Contacts of the helix formed by residues 130 - 141 (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 SER 130 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B PRO* 3.8 4.9 - - - +
126B GLN* 3.6 31.7 + - - +
127B GLY 2.6 25.4 + - - -
128B LEU 3.1 1.6 - - - -
129B ASP* 1.3 81.5 - - - +
131B ASP* 1.3 67.0 + - - +
132B ALA* 3.7 2.3 + - - +
133B GLU* 3.1 16.0 + - - +
134B LYS* 3.0 26.1 + - - +
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Residues in contact with ASP 131 (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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126B GLN* 4.3 5.2 + - - +
130B SER* 1.3 73.8 - - - +
132B ALA* 1.3 57.7 + - - +
134B LYS* 3.3 22.7 + - - +
135B GLU* 2.9 31.2 + - - +
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Residues in contact with ALA 132 (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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95B ASP* 3.8 14.1 - - - +
96B ILE* 4.4 5.8 - - + -
97B THR* 3.7 27.3 - - + +
124B PRO* 4.2 9.9 - - + -
126B GLN* 3.5 21.5 - - - +
130B SER* 3.1 3.6 - - - +
131B ASP* 1.3 80.1 - - - +
133B GLU* 1.3 57.3 + - - +
135B GLU* 3.4 1.6 + - - +
136B MET* 3.0 38.4 + - + +
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Residues in contact with GLU 133 (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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124B PRO* 4.0 8.9 - - + +
127B GLY 3.9 5.4 - - - +
128B LEU* 3.7 19.6 - - + +
129B ASP* 2.6 34.9 + - - +
130B SER* 3.1 19.8 + - - +
132B ALA* 1.3 79.9 - - - +
134B LYS* 1.3 61.0 + - - +
136B MET* 3.4 4.7 + - - +
137B LYS* 2.9 37.4 + - - +
166B ASP* 5.6 0.9 - - - +
167B ILE* 3.7 34.6 + - + +
168B ALA 5.2 0.5 + - - -
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Residues in contact with LYS 134 (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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129B ASP* 3.4 27.9 + - - +
130B SER 3.0 10.9 + - - +
131B ASP* 3.5 22.4 + - - +
133B GLU* 1.3 81.8 - - - +
135B GLU* 1.3 62.2 + - - +
137B LYS* 3.4 8.1 + - - +
138B ALA* 3.3 20.6 + - - +
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Residues in contact with GLU 135 (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* 4.1 25.1 - - + -
131B ASP 2.9 17.8 + - - +
132B ALA 3.7 4.5 - - - +
134B LYS* 1.3 78.2 - - - +
136B MET* 1.3 62.1 + - - +
138B ALA* 3.3 8.7 + - - +
139B ILE* 3.2 22.1 + - + +
152B VAL* 3.8 17.5 - - + +
157B SER* 5.4 0.9 - - - -
158B VAL* 2.8 35.6 + - - +
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Residues in contact with MET 136 (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* 3.7 17.0 - - - +
95B ASP* 4.0 11.0 - - - +
96B ILE* 3.6 35.9 - - + -
122B ALA* 3.8 16.4 - - + -
123B PHE 4.0 3.1 - - - +
124B PRO* 3.6 44.0 - - + -
132B ALA 3.0 21.4 + - - +
133B GLU* 4.0 4.3 - - - +
135B GLU* 1.3 73.0 - - - +
137B LYS* 1.3 65.9 + - - +
139B ILE* 4.2 4.7 - - - -
140B TRP* 2.9 49.1 + - + +
167B ILE* 4.3 2.5 - - + -
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Residues in contact with LYS 137 (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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133B GLU* 2.9 23.7 + - - +
134B LYS* 3.4 10.1 - - - +
136B MET* 1.3 76.4 - - - +
138B ALA* 1.3 62.5 + - - +
140B TRP* 3.5 1.3 + - - +
141B CYS* 3.1 47.0 + - - +
161B ALA 4.4 6.1 - - - +
162B SER* 3.8 11.3 + - - +
163B CYS 3.3 26.9 + - - +
165B VAL* 3.0 28.0 - - + +
166B ASP* 5.1 1.1 - - - +
167B ILE* 3.9 21.3 - - + +
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Residues in contact with ALA 138 (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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134B LYS 3.3 9.2 + - - +
135B GLU* 3.4 11.4 - - - +
136B MET 3.2 0.4 - - - -
137B LYS* 1.3 81.2 - - - +
139B ILE* 1.3 62.0 + - - +
141B CYS 3.3 1.2 + - - -
142B ALA* 3.2 18.9 + - - +
158B VAL* 3.9 14.9 - - + +
159B ALA 3.9 19.1 - - - +
160B PRO* 4.2 5.2 - - + -
161B ALA* 3.6 27.3 - - - +
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Residues in contact with ILE 139 (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 14.8 - - + -
96B ILE* 3.8 25.6 - - + -
135B GLU* 3.2 15.6 + - + +
136B MET* 3.2 9.8 + - + +
138B ALA* 1.3 77.2 - - - +
140B TRP* 1.3 66.4 + - + +
142B ALA* 3.1 19.2 + - - +
145B LYS* 3.8 8.7 - - - +
148B ALA* 4.1 11.2 - - + +
149B PHE* 3.7 36.6 - - + +
152B VAL* 3.6 39.7 - - + -
158B VAL* 4.3 4.5 - - + -
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Residues in contact with TRP 140 (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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77B GLU* 2.7 32.1 + - + -
79B ILE* 3.5 34.3 - - + +
94B THR* 4.2 3.8 - - + -
120B TYR* 3.7 21.0 + - + -
121B LEU 3.7 3.4 - - - -
122B ALA* 3.6 33.9 - - + -
136B MET* 2.9 57.6 + - + +
137B LYS 4.0 3.1 - - - +
139B ILE* 1.3 77.2 - - + +
141B CYS* 1.3 59.1 + - - +
142B ALA 3.4 0.4 - - - +
145B LYS* 3.7 29.2 - - + +
149B PHE* 3.9 25.1 - + - -
163B CYS* 4.1 1.1 - - - -
165B VAL* 4.0 28.8 - - + +
167B ILE* 4.5 3.4 - - + -
170B HIS* 3.6 15.7 - + - -
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Residues in contact with CYS 141 (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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137B LYS* 3.1 39.8 + - - +
138B ALA 3.7 1.3 - - - -
139B ILE 3.1 1.0 - - - -
140B TRP* 1.3 76.7 - - - +
142B ALA* 1.3 66.3 + - - +
143B LYS 3.9 0.2 + - - -
161B ALA* 3.7 26.0 - - + +
162B SER* 3.7 2.2 - - - +
163B CYS* 2.0 63.5 - - + +
165B VAL* 4.3 2.0 - - - -
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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