Contacts of the helix formed by residues 131 - 150 (chain B) in PDB entry 3LOC
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 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ASP 2.9 16.0 + - - -
128B GLU* 5.1 0.2 - - - -
129B LEU 3.1 1.0 + - - -
130B THR* 1.3 78.5 + - - +
132B ASP* 1.3 66.8 + - - -
133B LEU 3.1 2.5 + - - -
134B LYS 3.2 10.6 + - - -
135B ALA* 3.2 14.2 + - - +
88D ALA* 4.0 13.2 - - - -
91D ALA* 4.6 7.9 - - - -
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Residues in contact with ASP 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ARG* 4.6 1.6 + - - -
128B GLU* 3.0 34.7 + - - +
131B GLY* 1.3 70.5 - - - +
133B LEU* 1.3 64.7 + - - +
135B ALA* 3.3 7.2 + - - +
136B LEU* 3.0 23.9 + - - +
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A GLN* 3.2 39.3 - - + +
182A VAL* 4.3 7.6 - - + -
73B LEU* 4.9 5.6 - - + -
77B LEU* 3.9 32.1 - - + -
128B GLU* 3.4 6.3 + - - +
129B LEU* 3.3 30.5 - - + +
131B GLY 3.3 0.6 - - - -
132B ASP* 1.3 77.8 - - - +
134B LYS* 1.3 53.9 + - - +
136B LEU* 3.0 7.9 + - + +
137B ILE* 2.8 61.3 + - + +
166B TRP* 4.2 8.5 - - + -
212B URA 4.4 3.1 - - + -
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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
----------------------------------------------------------
181A ALA 3.7 20.0 - - - +
182A VAL* 3.8 26.5 - - + +
129B LEU 3.1 7.7 + - - +
130B THR 3.4 24.9 - - - +
131B GLY 3.2 0.2 + - - -
133B LEU* 1.3 77.3 - - - +
135B ALA* 1.3 60.5 + - - +
137B ILE* 3.0 3.0 + - - +
138B ASP* 2.8 60.7 + - - +
152D LYS* 6.1 3.4 - - - +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B GLY 3.2 10.3 + - - +
132B ASP* 3.6 10.8 - - - +
134B LYS* 1.3 81.0 - - - +
136B LEU* 1.3 62.9 + - - +
138B ASP* 3.4 9.5 + - - +
139B GLU* 3.2 23.2 + - - +
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 4.5 15.0 - - + -
80B LEU* 4.0 18.4 - - + -
81B LYS* 3.9 29.8 - - + -
132B ASP 3.0 11.6 + - - +
133B LEU* 3.0 12.6 + - + +
135B ALA* 1.3 79.5 - - - +
137B ILE* 1.3 79.4 + - + +
139B GLU* 3.3 23.7 + - - +
140B LYS* 3.3 31.4 + - + +
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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
----------------------------------------------------------
182A VAL* 4.3 20.0 - - + -
77B LEU* 4.7 0.4 - - + -
80B LEU* 3.8 28.3 - - + -
133B LEU* 2.8 39.5 + - + +
134B LYS* 3.0 5.6 + - - +
136B LEU* 1.3 77.2 - - + +
138B ASP* 1.3 58.2 + - - +
140B LYS* 3.3 2.5 + - - +
141B SER* 2.8 50.5 + - - +
159B GLN* 4.6 13.7 - - + +
162B ILE* 3.9 18.2 - - + -
163B PHE* 5.7 1.3 - - + -
166B TRP* 3.9 22.0 - - + -
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Residues in contact with ASP 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A VAL* 4.7 6.9 - - - +
134B LYS* 2.8 45.1 + - - +
135B ALA* 3.6 8.6 - - - +
137B ILE* 1.3 75.8 - - - +
139B GLU* 1.3 62.3 + - - +
141B SER* 3.7 6.2 + - - -
142B ALA* 3.2 23.6 + - - +
159B GLN* 4.7 7.8 + - - -
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Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ALA 3.2 10.5 + - - +
136B LEU* 3.4 19.6 - - - +
138B ASP* 1.3 82.7 - - - +
140B LYS* 1.3 81.3 + - + +
142B ALA* 3.6 6.1 - - - +
143B LEU* 3.3 24.2 + - + +
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Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 3.5 46.7 + - + +
81B LYS* 3.2 22.6 + - - +
83B PHE* 2.8 36.6 + - + -
84B ARG* 3.6 6.9 - - - +
136B LEU* 3.3 20.4 + - + +
137B ILE* 4.1 2.7 - - - +
139B GLU* 1.3 104.1 + - + +
141B SER* 1.3 60.4 + - - +
143B LEU* 3.3 15.8 - - + +
144B ILE* 3.0 35.8 + - + +
162B ILE* 4.9 4.0 - - + -
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Residues in contact with SER 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ILE* 2.8 28.4 + - - +
138B ASP* 3.7 7.6 - - - -
140B LYS* 1.3 74.9 - - - +
142B ALA* 1.3 56.9 + - - +
144B ILE* 3.0 3.5 + - - -
145B ALA* 2.7 33.6 + - - +
158B PRO* 3.5 28.3 - - - +
159B GLN* 3.6 26.3 + - - +
162B ILE* 4.1 2.8 - - - +
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ASP 3.2 10.6 + - - +
139B GLU* 3.6 11.7 - - - +
141B SER* 1.3 77.7 - - - +
143B LEU* 1.3 62.7 + - - +
145B ALA* 3.0 10.6 + - - +
146B GLY* 2.9 20.6 + - - -
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 3.8 35.0 - - + +
84B ARG* 3.8 18.8 - - - +
85B GLU* 4.0 30.7 - - + +
139B GLU* 3.3 11.7 + - + +
140B LYS* 3.3 21.5 - - + +
141B SER 3.2 0.4 - - - -
142B ALA* 1.3 78.2 - - - +
144B ILE* 1.3 56.9 + - - +
146B GLY* 3.1 6.8 + - - -
147B TRP* 3.0 40.8 + - + +
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Residues in contact with ILE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 5.5 0.9 - - + -
83B PHE* 5.1 15.9 - - + -
93B ILE* 5.9 3.8 - - + -
140B LYS* 3.0 18.3 + - + +
141B SER 3.5 5.6 - - - +
143B LEU* 1.3 77.0 - - + +
145B ALA* 1.3 66.6 + - - +
146B GLY 3.0 1.6 - - - -
147B TRP* 2.8 33.2 + - + +
148B VAL* 2.9 17.3 + - + +
153B LEU* 4.2 18.2 - - + -
156B ILE* 5.0 2.2 - - + -
158B PRO* 3.9 24.9 - - + +
161B LEU* 4.5 15.0 - - + -
162B ILE* 4.1 30.1 - - + -
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Residues in contact with ALA 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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141B SER 2.7 16.7 + - - +
142B ALA* 3.4 12.1 - - - +
144B ILE* 1.3 72.6 - - - +
146B GLY* 1.3 51.8 + - - +
148B VAL* 3.1 13.6 + - - +
149B LYS* 2.6 36.5 + - - +
158B PRO* 4.0 12.5 - - + +
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Residues in contact with GLY 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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142B ALA 2.9 12.1 + - - -
143B LEU* 3.3 7.0 - - - -
145B ALA* 1.3 74.5 - - - +
147B TRP* 1.3 67.0 + - - +
149B LYS* 3.8 9.6 - - - +
150B SER* 3.1 26.9 + - - -
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Residues in contact with TRP 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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83B PHE* 4.9 10.8 - + - -
84B ARG 3.2 13.2 - - - -
85B GLU* 2.5 46.0 - - + -
86B ASP* 4.5 0.4 - - - -
87B PHE* 3.6 26.5 - - + -
89B PRO* 3.6 35.2 - - + +
92B ALA* 6.1 1.5 - - + +
93B ILE* 5.4 4.1 - - + +
143B LEU* 3.0 29.2 + - + +
144B ILE* 2.8 36.7 + - + +
146B GLY* 1.3 74.5 - - - +
148B VAL* 1.3 64.0 + - - +
150B SER* 3.4 3.4 + - - -
151B GLY 3.3 4.2 + - - -
152B LYS* 3.0 40.9 + - + -
153B LEU* 3.7 27.4 - - + -
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ILE* 2.9 25.2 + - + +
145B ALA* 3.2 13.0 - - - +
147B TRP* 1.3 77.0 - - - +
149B LYS* 1.3 62.8 + - - +
151B GLY* 3.0 14.9 + - - -
153B LEU* 4.0 16.7 - - + +
154B ALA 3.9 14.4 - - - +
155B PRO* 3.7 28.5 - - + -
156B ILE* 3.9 19.7 - - + +
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Residues in contact with LYS 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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145B ALA 2.6 20.1 + - - +
146B GLY* 4.1 9.4 - - - +
147B TRP 3.4 0.2 - - - -
148B VAL* 1.3 73.8 - - - +
150B SER* 1.3 63.7 + - - +
151B GLY 3.3 1.3 + - - -
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Residues in contact with SER 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLY 3.1 20.7 + - - -
147B TRP* 3.4 2.3 + - - -
148B VAL 3.2 0.2 - - - -
149B LYS* 1.3 79.9 - - - +
151B GLY* 1.3 57.2 + - - +
152B LYS* 3.4 34.5 + - - +
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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
------------------------------------------------------------
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