Contacts of the helix formed by residues 137 - 150 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135J MET* 3.2 2.0 - - - +
136J ALA* 1.3 81.1 - - - +
138J GLY* 1.3 64.8 + - - +
139J MET* 4.1 0.5 - - - +
140J CYS* 3.3 12.0 + - - +
141J ALA 3.2 13.7 + - - -
270J LEU* 4.5 6.3 - - - -
271J ALA* 3.5 9.4 - - - +
272J GLY* 3.1 15.8 - - - -
500J PLP 3.3 16.6 + - - -
110L ARG* 4.1 12.7 - - - -
292L GLY* 3.0 27.4 + - - -
294L ALA* 5.8 1.8 - - - -
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Residues in contact with GLY 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137J SER* 1.3 68.7 - - - +
139J MET* 1.3 55.5 + - - -
141J ALA* 2.7 25.3 + - - +
142J SER* 3.0 15.5 + - - -
256J LEU* 4.6 3.2 - - - +
257J HIS 4.2 9.4 - - - -
258J SER* 3.9 8.7 - - - -
271J ALA 3.5 4.6 + - - -
272J GLY* 3.8 10.3 - - - -
500J PLP 2.7 28.7 + - - -
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Residues in contact with MET 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137J SER* 4.1 2.2 - - - +
138J GLY* 1.3 69.8 - - - +
140J CYS* 1.3 57.9 + - - +
142J SER* 3.3 8.3 + - - +
143J THR* 2.8 40.3 + - - +
163J TYR* 3.8 19.5 - - - -
165J LYS* 3.9 10.3 - - + +
166J THR* 3.7 37.5 - - - +
169J PHE* 5.2 3.4 - - + -
500J PLP 2.5 22.3 + - - +
110L ARG* 3.2 39.5 - - - +
290L ILE* 3.4 29.2 - - + +
291L LEU 3.8 2.7 - - - +
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Residues in contact with CYS 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J MET* 3.8 22.9 - - + -
136J ALA 4.5 0.4 - - - -
137J SER* 3.3 16.5 + - - +
138J GLY 3.1 0.4 - - - -
139J MET* 1.3 78.6 - - - +
141J ALA* 1.3 57.6 + - - +
143J THR* 4.2 1.3 - - - -
144J VAL* 3.0 47.1 + - - +
288J HIS* 5.2 0.4 - - - -
291J LEU* 6.4 0.4 - - - -
293J GLY* 4.1 20.9 - - - -
291L LEU 3.0 13.6 + - - -
292L GLY 2.9 25.4 - - - +
293L GLY* 5.1 0.7 - - - -
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Residues in contact with ALA 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J MET* 3.6 17.6 - - - +
137J SER 3.2 10.7 + - - +
138J GLY* 2.7 18.9 + - - +
140J CYS* 1.3 68.8 - - - +
142J SER* 1.3 66.2 + - - +
145J MET* 3.0 26.0 + - - +
256J LEU* 4.3 5.4 - - + -
273J CYS 4.1 17.0 - - - +
274J ILE* 3.2 27.7 - - + +
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Residues in contact with SER 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J GLY 3.0 14.5 + - - -
139J MET* 3.5 12.4 + - - +
141J ALA* 1.3 75.1 - - - +
143J THR* 1.3 65.6 + - - +
145J MET* 3.4 3.9 - - - +
146J LEU* 2.8 34.6 + - - +
166J THR* 4.5 24.3 + - - -
205J PHE* 4.7 8.8 - - - -
256J LEU* 4.2 25.6 - - - +
500J PLP 5.2 4.2 - - - -
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Residues in contact with THR 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J MET* 2.8 27.2 + - - +
140J CYS* 3.7 6.1 - - - +
142J SER* 1.3 78.4 - - - +
144J VAL* 1.3 69.1 + - + +
146J LEU* 3.1 3.4 + - - +
147J LEU* 3.0 33.1 + - + +
169J PHE* 3.7 29.2 - - + -
291J LEU* 5.2 2.2 - - + -
290L ILE 3.7 14.7 + - - -
291L LEU* 3.5 32.6 - - + +
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Residues in contact with VAL 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J MET* 3.3 20.0 - - + -
140J CYS* 3.0 27.1 + - - +
143J THR* 1.3 83.2 - - + +
145J MET* 1.3 57.9 + - - +
147J LEU* 3.3 6.0 + - - -
148J ALA* 2.8 29.1 + - - +
284J ILE* 3.6 29.8 - - + +
287J LEU* 3.6 16.2 - - + +
288J HIS* 4.0 12.6 - - - +
291J LEU* 3.7 23.6 - - + -
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Residues in contact with MET 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141J ALA 3.0 20.2 + - - +
142J SER* 3.4 4.5 - - - +
144J VAL* 1.3 76.0 - - - +
146J LEU* 1.3 106.4 + - + +
148J ALA* 3.8 0.3 - - - -
149J LEU* 3.0 44.4 + - + +
203J LEU* 3.9 24.5 - - + -
205J PHE* 4.5 5.8 - - + -
234J CYS* 3.6 30.3 - - - -
254J LEU* 4.6 3.4 - - + -
256J LEU* 4.4 8.1 - - + -
274J ILE* 3.9 15.0 - - + -
284J ILE* 3.8 20.4 - - + +
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Residues in contact with LEU 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J SER* 2.8 23.0 + - - +
143J THR 3.5 4.7 - - - +
145J MET* 1.3 97.3 - - + +
147J LEU* 1.3 63.0 + - - +
148J ALA 3.1 0.2 + - - -
150J VAL* 3.0 35.1 + - + +
156J ILE* 3.3 34.3 - - + -
166J THR* 4.9 8.7 - - + -
169J PHE* 3.4 35.4 - - + -
170J ILE* 4.1 17.0 - - + -
174J LEU* 4.3 10.3 - - + +
203J LEU* 4.1 2.9 - - + -
205J PHE* 5.1 8.7 - - + -
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Residues in contact with LEU 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J THR* 3.0 35.4 + - + +
144J VAL 3.8 0.2 - - - +
146J LEU* 1.3 77.2 - - - +
148J ALA* 1.3 58.1 - - - +
150J VAL 4.0 9.5 - - - +
169J PHE* 3.8 18.8 - - + -
173J ILE* 5.3 6.7 - - + -
174J LEU* 4.3 8.1 - - + -
177J MET* 3.9 33.6 - - + +
287J LEU* 3.6 17.7 - - + +
291J LEU* 4.1 18.8 - - + -
147L LEU* 5.3 12.6 - - + -
173L ILE* 6.0 7.0 - - + -
176L LYS* 4.3 14.6 + - - -
291L LEU* 5.2 4.0 - - + -
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Residues in contact with ALA 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144J VAL 2.8 17.6 + - - +
145J MET 3.9 2.2 - - - +
147J LEU* 1.3 79.6 - - - +
149J LEU* 1.3 65.3 + - - +
150J VAL 4.8 0.4 - - - -
283J GLU* 4.1 16.5 - - - +
284J ILE* 4.0 28.7 - - + +
287J LEU* 3.6 19.1 - - + -
176L LYS* 5.8 1.3 + - - -
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Residues in contact with LEU 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J MET* 3.0 36.6 + - + +
148J ALA* 1.3 82.5 - - - +
150J VAL* 1.3 68.0 + - + +
151J PRO* 3.6 9.5 - - - +
202J ASN* 5.4 1.0 + - - +
203J LEU* 4.5 9.2 - - + -
232J LEU* 4.5 11.9 - - + -
254J LEU* 3.4 33.0 - - + -
280J LEU* 4.1 23.1 - - + +
283J GLU* 4.5 12.6 - - + -
284J ILE* 4.1 18.2 - - + -
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Residues in contact with VAL 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146J LEU* 3.0 25.5 + - + +
147J LEU 4.0 10.4 - - - +
148J ALA 4.8 0.5 - - - -
149J LEU* 1.3 78.2 - - + +
151J PRO* 1.3 71.3 - - + +
154J GLY* 4.4 9.4 - - - -
155J HIS 4.7 3.1 - - - +
156J ILE* 4.3 12.1 - - + -
174J LEU* 6.0 1.6 - - + -
177J MET* 4.4 3.6 - - - +
179J ILE* 3.5 43.8 - - + +
202J ASN* 4.6 8.3 - - + -
203J LEU* 4.0 32.8 - - + -
176L LYS* 5.2 1.9 + - - -
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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