Contacts of the helix formed by residues 148 - 163 (chain A) in PDB entry 1L6N
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 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A ALA 3.9 2.0 + - - -
147A ILE* 1.3 79.4 - - - +
149A PRO* 1.4 72.3 - - - +
150A ARG* 2.8 28.2 + - - +
151A THR* 3.2 26.3 + - - +
152A LEU* 3.4 8.7 + - - +
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Residues in contact with PRO 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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147A ILE 4.5 1.1 - - - +
148A SER* 1.4 91.2 - - - +
150A ARG* 1.3 67.1 + - + +
151A THR 3.2 0.7 - - - -
152A LEU* 3.3 14.2 + - + +
153A ASN* 3.1 23.0 + - - +
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Residues in contact with ARG 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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148A SER* 2.8 11.8 + - - +
149A PRO* 1.3 85.0 - - + +
151A THR* 1.3 61.4 + - - +
153A ASN* 3.6 6.6 + - - +
154A ALA* 3.2 19.4 + - - +
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Residues in contact with THR 151 (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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147A ILE* 3.2 39.5 - - + -
148A SER* 3.2 18.0 + - - +
149A PRO 3.2 0.2 - - - -
150A ARG* 1.3 79.3 - - - +
152A LEU* 1.3 63.1 + - - +
153A ASN 3.1 0.2 - - - -
154A ALA* 2.9 8.8 + - - +
155A TRP* 2.8 27.4 + - - +
175A LEU* 2.7 31.4 + - + +
187A MET* 6.0 0.2 - - + -
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Residues in contact with LEU 152 (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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147A ILE* 4.1 7.6 - - + +
148A SER 3.4 13.4 + - - +
149A PRO* 3.3 16.1 + - + +
151A THR* 1.3 83.3 - - + +
153A ASN* 1.3 50.4 + - - +
155A TRP* 3.3 4.7 + - - +
156A VAL* 2.7 41.9 + - - +
186A THR* 3.1 41.1 - - + +
187A MET* 3.4 16.2 - - + -
190A THR* 3.3 32.7 - - + +
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Residues in contact with ASN 153 (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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149A PRO 3.1 12.5 + - - +
150A ARG* 3.6 10.8 - - - +
152A LEU* 1.3 73.3 - - - +
154A ALA* 1.3 66.9 - - - +
156A VAL* 3.1 16.6 + - - +
157A LYS* 3.0 24.6 + - - +
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Residues in contact with ALA 154 (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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150A ARG 3.2 11.2 + - - +
151A THR* 2.9 14.7 + - - +
153A ASN* 1.3 80.2 - - - +
155A TRP* 1.3 61.7 + - - +
157A LYS* 3.1 10.8 + - - +
158A VAL* 3.1 23.7 + - + +
175A LEU* 4.3 12.8 - - + -
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Residues in contact with TRP 155 (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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151A THR 2.8 11.6 + - - +
152A LEU 3.6 5.2 - - - +
154A ALA* 1.3 72.8 - - - +
156A VAL* 1.3 58.5 + - - +
158A VAL* 2.5 66.9 + - + +
159A VAL* 2.7 38.1 + - + +
163A ALA* 5.2 5.4 - - - -
168A VAL* 4.4 11.4 - - + -
171A MET 4.9 1.6 - - - -
172A PHE* 3.3 45.5 - + + -
175A LEU* 4.1 7.5 - - + +
187A MET* 3.1 68.1 + - + -
190A THR* 3.5 13.2 - - + -
191A VAL* 3.6 15.4 - - + +
270A LEU* 5.9 5.2 - - + -
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Residues in contact with VAL 156 (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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152A LEU 2.7 29.5 + - - +
153A ASN* 3.2 20.0 - - - +
155A TRP* 1.3 75.6 - - - +
157A LYS* 1.3 57.9 + - + +
159A VAL* 3.3 10.2 + - - +
160A GLU* 2.9 38.5 + - - +
190A THR* 2.8 39.7 - - + +
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Residues in contact with LYS 157 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A ASN* 3.0 13.6 + - - +
154A ALA* 3.3 11.2 - - - +
155A TRP 3.0 0.2 - - - -
156A VAL* 1.3 74.2 - - - +
158A VAL* 1.3 61.9 - - + +
160A GLU* 3.3 12.0 + - + +
161A GLU* 2.8 38.6 + - + +
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Residues in contact with VAL 158 (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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154A ALA 3.1 17.0 - - - +
155A TRP* 2.5 48.2 + - + +
157A LYS* 1.3 69.4 - - + +
159A VAL* 1.3 56.9 + - - -
161A GLU* 2.9 10.1 + - + +
162A LYS 2.9 25.6 + - - -
163A ALA 3.8 1.2 + - - -
168A VAL* 3.8 13.2 - - + +
171A MET* 3.2 49.6 - - + -
175A LEU* 4.3 4.3 - - + -
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Residues in contact with VAL 159 (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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155A TRP* 2.7 65.7 + - + +
156A VAL* 3.6 8.7 - - + +
158A VAL* 1.3 72.8 - - - +
160A GLU* 1.3 60.3 + - - +
162A LYS* 3.9 0.2 - - - -
163A ALA* 2.6 51.2 + - + +
191A VAL* 3.5 10.1 - - + -
192A GLY 3.2 39.6 - - - +
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Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A VAL* 2.9 28.4 + - + +
157A LYS* 3.5 12.5 - - + +
158A VAL 3.3 0.2 - - - -
159A VAL* 1.3 77.5 - - - +
161A GLU* 1.3 60.6 + - - +
192A GLY 5.7 0.9 - - - -
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Residues in contact with GLU 161 (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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157A LYS* 2.8 24.2 + - + +
158A VAL* 2.9 14.3 + - + +
160A GLU* 1.3 82.0 - - - +
162A LYS* 1.3 79.3 + - + +
168A VAL* 6.0 0.2 - - + -
171A MET* 6.2 1.3 - - - -
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Residues in contact with LYS 162 (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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158A VAL 2.9 5.3 + - - -
159A VAL 3.9 0.2 - - - -
161A GLU* 1.3 85.5 - - + +
163A ALA* 1.3 66.4 - - - +
164A PHE 2.8 9.4 + - - +
165A SER* 3.1 27.4 + - - +
167A GLU* 5.7 6.3 - - + -
168A VAL* 2.6 29.8 - - + +
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Residues in contact with ALA 163 (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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155A TRP* 5.2 4.1 - - - -
159A VAL* 2.6 53.7 + - + +
162A LYS* 1.3 69.1 - - - +
164A PHE* 1.3 79.2 + - + +
168A VAL* 2.8 21.5 - - - +
191A VAL* 5.6 1.8 - - + -
192A GLY 4.5 0.4 - - - +
193A GLY* 4.4 11.4 - - - -
270A LEU* 5.4 6.2 - - - +
274A VAL* 4.7 0.9 - - - +
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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