Contacts of the helix formed by residues 144 - 154 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142B ALA* 3.8 3.1 - - - +
143B LYS* 1.3 83.4 - - + +
145B LYS* 1.3 63.7 + - - +
146B ASN* 3.2 14.6 + - - +
147B LYS* 3.0 35.9 + - + +
148B ALA* 3.0 22.2 + - - +
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Residues in contact with LYS 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LYS 3.0 27.1 + - - -
77B GLU* 3.8 12.8 - - - +
78B MET 3.9 12.3 + - - +
79B ILE* 3.8 31.5 - - + +
139B ILE* 3.8 15.8 - - - +
140B TRP* 3.7 29.2 - - + +
142B ALA 3.9 8.2 + - - +
144B ASP* 1.3 72.6 + - - +
146B ASN* 1.3 60.9 + - - +
148B ALA* 3.4 1.9 + - - +
149B PHE* 2.9 31.0 + - - +
165B VAL* 5.6 2.7 - - - -
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Residues in contact with ASN 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ILE* 3.7 11.4 - - - +
80B VAL 2.9 31.7 + - - +
81B TYR* 3.1 36.4 + - + +
144B ASP* 3.2 8.9 + - - +
145B LYS* 1.3 79.0 + - - +
147B LYS* 1.3 57.7 + - - +
149B PHE 3.2 1.0 + - - -
150B ASP* 2.9 36.4 + - - +
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Residues in contact with LYS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ASP* 3.0 31.5 + - + +
146B ASN* 1.3 75.8 - - - +
148B ALA* 1.3 57.5 + - - +
150B ASP* 3.2 10.7 + - + +
151B ASP* 2.8 55.8 + - - +
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ILE* 3.9 10.8 - - + +
142B ALA* 3.4 32.3 - - + -
144B ASP 3.0 9.8 + - - +
145B LYS 3.7 4.0 - - - +
147B LYS* 1.3 74.2 - - - +
149B PHE* 1.3 64.2 + - - +
151B ASP* 3.3 8.9 + - - +
152B VAL* 3.1 28.4 + - - +
158B VAL* 4.0 18.5 - - + +
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Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ILE* 3.9 20.4 - - + -
81B TYR* 3.6 10.5 - - - +
94B THR* 3.9 15.5 - - + -
96B ILE* 3.9 15.9 - - + -
105B HIS* 3.3 33.2 - + - -
120B TYR* 3.5 19.3 - + - -
139B ILE* 3.7 21.0 - - + +
140B TRP* 3.9 18.8 - + - -
145B LYS 2.9 18.8 + - - +
148B ALA* 1.3 75.1 - - - +
150B ASP* 1.3 64.8 + - - +
152B VAL* 3.4 1.2 + - - +
153B MET* 2.9 65.6 + - + +
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Residues in contact with ASP 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B TYR* 2.8 20.2 + - - -
105B HIS* 2.7 34.9 + - - -
146B ASN* 2.9 23.6 + - - +
147B LYS* 3.4 12.5 + - + +
149B PHE* 1.3 76.3 - - - +
151B ASP* 1.3 63.8 + - - +
153B MET* 3.5 1.9 + - - +
154B ALA* 2.9 25.2 + - - +
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Residues in contact with ASP 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LYS* 2.8 52.2 + - - +
148B ALA* 3.6 9.2 - - - +
149B PHE 3.3 0.2 - - - -
150B ASP* 1.3 74.8 - - - +
152B VAL* 1.3 64.1 + - + +
154B ALA* 3.0 17.8 + - - +
156B LYS* 3.0 46.0 + - + +
157B SER 5.5 4.9 - - - +
158B VAL* 5.7 2.9 - - + +
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ILE* 4.4 21.1 - - + +
135B GLU* 3.8 14.6 - - + +
139B ILE* 3.6 26.7 - - + -
148B ALA 3.1 19.7 + - - +
149B PHE 3.9 1.3 - - - +
151B ASP* 1.3 76.0 - - - +
153B MET* 1.3 60.6 + - + +
155B GLY* 2.8 22.2 + - - -
156B LYS 3.6 11.1 - - - +
158B VAL* 3.6 35.7 - - + +
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Residues in contact with MET 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B THR* 4.6 0.7 - - - +
96B ILE* 4.3 20.9 - - + +
101B CYS* 3.4 40.6 - - + +
102B HIS* 3.6 31.8 - - + +
105B HIS* 3.7 21.3 - - + -
106B GLU* 4.8 13.0 - - + +
120B TYR* 5.2 0.4 - - - +
149B PHE* 2.9 61.1 + - + +
150B ASP 3.9 1.8 - - - +
152B VAL* 1.3 75.3 - - - +
154B ALA* 1.3 57.8 + - - +
155B GLY 3.2 1.6 + - - -
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Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ASP 2.9 18.2 + - - +
151B ASP* 3.0 10.5 + - - +
153B MET* 1.3 76.8 - - - +
155B GLY* 1.3 59.4 + - - +
156B LYS* 3.4 17.3 + - + +
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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