Contacts of the helix formed by residues 137 - 150 (chain A) in PDB entry 1I43
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 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A MET* 3.2 1.5 - - - +
136A ALA* 1.3 80.5 - - - +
138A GLY* 1.3 63.7 + - - +
139A MET* 3.7 0.3 + - - +
140A CYS* 3.3 12.7 + - - +
141A ALA 3.1 14.2 + - - -
270A LEU* 4.6 7.4 - - - -
271A ALA* 3.5 9.2 - - - +
272A GLY* 3.1 15.8 - - - -
500A PLP 3.2 16.5 + - - -
110C ARG* 4.0 11.6 - - - -
292C GLY* 2.7 30.8 + - - -
294C ALA* 5.5 2.0 - - - -
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Residues in contact with GLY 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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137A SER* 1.3 71.6 - - - +
139A MET* 1.3 63.1 + - - +
141A ALA* 3.0 13.2 + - - +
142A SER* 3.0 17.1 + - - -
256A LEU* 4.3 2.8 - - - +
257A HIS 4.1 11.7 - - - -
258A SER* 4.2 3.6 - - - -
271A ALA 3.3 9.6 + - - -
272A GLY* 3.9 9.6 - - - -
500A PLP 2.8 26.4 + - - -
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Residues in contact with MET 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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137A SER* 4.0 2.9 - - - +
138A GLY* 1.3 71.4 - - - +
140A CYS* 1.3 58.2 + - - +
142A SER* 3.3 8.1 + - - +
143A THR* 2.8 41.0 + - - +
163A TYR* 3.8 24.9 - - - -
165A LYS* 4.0 10.5 - - + +
166A THR* 3.8 31.9 - - + +
169A PHE* 5.2 1.8 - - + -
500A PLP 2.7 20.5 + - - +
110C ARG* 3.3 39.5 - - - +
290C ILE* 3.3 30.1 - - + +
291C LEU 3.8 2.2 - - - -
292C GLY* 4.3 0.7 - - - -
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Residues in contact with CYS 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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135A MET* 3.8 22.4 - - + -
136A ALA 4.4 0.2 - - - -
137A SER* 3.3 15.7 + - - +
138A GLY 3.2 0.2 - - - -
139A MET* 1.3 79.2 - - - +
141A ALA* 1.3 57.5 + - - +
143A THR* 3.7 1.3 - - - -
144A VAL* 2.9 47.3 + - - +
288A HIS* 5.1 0.4 - - - -
291A LEU* 6.4 0.9 - - - -
293A GLY* 4.1 23.1 - - - -
291C LEU 2.9 16.0 + - - +
292C GLY 3.2 23.1 - - - +
293C GLY* 5.1 0.9 - - - -
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Residues in contact with ALA 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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135A MET* 3.5 19.9 - - - -
137A SER 3.1 10.4 + - - +
138A GLY 3.0 10.9 + - - +
140A CYS* 1.3 77.3 - - - +
142A SER* 1.3 63.5 + - - +
144A VAL* 4.0 0.5 - - - +
145A MET* 2.9 25.8 + - - +
256A LEU* 4.2 6.3 - - + -
273A CYS 4.0 16.4 - - - +
274A ILE* 3.3 27.3 - - + +
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Residues in contact with SER 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 GLY 3.0 15.1 + - - -
139A MET* 3.9 9.8 + - - -
141A ALA* 1.3 76.5 - - - +
143A THR* 1.3 64.6 + - - +
145A MET* 3.6 3.5 - - - +
146A LEU* 2.9 33.1 + - - +
166A THR* 4.7 18.4 + - - -
205A PHE* 4.7 13.7 - - - -
236A ASP* 5.7 0.3 + - - -
256A LEU* 3.9 27.9 - - - +
500A PLP 5.3 4.3 - - - -
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Residues in contact with THR 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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139A MET* 2.8 23.4 + - - +
140A CYS* 3.7 6.1 - - - +
142A SER* 1.3 78.0 - - - +
144A VAL* 1.3 71.4 + - + +
146A LEU* 3.6 2.4 - - - +
147A LEU* 3.0 36.9 + - + +
169A PHE* 3.7 30.4 - - + -
291A LEU* 5.3 2.2 - - + -
290C ILE 3.9 9.0 + - - -
291C LEU* 3.4 37.7 - - + +
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Residues in contact with VAL 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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135A MET* 3.5 17.0 - - + -
140A CYS* 2.9 38.8 + - - +
143A THR* 1.3 77.0 - - + +
145A MET* 1.3 57.2 + - - +
147A LEU* 3.2 6.0 + - - -
148A ALA* 2.8 28.9 + - - +
284A ILE* 3.6 30.3 - - + +
287A LEU* 3.7 14.8 - - + +
288A HIS* 4.2 13.2 - - - +
291A LEU* 3.9 21.5 - - + -
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Residues in contact with MET 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 ALA 2.9 19.3 + - - +
142A SER 3.6 5.4 - - - +
144A VAL* 1.3 76.7 - - - +
146A LEU* 1.3 97.5 + - + +
148A ALA* 3.2 0.3 + - - -
149A LEU* 2.9 48.9 + - + +
150A VAL* 5.3 0.2 - - + -
203A LEU* 3.7 29.2 - - + -
205A PHE* 4.4 7.4 - - + -
234A CYS* 3.8 27.1 - - - -
254A LEU* 4.7 3.4 - - + -
256A LEU* 4.4 9.2 - - + -
274A ILE* 3.9 14.8 - - + -
284A ILE* 4.1 18.8 - - + +
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Residues in contact with LEU 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 SER* 2.9 25.0 + - - +
143A THR 3.6 3.4 - - - +
145A MET* 1.3 99.2 - - + +
147A LEU* 1.3 63.9 + - - +
148A ALA 3.0 1.6 + - - -
150A VAL* 3.1 33.4 + - + +
156A ILE* 3.2 33.4 - - + -
166A THR* 4.7 9.0 - - + -
169A PHE* 3.6 33.0 - - + -
170A ILE* 4.2 17.3 - - + -
174A LEU* 4.5 9.5 - - + +
203A LEU* 4.1 2.0 - - + -
205A PHE* 5.1 8.5 - - + -
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Residues in contact with LEU 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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143A THR* 3.0 36.9 + - + +
144A VAL 3.7 4.0 - - - +
146A LEU* 1.3 76.2 - - - +
148A ALA* 1.3 58.8 + - - +
150A VAL 4.1 8.7 - - - +
169A PHE* 3.7 19.7 - - + -
173A ILE* 5.5 6.3 - - + -
174A LEU* 4.3 7.2 - - + -
177A MET* 3.7 36.0 - - + +
287A LEU* 3.7 14.9 - - + +
291A LEU* 4.3 17.0 - - + -
147C LEU* 5.2 15.7 - - + -
173C ILE* 5.9 8.0 - - + +
176C LYS* 4.1 15.6 + - - -
291C LEU* 5.1 4.0 - - + -
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Residues in contact with ALA 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 VAL 2.8 17.2 + - - +
145A MET 3.8 2.7 - - - +
146A LEU 3.0 0.2 - - - -
147A LEU* 1.3 80.4 - - - +
149A LEU* 1.3 64.6 + - - +
150A VAL 4.8 1.0 - - - +
283A GLU* 4.3 14.3 - - - +
284A ILE* 4.0 30.7 - - + +
287A LEU* 3.6 18.4 - - + -
176C LYS* 5.6 2.1 + - - -
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Residues in contact with LEU 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 MET* 2.9 34.8 + - + +
148A ALA* 1.3 80.5 - - - +
150A VAL* 1.3 69.4 + - + +
151A PRO* 3.5 10.2 - - - +
202A ASN* 5.5 1.4 + - - +
203A LEU* 4.5 9.6 - - + -
232A LEU* 4.5 13.9 - - + +
254A LEU* 3.5 32.1 - - + -
280A LEU* 4.0 24.7 - - + +
283A GLU* 4.5 13.2 - - + +
284A ILE* 4.2 18.2 - - + -
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Residues in contact with VAL 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 LEU* 3.1 24.1 + - + +
147A LEU 4.1 9.9 - - - +
148A ALA 4.8 0.6 - - - -
149A LEU* 1.3 79.1 - - + +
151A PRO* 1.3 79.5 - - + +
154A GLY* 4.5 9.4 - - - -
155A HIS 4.7 2.5 - - - +
156A ILE* 4.1 24.5 - - + -
174A LEU* 5.9 1.8 - - + -
177A MET* 4.4 3.3 - - - +
179A ILE* 3.7 35.6 - - + +
202A ASN* 4.5 9.6 - - + -
203A LEU* 4.1 20.6 - - + -
176C LYS* 5.2 1.6 + - - -
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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