Contacts of the helix formed by residues 131 - 150 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ASP 2.8 18.6 + - - -
129A LEU 3.3 0.8 - - - -
130A THR* 1.3 77.1 + - - +
132A ASP* 1.3 67.8 + - - -
133A LEU 3.2 2.2 + - - -
134A LYS 3.3 2.1 + - - -
135A ALA* 2.9 24.4 + - - +
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Residues in contact with ASP 132 (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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70A ARG* 4.6 20.3 + - - +
127A ASP 4.5 0.4 + - - -
128A GLU* 3.6 15.9 + - - +
131A GLY* 1.3 71.4 - - - +
133A LEU* 1.3 57.7 + - - +
135A ALA* 3.4 7.6 + - - +
136A LEU* 2.9 28.1 + - - +
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Residues in contact with LEU 133 (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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70A ARG* 5.4 4.9 - - - +
73A LEU* 4.5 7.9 - - + -
77A LEU* 3.9 38.4 - - + -
128A GLU 3.1 18.6 + - - +
129A LEU* 3.5 24.0 - - + +
132A ASP* 1.3 74.0 - - - +
134A LYS* 1.3 67.8 + - - +
136A LEU* 3.2 6.2 + - + +
137A ILE* 2.8 41.4 + - + +
166A TRP* 4.4 9.4 - - + -
212A URA 4.5 4.3 - - + -
178B GLN* 3.7 32.3 - - + +
182B VAL* 4.7 7.4 - - + -
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Residues in contact with LYS 134 (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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129A LEU 3.0 20.7 + - - +
130A THR* 3.5 19.1 - - - +
131A GLY 3.3 0.2 + - - -
133A LEU* 1.3 74.0 - - - +
135A ALA* 1.3 65.8 + - - +
137A ILE* 2.9 6.2 + - - +
138A ASP* 2.8 58.4 + - - +
181B ALA 3.4 20.6 - - - +
182B VAL* 3.7 28.4 + - + -
183B THR 5.9 0.4 - - - -
184B GLY 5.8 1.3 - - - +
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Residues in contact with ALA 135 (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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131A GLY 2.9 18.1 + - - +
132A ASP* 3.5 9.9 - - - +
134A LYS* 1.3 78.9 - - - +
136A LEU* 1.3 62.2 + - - +
138A ASP* 3.5 8.6 - - - +
139A GLU* 3.3 18.7 + - - +
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Residues in contact with LEU 136 (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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77A LEU* 3.9 35.7 - - + -
80A LEU* 5.1 2.9 - - + -
81A LYS* 3.8 33.9 - - + +
132A ASP 2.9 17.7 + - - +
133A LEU* 3.6 6.1 - - + +
134A LYS 3.2 0.2 - - - -
135A ALA* 1.3 76.4 - - - +
137A ILE* 1.3 60.8 + - + +
139A GLU* 3.1 14.3 + - - +
140A LYS* 3.0 57.2 + - + +
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Residues in contact with ILE 137 (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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77A LEU* 4.8 1.6 - - + -
80A LEU* 3.6 22.9 - - + -
133A LEU* 2.8 39.2 + - + +
134A LYS* 2.9 5.4 + - - +
136A LEU* 1.3 72.3 - - + +
138A ASP* 1.3 61.7 + - - +
140A LYS* 4.5 2.2 - - - +
141A SER* 2.8 44.6 + - - +
159A GLN* 4.8 6.5 - - + +
162A ILE* 4.2 17.0 - - + -
163A PHE* 5.5 1.8 - - + -
166A TRP* 3.6 33.4 - - + -
182B VAL* 4.5 25.4 - - + -
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Residues in contact with ASP 138 (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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134A LYS* 2.8 51.2 + - - +
135A ALA* 3.5 8.6 - - - +
137A ILE* 1.3 77.7 - - - +
139A GLU* 1.3 64.4 + - - +
141A SER* 3.5 6.7 - - - -
142A ALA* 3.1 20.4 + - - +
159A GLN* 4.7 8.3 + - - -
182B VAL* 4.5 7.8 - - - +
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Residues in contact with GLU 139 (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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84A ARG* 5.6 0.5 + - - -
135A ALA 3.3 8.8 + - - +
136A LEU* 3.1 16.1 + - - +
138A ASP* 1.3 78.5 - - - +
140A LYS* 1.3 90.7 + - + +
142A ALA* 2.8 29.9 + - + +
143A LEU* 3.1 18.5 + - + +
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Residues in contact with LYS 140 (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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80A LEU* 3.5 48.9 - - + +
81A LYS* 3.1 13.7 + - - +
83A PHE* 2.9 27.5 + - + -
84A ARG* 3.6 10.1 - - - +
136A LEU* 3.0 41.2 + - + +
137A ILE* 4.5 2.2 - - - +
139A GLU* 1.3 100.7 + - - +
141A SER* 1.3 61.8 + - - +
143A LEU* 3.4 19.2 + - + +
144A ILE* 3.1 30.9 + - + +
162A ILE* 5.0 1.8 - - + -
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Residues in contact with SER 141 (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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137A ILE* 2.8 26.8 + - - +
138A ASP* 3.5 8.5 - - - -
140A LYS* 1.3 73.9 - - - +
142A ALA* 1.3 56.5 + - - +
144A ILE* 3.2 2.7 + - - +
145A ALA* 2.6 38.7 + - - +
158A PRO* 3.6 22.0 - - - +
159A GLN* 3.7 27.0 + - - +
162A ILE* 4.3 2.7 - - - +
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Residues in contact with ALA 142 (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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138A ASP 3.1 8.9 + - - +
139A GLU* 2.8 19.3 + - + +
141A SER* 1.3 75.4 - - - +
143A LEU* 1.3 66.1 + - + +
145A ALA* 3.2 8.7 + - - +
146A GLY* 2.7 20.3 + - - -
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Residues in contact with LEU 143 (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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83A PHE* 3.5 39.9 - - + +
84A ARG* 3.5 20.4 - - - +
85A GLU* 4.1 14.4 - - + +
139A GLU* 3.1 31.2 + - + +
140A LYS* 3.4 14.8 - - + +
142A ALA* 1.3 78.0 - - + +
144A ILE* 1.3 56.1 + - + +
146A GLY* 2.7 23.5 + - - -
147A TRP* 3.1 30.7 + - + -
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Residues in contact with ILE 144 (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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80A LEU* 5.1 1.6 - - + -
83A PHE* 4.3 23.6 - - + -
93A ILE* 5.5 3.6 - - + -
140A LYS* 3.1 21.3 + - + +
141A SER* 3.7 2.9 - - - +
143A LEU* 1.3 78.2 - - + +
145A ALA* 1.3 64.5 + - - +
147A TRP* 2.9 35.7 + - + +
148A VAL* 3.1 16.6 + - + +
153A LEU* 4.3 18.2 - - + -
156A ILE* 4.9 1.6 - - + -
158A PRO* 3.7 23.6 - - + +
161A LEU* 4.8 12.1 - - + -
162A ILE* 3.9 30.3 - - + -
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Residues in contact with ALA 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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141A SER 2.6 20.9 + - - +
142A ALA* 3.2 10.3 - - - +
144A ILE* 1.3 73.6 - - - +
146A GLY* 1.3 56.8 + - - +
148A VAL* 2.9 29.3 - - + +
149A LYS* 3.0 13.4 + - - +
158A PRO* 3.7 15.0 - - + +
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Residues in contact with GLY 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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142A ALA 2.7 9.0 + - - -
143A LEU 2.7 16.7 + - - -
145A ALA* 1.3 67.5 - - - +
147A TRP* 1.3 68.2 + - - -
148A VAL 3.1 0.3 + - - -
149A LYS* 3.1 7.9 + - - +
150A SER* 3.0 25.8 + - - -
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Residues in contact with TRP 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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83A PHE* 4.8 14.8 - + - -
84A ARG 3.0 29.2 - - - -
85A GLU* 2.7 33.2 - - + -
87A PHE* 4.4 13.0 - - + -
89A PRO* 3.3 46.8 + - + +
92A ALA* 6.1 0.2 - - - +
93A ILE* 5.0 2.4 - - + +
143A LEU* 3.1 36.0 + - + -
144A ILE* 2.9 33.8 + - + +
146A GLY* 1.3 71.6 - - - +
148A VAL* 1.3 60.5 + - - +
150A SER* 3.1 12.2 + - - -
152A LYS* 2.8 35.3 + - + -
153A LEU* 3.7 22.2 - - + -
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Residues in contact with VAL 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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144A ILE* 3.1 15.0 + - + +
145A ALA* 2.9 26.5 - - + +
146A GLY 3.1 0.2 + - - -
147A TRP* 1.3 73.8 - - - +
149A LYS* 1.3 60.2 + - + +
151A GLY* 2.9 21.8 + - - -
153A LEU* 3.8 24.2 - - + +
154A ALA 3.7 24.2 - - - +
155A PRO* 5.0 3.4 - - + -
156A ILE* 4.2 30.1 - - + +
158A PRO* 5.6 0.9 - - + -
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Residues in contact with LYS 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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145A ALA 3.0 13.7 + - - +
146A GLY* 3.1 10.5 + - - +
148A VAL* 1.3 78.1 - - + +
150A SER* 1.3 60.7 + - - +
151A GLY* 3.3 1.0 + - - -
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Residues in contact with SER 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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146A GLY 3.0 13.5 + - - -
147A TRP* 3.1 15.8 + - - -
148A VAL 3.2 0.2 - - - -
149A LYS* 1.3 75.1 - - - +
151A GLY* 1.3 58.7 + - - +
152A LYS* 3.5 22.4 + - - +
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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