.1 45.9 + - + +
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Residues in contact with ASP 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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81A TYR* 3.0 17.1 + - - -
105A HIS* 2.5 38.2 + - + +
146A ASN* 3.0 20.8 + - - +
147A LYS* 3.6 9.6 - - + +
149A PHE* 1.3 76.8 - - - +
151A ASP* 1.3 59.4 + - - +
153A MET* 3.3 2.3 + - - +
154A ALA* 2.9 31.5 + - - +
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Residues in contact with ASP 151 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A LYS* 2.9 48.3 + - - +
148A ALA* 3.7 7.9 - - - +
150A ASP* 1.3 79.2 - - - +
152A VAL* 1.3 62.0 + - + +
154A ALA* 3.1 3.7 + - - -
155A GLY 3.1 5.7 + - - -
156A LYS* 2.8 62.1 + - + +
157A SER 5.7 2.7 - - - +
158A VAL* 5.7 3.4 - - - -
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Residues in contact with VAL 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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96A ILE* 3.9 29.3 - - + +
135A GLU* 4.4 10.1 - - - +
139A ILE* 3.5 35.7 - - + -
148A ALA 3.1 17.3 + - - +
149A PHE 3.8 2.2 - - - +
151A ASP* 1.3 75.7 - - - +
153A MET* 1.3 64.6 + - - +
155A GLY* 3.2 12.3 + - - -
156A LYS 3.9 7.4 - - - +
158A VAL* 3.5 29.6 - - + -
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Residues in contact with MET 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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94A THR* 4.4 0.7 - - - +
95A ASP 4.4 0.4 - - - +
96A ILE* 3.9 33.7 - - + +
101A CYS* 3.6 41.1 - - + +
102A HIS* 3.0 45.0 + - + +
105A HIS* 4.0 15.3 - - + -
149A PHE* 3.1 51.3 + - + +
150A ASP 3.6 7.4 - - - +
152A VAL* 1.3 77.3 - - - +
154A ALA* 1.3 57.6 + - - +
155A GLY 3.1 4.2 + - - -
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Residues in contact with ALA 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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102A HIS* 4.7 4.5 - - - -
150A ASP 2.9 18.0 + - - +
151A ASP* 3.1 3.8 + - - +
153A MET* 1.3 74.6 - - - +
155A GLY* 1.3 59.8 + - - +
156A LYS* 3.4 27.5 + - - +
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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