Contacts of the helix formed by residues 137 - 150 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135F MET* 3.2 1.5 - - - +
136F ALA* 1.3 80.8 - - - +
138F GLY* 1.3 64.9 + - - +
139F MET* 3.6 1.2 + - - +
140F CYS* 3.1 18.5 + - - +
141F ALA 3.1 6.9 + - - -
270F LEU* 4.5 7.6 - - - -
271F ALA* 3.4 10.5 - - - +
272F GLY* 3.1 15.5 - - - -
500F PLP 3.3 14.1 + - - -
110H ARG* 4.2 12.9 - - - -
292H GLY* 2.9 31.2 + - - -
294H ALA* 5.6 1.6 - - - -
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Residues in contact with GLY 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F SER* 1.3 71.0 - - - +
139F MET* 1.3 57.9 + - - -
141F ALA* 3.2 10.4 + - - +
142F SER* 2.8 21.7 + - - -
256F LEU* 4.4 3.0 - - - +
257F HIS 4.1 11.0 - - - -
258F SER* 4.1 3.8 - - - -
271F ALA 3.3 9.8 + - - -
272F GLY* 3.8 10.3 - - - -
500F PLP 2.5 31.0 + - - -
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Residues in contact with MET 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F SER* 4.0 2.7 - - - +
138F GLY* 1.3 73.1 - - - +
140F CYS* 1.3 64.5 + - - +
142F SER* 3.5 7.1 + - - +
143F THR* 2.9 36.6 + - - +
163F TYR* 3.9 17.9 - - - -
165F LYS* 4.1 8.1 - - + -
166F THR* 3.9 36.3 - - + +
169F PHE* 5.2 2.5 - - + -
500F PLP 2.5 17.4 + - - +
110H ARG* 3.2 44.0 - - - +
289H HIS 4.9 0.2 - - - +
290H ILE* 3.3 30.1 - - + +
291H LEU 3.8 1.8 - - - -
292H GLY* 4.4 1.1 - - - -
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Residues in contact with CYS 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F MET* 4.0 13.2 - - + -
136F ALA 4.5 0.2 - - - -
137F SER* 3.1 19.1 + - - +
139F MET* 1.3 79.5 - - - +
141F ALA* 1.3 56.5 + - - +
143F THR* 4.3 1.1 - - - -
144F VAL* 2.8 51.8 + - - +
288F HIS* 5.3 0.2 - - - -
291F LEU* 6.3 0.9 - - - -
293F GLY* 4.1 26.2 - - - -
291H LEU 3.1 13.8 + - - -
292H GLY 3.1 22.7 - - - +
293H GLY* 4.9 2.0 - - - -
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Residues in contact with ALA 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F MET* 3.7 19.2 - - - -
137F SER 3.1 11.8 + - - +
138F GLY 3.3 10.1 - - - +
140F CYS* 1.3 72.8 - - - +
142F SER* 1.3 57.2 + - - +
144F VAL* 3.8 0.3 - - - +
145F MET* 2.8 36.7 + - - +
256F LEU* 4.4 5.4 - - + -
273F CYS 4.0 16.4 - - - +
274F ILE* 3.3 29.1 - - + +
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Residues in contact with SER 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F GLY 2.8 17.3 + - - -
139F MET* 3.7 12.4 + - - +
141F ALA* 1.3 74.1 - - - +
143F THR* 1.3 65.7 + - - +
145F MET* 3.0 6.5 + - - +
146F LEU* 2.8 32.7 + - - +
166F THR* 4.7 15.1 + - - -
205F PHE* 4.7 14.3 - - - -
236F ASP* 5.6 0.3 + - - -
256F LEU* 4.1 26.6 - - - +
500F PLP 5.2 4.0 - - - -
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Residues in contact with THR 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F MET* 2.9 28.2 + - - +
140F CYS* 3.6 5.4 - - - +
142F SER* 1.3 77.4 - - - +
144F VAL* 1.3 70.2 + - + +
146F LEU* 3.2 2.1 + - - +
147F LEU* 3.0 39.1 + - + +
169F PHE* 3.9 21.9 - - + -
291F LEU* 5.3 1.8 - - + -
290H ILE 3.8 13.7 + - - -
291H LEU* 3.4 36.8 - - + +
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Residues in contact with VAL 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F MET* 3.4 17.7 - - + -
140F CYS* 2.8 39.2 + - - +
143F THR* 1.3 78.4 - - + +
145F MET* 1.3 62.8 + - - +
147F LEU* 3.4 3.1 + - - -
148F ALA* 3.0 22.0 + - - +
284F ILE* 3.6 29.4 - - + +
287F LEU* 3.8 13.5 - - + +
288F HIS* 4.2 12.6 - - - +
291F LEU* 3.7 25.8 - - + -
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Residues in contact with MET 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F ALA 2.8 23.3 + - - +
142F SER 3.3 5.2 - - - +
144F VAL* 1.3 74.2 - - - +
146F LEU* 1.3 104.1 + - + +
148F ALA* 3.3 0.9 + - - +
149F LEU* 3.0 43.7 + - + +
150F VAL* 5.3 0.2 - - + -
203F LEU* 3.8 25.8 - - + -
205F PHE* 4.3 7.6 - - + -
234F CYS* 3.4 31.2 - - - -
254F LEU* 4.7 4.3 - - + -
256F LEU* 4.4 6.1 - - + -
274F ILE* 3.9 14.6 - - + -
284F ILE* 4.0 19.0 - - + +
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Residues in contact with LEU 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F SER* 2.8 23.7 + - - +
143F THR 3.6 3.4 - - - +
145F MET* 1.3 99.3 - - + +
147F LEU* 1.3 62.2 + - - +
148F ALA 3.0 1.6 + - - -
150F VAL* 3.1 34.3 + - + +
156F ILE* 3.3 32.1 - - + -
166F THR* 4.8 9.2 - - + -
169F PHE* 3.6 32.3 - - + -
170F ILE* 4.2 19.1 - - + -
174F LEU* 4.3 11.6 - - + +
203F LEU* 4.1 2.2 - - + -
205F PHE* 5.0 8.5 - - + -
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Residues in contact with LEU 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F THR* 3.0 39.0 + - + +
144F VAL 4.0 0.7 - - - +
146F LEU* 1.3 76.8 - - - +
148F ALA* 1.3 59.2 + - - +
150F VAL 4.3 6.1 - - - +
169F PHE* 3.7 20.6 - - + -
173F ILE* 5.3 5.8 - - + -
174F LEU* 4.4 7.2 - - + -
177F MET* 3.8 34.5 - - + +
287F LEU* 3.8 18.9 - - + +
291F LEU* 4.5 15.7 - - + -
147H LEU* 5.3 15.5 - - + -
173H ILE* 5.9 7.6 - - + +
176H LYS* 4.1 17.2 + - - -
177H MET* 6.2 0.4 - - - -
291H LEU* 4.9 3.8 - - + -
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Residues in contact with ALA 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F VAL 3.0 17.6 + - - +
145F MET 3.7 3.1 - - - +
146F LEU 3.0 1.0 - - - -
147F LEU* 1.3 79.9 - - - +
149F LEU* 1.3 66.6 + - - +
150F VAL 4.8 1.3 - - - +
283F GLU* 4.4 13.9 - - - +
284F ILE* 4.0 28.9 - - + +
287F LEU* 3.9 15.7 - - + -
176H LYS* 5.4 3.1 + - - -
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Residues in contact with LEU 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F MET* 3.0 33.8 + - + +
148F ALA* 1.3 79.8 - - - +
150F VAL* 1.3 67.9 + - + +
151F PRO* 3.4 11.4 - - - +
202F ASN* 5.6 0.7 - - - +
203F LEU* 4.5 9.6 - - + -
232F LEU* 4.6 13.9 - - + +
254F LEU* 3.5 31.9 - - + -
280F LEU* 4.0 24.9 - - + +
283F GLU* 4.6 13.0 - - + -
284F ILE* 4.2 18.8 - - + -
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Residues in contact with VAL 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F LEU* 3.1 26.6 + - + +
147F LEU 4.3 8.7 - - - +
148F ALA 4.8 1.6 - - - +
149F LEU* 1.3 79.1 - - + +
151F PRO* 1.3 78.7 - - + +
154F GLY* 4.6 5.6 - - - -
155F HIS 4.8 2.5 - - - +
156F ILE* 4.2 14.1 - - + -
174F LEU* 6.0 1.8 - - + -
177F MET* 4.4 4.3 - - - +
179F ILE* 3.6 35.6 - - + +
202F ASN* 4.6 12.8 - - + -
203F LEU* 4.1 31.2 - - + -
176H LYS* 5.0 1.7 + - - -
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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