Contacts of the helix formed by residues 128 - 145 (chain B) in PDB entry 5EJC
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 GLU 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B PHE* 4.7 14.0 - - + -
126B PRO 3.7 7.6 + - - +
127B LEU* 1.3 76.2 - - - +
129B PRO* 1.4 77.9 - - + +
130B ASP* 3.3 4.0 - - + +
131B ASP* 2.9 31.0 + - - +
132B GLU* 3.3 9.2 + - - +
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Residues in contact with PRO 129 (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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127B LEU 4.7 0.2 - - - +
128B GLU* 1.4 88.7 - - + +
130B ASP* 1.3 67.6 + - - +
132B GLU* 3.2 24.4 + - - +
133B VAL* 3.3 17.1 + - - +
209B ARG* 5.5 0.3 + - - -
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Residues in contact with ASP 130 (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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118B LYS* 5.8 2.3 + - - -
128B GLU* 3.1 3.6 + - + +
129B PRO* 1.3 83.5 - - - +
131B ASP* 1.3 67.5 + - - +
133B VAL* 3.3 11.3 + - - +
134B PHE* 3.2 20.3 + - - +
208B LYS* 5.5 7.1 + - - +
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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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109B LEU* 4.1 23.9 - - + +
112B TYR* 5.9 2.1 - - - -
113B GLN* 3.3 30.1 + - - +
118B LYS* 5.1 8.0 - - - +
127B LEU* 4.2 13.7 - - + -
128B GLU* 2.9 36.3 + - - +
130B ASP* 1.3 81.0 - - - +
132B GLU* 1.3 58.5 + - - +
134B PHE* 3.4 5.3 + - - +
135B LEU* 3.0 27.3 + - - +
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Residues in contact with GLU 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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127B LEU* 4.0 33.1 - - + +
128B GLU 3.7 8.3 - - - +
129B PRO* 3.2 18.9 + - - +
131B ASP* 1.3 73.8 - - - +
133B VAL* 1.3 64.0 + - - +
135B LEU* 3.8 10.1 - - + +
136B ALA* 3.2 22.2 + - - +
209B ARG* 3.8 21.7 + - - +
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Residues in contact with VAL 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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129B PRO 3.3 15.1 + - - +
130B ASP* 3.3 13.6 + - - +
131B ASP 3.3 0.2 - - - -
132B GLU* 1.3 74.6 - - - +
134B PHE* 1.3 66.1 + - - +
136B ALA* 3.2 5.0 + - - +
137B ILE* 3.1 29.7 + - + +
159B VAL* 6.0 3.6 - - + -
162B LEU* 5.6 1.3 - - + -
204B ASP* 6.3 1.1 - - + -
208B LYS* 3.4 47.1 - - + +
209B ARG* 4.0 26.9 - - + +
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Residues in contact with PHE 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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108B TYR* 3.6 15.3 - - + -
109B LEU* 3.4 43.5 - - + -
112B TYR* 3.4 53.4 - + + -
130B ASP 3.2 9.5 + - - +
131B ASP* 3.5 9.6 - - - +
133B VAL* 1.3 79.6 - - - +
135B LEU* 1.3 55.4 + - - +
137B ILE* 3.2 6.7 + - - +
138B ALA* 2.7 42.3 + - + -
152B TYR* 4.9 5.2 - + - -
155B THR* 3.9 22.8 - - + +
156B ARG* 4.8 2.5 - - - -
159B VAL* 4.0 26.0 - - + +
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Residues in contact with LEU 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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105B ALA* 3.3 36.8 - - + +
106B GLU* 3.7 16.8 - - + +
109B LEU* 4.1 15.3 - - + -
127B LEU* 4.0 23.8 - - + -
131B ASP 3.0 15.5 + - - +
132B GLU* 3.9 9.0 - - + +
133B VAL 3.2 0.6 - - - -
134B PHE* 1.3 78.2 - - - +
136B ALA* 1.3 62.0 + - - +
138B ALA* 3.8 2.4 - - - +
139B LYS* 3.1 53.0 + - - +
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Residues in contact with ALA 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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132B GLU 3.2 13.8 + - - +
133B VAL 3.2 8.6 + - - +
135B LEU* 1.3 77.9 - - - +
137B ILE* 1.3 60.3 + - - +
139B LYS* 3.5 12.2 + - - +
140B ALA* 3.3 15.4 + - - +
209B ARG* 3.9 30.5 - - + +
212B ALA* 3.7 23.5 - - + +
213B GLY* 5.1 1.2 + - - -
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Residues in contact with ILE 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 VAL* 3.1 20.0 + - + +
134B PHE 3.7 5.8 - - - +
136B ALA* 1.3 73.2 - - - +
138B ALA* 1.3 61.3 + - - +
140B ALA* 3.0 3.2 + - - +
141B MSE 2.8 37.1 + - + +
155B THR* 4.2 9.2 - - + -
158B PHE* 3.9 20.6 - - + -
159B VAL* 4.1 18.4 - - + -
162B LEU* 4.3 11.4 - - + -
208B LYS 4.0 20.2 - - - +
209B ARG* 3.8 21.5 - - - +
212B ALA* 4.0 8.7 - - + -
224B TRP* 3.8 16.8 - - + -
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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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105B ALA* 4.1 19.1 - - + +
108B TYR* 4.4 8.8 - - + -
134B PHE* 2.7 41.7 + - + +
135B LEU 3.8 5.4 - - - +
137B ILE* 1.3 73.6 - - - +
139B LYS* 1.3 56.7 + - - +
141B MSE 3.8 1.9 - - - +
142B GLU* 3.1 31.4 + - - +
151B CYS* 4.5 2.9 - - - -
155B THR* 3.8 16.3 - - + +
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Residues in contact with LYS 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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103B PRO* 6.4 1.6 - - - -
105B ALA* 3.7 16.4 - - + -
135B LEU* 3.1 47.7 + - - +
136B ALA* 3.6 9.4 - - - +
137B ILE 3.2 0.2 - - - -
138B ALA* 1.3 73.2 - - - +
140B ALA* 1.3 66.1 + - - +
142B GLU* 3.4 22.2 - - - +
143B GLU* 3.8 12.8 + - - +
217B GLU* 5.1 0.4 - - - -
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Residues in contact with ALA 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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136B ALA 3.3 9.6 + - - +
137B ILE 3.0 8.4 + - - +
139B LYS* 1.3 77.5 - - - +
141B MSE 1.3 64.7 + - - +
143B GLU 3.1 11.1 + - - -
144B MSE 3.5 15.0 + - + +
212B ALA* 4.1 9.6 - - + -
213B GLY 5.3 0.9 - - - +
217B GLU* 3.4 33.7 - - - +
220B LEU* 4.4 3.1 - - + -
224B TRP* 3.8 21.8 - - + -
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Residues in contact with MSE 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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60B TRP* 3.8 18.6 - - + -
137B ILE* 2.8 28.7 + - + +
138B ALA 3.8 1.8 - - - +
140B ALA* 1.3 72.5 - - - +
142B GLU* 1.3 56.2 + - - +
144B MSE 2.9 8.6 + - + +
145B VAL* 2.8 69.6 + - + +
151B CYS* 3.6 8.8 - - - +
154B ILE* 3.6 32.5 - - + -
155B THR* 3.4 27.4 - - - +
158B PHE* 5.4 4.9 - - - -
224B TRP* 3.8 23.3 - - + -
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Residues in contact with GLU 142 (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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104B GLN* 3.4 30.0 + - + +
105B ALA* 3.8 24.9 + - - +
108B TYR* 4.5 7.2 - - + +
138B ALA 3.1 12.0 + - - +
139B LYS* 3.4 17.0 - - - +
140B ALA 3.1 0.4 - - - -
141B MSE 1.3 77.6 - - - +
143B GLU* 1.3 67.0 + - - +
145B VAL 3.2 15.3 - - - +
146B GLU* 4.7 3.1 - - - -
151B CYS* 3.6 16.4 - - - -
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Residues in contact with GLU 143 (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 LYS 3.8 13.2 - - - +
140B ALA 3.1 6.1 + - - +
142B GLU* 1.3 86.8 - - - +
144B MSE 1.3 62.2 + - - +
145B VAL 5.0 0.6 - - - -
217B GLU* 3.8 32.0 - - + +
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Residues in contact with MSE 144 (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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56B ARG* 5.7 2.4 - - - -
60B TRP* 4.0 11.9 - - + -
140B ALA* 3.6 10.1 - - + +
141B MSE 2.9 14.1 + - + +
143B GLU* 1.3 81.1 - - - +
145B VAL* 1.3 62.8 + - + +
146B GLU 4.2 0.9 + - - -
217B GLU* 3.7 36.3 - - + +
220B LEU* 3.8 24.5 - - + -
221B GLN* 3.8 37.7 - - + +
224B TRP* 3.7 40.6 - - + -
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Residues in contact with VAL 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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56B ARG* 6.5 0.9 - - + -
57B ALA* 4.9 14.6 - - + -
60B TRP* 5.2 4.3 - - + -
141B MSE 2.8 41.5 + - + +
142B GLU* 3.2 16.5 - - - +
143B GLU 5.0 0.4 - - - -
144B MSE 1.3 78.1 - - + +
146B GLU* 1.3 63.9 + - - +
147B ASP* 3.6 9.4 - - + +
150B ASP* 3.6 14.6 - - + +
151B CYS* 3.4 36.6 - - - +
154B ILE* 3.8 14.8 - - + -
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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