Contacts of the helix formed by residues 226 - 244 (chain T) in PDB entry 1L9J
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 THR 226 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119T ASP* 2.6 29.4 + - - +
120T LEU* 3.1 44.9 - - + +
121T PRO* 3.7 7.4 - - + -
220T LYS* 3.8 14.4 - - - +
224T GLU* 5.0 5.8 - - - +
225T VAL* 1.3 74.2 - - - +
227T LEU* 1.3 65.7 + - - +
229T GLU* 2.7 34.7 + - - +
230T GLU* 3.1 8.0 + - - +
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Residues in contact with LEU 227 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233S ARG* 4.2 3.4 - - - +
236S GLU* 4.4 17.5 - - + +
240S ASP* 3.7 21.5 - - + +
70T ARG* 6.0 1.3 - - - +
117T ARG* 3.9 32.8 - - + +
118T ARG* 3.5 15.5 - - + +
120T LEU 3.0 20.8 + - - +
121T PRO* 4.3 0.4 - - - +
122T GLU* 3.5 42.2 - - + +
225T VAL 3.8 0.8 + - - -
226T THR* 1.3 68.9 - - - +
228T LEU* 1.3 57.6 + - - +
230T GLU* 2.5 49.1 + - - +
231T ASP* 3.2 6.4 + - - +
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Residues in contact with LEU 228 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114T TRP* 3.7 28.5 - - + -
115T VAL 4.2 0.7 - - - +
116T ALA* 3.8 5.8 - - + -
117T ARG* 3.1 41.6 - - - +
118T ARG 3.4 3.2 + - - -
119T ASP* 3.6 32.5 - - + +
226T THR* 3.9 7.6 - - - +
227T LEU* 1.3 77.6 - - - +
229T GLU* 1.3 62.2 + - + +
231T ASP* 3.7 4.7 + - - +
232T LYS* 3.0 34.0 + - + +
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Residues in contact with GLU 229 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119T ASP* 4.5 2.9 - - - +
217T PRO* 6.5 0.4 - - + -
218T THR 3.2 19.7 - - - +
219T ILE* 3.7 16.1 - - + +
220T LYS* 3.4 32.2 + - - +
224T GLU 4.2 1.2 - - - +
225T VAL* 3.2 21.5 - - + +
226T THR* 2.7 43.1 + - - +
227T LEU 2.7 4.0 + - - -
228T LEU* 1.3 74.3 - - + +
230T GLU* 1.3 58.5 + - - +
232T LYS* 2.8 28.7 + - + +
233T ILE* 2.8 17.9 + - + +
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Residues in contact with GLU 230 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229S PHE 6.1 0.3 - - - -
230S GLY* 5.6 1.0 - - - -
233S ARG* 3.2 38.3 + - - -
117T ARG* 5.4 3.9 + - - +
122T GLU* 5.1 1.2 + - - +
131T ILE* 3.4 22.7 - - - +
178T PHE* 4.0 25.6 - - + -
225T VAL* 3.9 16.0 - - + +
226T THR 3.1 10.8 + - - +
227T LEU* 2.5 29.6 + - - +
229T GLU* 1.3 70.2 - - - +
231T ASP* 1.3 65.6 + - - +
233T ILE* 3.1 7.6 + - - -
234T CYS* 3.0 33.6 + - - -
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Residues in contact with ASP 231 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229S PHE 5.3 3.6 - - - +
237S GLN* 5.4 0.2 + - - -
242S GLY* 4.7 0.2 - - - -
243S THR* 3.4 27.7 + - + +
244S ALA 5.6 0.3 + - - -
113T SER 4.2 0.3 - - - +
114T TRP* 3.7 22.6 - - + +
115T VAL 3.3 18.0 + - - +
117T ARG* 3.0 49.4 + - - +
227T LEU 3.2 2.0 + - - -
228T LEU 3.9 8.3 - - - +
229T GLU 3.2 0.4 - - - -
230T GLU* 1.3 77.2 - - - +
232T LYS* 1.3 57.1 + - - +
234T CYS* 5.1 2.2 - - - -
235T GLY* 2.9 31.1 + - - +
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Residues in contact with LYS 232 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114T TRP* 3.2 63.2 - - + +
217T PRO* 3.8 30.5 - - + +
228T LEU* 3.0 30.3 - - + +
229T GLU* 2.8 16.2 + - + +
231T ASP* 1.3 77.9 - - - +
233T ILE* 1.3 58.4 + - - +
236T TYR* 3.1 25.6 + - - +
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Residues in contact with ILE 233 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178T PHE* 4.0 14.1 - - + -
190T LEU* 3.7 46.0 - - + +
192T PRO* 3.8 19.7 - - + -
216T ILE* 5.1 4.2 - - + +
217T PRO* 4.5 26.2 - - + +
218T THR 6.2 0.2 - - - -
219T ILE* 4.4 20.0 - - + -
225T VAL* 4.5 9.0 - - + -
229T GLU* 2.8 16.6 + - + +
230T GLU* 3.5 6.7 - - - +
232T LYS* 1.3 72.8 - - - +
234T CYS* 1.3 68.8 + - - +
236T TYR* 3.1 5.9 + - - +
237T VAL* 3.1 26.0 + - + +
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Residues in contact with CYS 234 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228S ARG* 3.9 20.0 - - + +
229S PHE* 3.9 24.0 - - + -
178T PHE* 4.1 19.1 - - - -
192T PRO* 3.8 28.7 - - + -
195T MET* 5.3 0.9 - - - +
230T GLU* 3.0 25.7 + - - +
231T ASP* 4.7 1.3 - - - +
233T ILE* 1.3 77.1 - - - +
235T GLY* 1.3 58.7 + - - +
236T TYR 3.2 0.2 + - - -
237T VAL* 3.2 2.4 + - - +
238T ALA* 2.8 32.2 + - - +
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Residues in contact with GLY 235 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229S PHE* 3.9 16.0 - - - -
243S THR* 5.5 0.7 - - - -
247S ARG* 4.1 1.1 - - - -
111T PRO 3.5 1.2 - - - +
112T ALA* 3.0 28.8 - - - -
113T SER 3.6 17.0 - - - -
114T TRP* 6.4 0.2 - - - -
231T ASP 2.9 19.4 + - - -
234T CYS* 1.3 76.5 - - - +
236T TYR* 1.3 56.9 + - - +
238T ALA* 3.9 0.2 - - - +
239T GLY 3.1 11.4 + - - -
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Residues in contact with TYR 236 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105T MET* 3.0 60.5 - - + +
106T LYS* 4.3 6.5 - - - -
112T ALA* 5.0 4.9 - - - -
208T LEU* 3.7 11.9 - - + -
212T LEU* 2.6 32.8 + - - +
215T GLY* 2.9 28.0 - - - -
216T ILE* 3.2 40.2 - - + -
217T PRO* 3.9 9.2 - - + -
232T LYS 3.1 21.3 + - - +
233T ILE 3.1 5.6 + - - +
234T CYS 3.1 0.6 - - - -
235T GLY* 1.3 74.2 - - - +
237T VAL* 1.3 71.0 + - + +
239T GLY* 2.9 12.3 + - - -
240T GLY 3.2 6.9 + - - -
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Residues in contact with VAL 237 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191T LEU* 4.2 15.5 - - + -
192T PRO* 3.8 21.5 - - + -
195T MET* 3.7 38.1 - - + -
205T VAL* 5.2 2.2 - - + -
207T ALA* 3.8 15.6 - - + +
208T LEU* 3.9 23.0 - - + +
216T ILE* 5.3 2.2 - - + -
233T ILE* 3.1 17.9 + - + +
234T CYS* 3.6 5.4 - - - +
236T TYR* 1.3 78.4 - - + +
238T ALA* 1.3 55.9 + - - +
240T GLY* 2.7 28.2 + - - -
241T LEU 3.7 2.3 + - - -
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Residues in contact with ALA 238 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112R GLY* 4.0 9.4 - - - +
228S ARG* 4.7 1.3 - - - -
229S PHE* 3.3 31.9 - - + -
247S ARG* 4.0 1.3 - - - +
111T PRO* 3.3 15.7 - - - +
195T MET* 3.6 19.0 - - + +
234T CYS 2.8 21.1 + - - +
235T GLY 3.9 1.6 - - - +
237T VAL* 1.3 73.7 - - - +
239T GLY* 1.3 61.6 + - - +
240T GLY 3.3 0.3 + - - -
241T LEU* 3.4 21.3 + - - +
242T MET 4.4 1.0 + - - -
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Residues in contact with GLY 239 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105T MET* 3.4 6.5 - - - -
111T PRO* 2.9 21.1 + - - -
112T ALA* 3.5 17.5 - - - -
235T GLY 3.1 3.4 + - - -
236T TYR 2.9 10.1 + - - -
238T ALA* 1.3 75.1 - - - +
240T GLY* 1.3 64.9 + - - +
242T MET* 3.3 3.8 + - - +
243T TYR* 3.1 27.5 + - - -
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Residues in contact with GLY 240 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105T MET* 3.4 4.9 - - - -
207T ALA 3.2 15.7 - - - +
208T LEU* 3.6 14.1 - - - -
236T TYR 3.2 4.6 + - - -
237T VAL 2.7 19.1 + - - -
239T GLY* 1.3 69.8 - - - +
241T LEU* 1.3 63.0 + - - +
244T ALA* 2.4 38.6 + - - +
248T ARG* 3.8 0.3 + - - -
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Residues in contact with LEU 241 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112R GLY* 4.7 12.3 - - - +
113R ILE 5.8 0.4 - - - +
228S ARG* 4.0 24.5 - - - +
195T MET* 4.1 13.2 - - + -
206T ASN* 4.5 6.5 - - + +
207T ALA* 3.5 32.5 + - + +
237T VAL 3.7 1.0 + - - -
238T ALA 3.4 13.4 + - - +
239T GLY 3.3 0.4 - - - -
240T GLY* 1.3 76.4 - - - +
242T MET* 1.3 59.5 + - + +
245T ALA* 4.0 4.2 - - - +
248T ARG* 3.7 26.7 + - - +
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Residues in contact with MET 242 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11R VAL* 4.9 1.8 - - + -
12R PRO 4.4 6.1 - - - +
13R GLY* 3.2 43.1 - - - +
14R GLY* 3.5 8.7 - - - +
109R ARG 4.6 6.1 - - - +
110R LYS* 4.2 16.2 - - + +
112R GLY* 6.4 0.2 - - - -
111T PRO* 3.4 36.6 - - + -
238T ALA 4.4 0.4 + - - -
239T GLY 3.3 3.3 + - - +
240T GLY 3.1 0.6 - - - -
241T LEU* 1.3 78.8 - - + +
243T TYR* 1.3 90.6 + - + +
245T ALA* 3.8 12.2 - - - +
246T PRO* 4.8 1.6 - - - +
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Residues in contact with TYR 243 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11R VAL* 3.8 20.8 - - - +
12R PRO 5.3 3.1 + - - -
100T PRO* 4.5 7.9 - - + +
104T PRO* 3.6 40.8 - - + +
105T MET* 3.8 23.6 - - + -
109T VAL* 4.4 2.1 - - - +
110T GLY* 4.3 2.9 - - - -
111T PRO* 4.1 8.1 - - + +
112T ALA* 4.3 13.0 - - + -
239T GLY* 3.1 21.6 + - - +
242T MET* 1.3 107.8 - - + +
244T ALA* 1.3 56.7 + - - +
245T ALA 3.0 5.6 - - - -
246T PRO* 3.0 20.3 - - - +
247T LYS* 5.7 0.9 - - - -
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Residues in contact with ALA 244 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105T MET* 5.4 0.6 - - - +
156T CYS* 3.8 9.5 - - - -
207T ALA 3.2 18.8 - - - +
208T LEU* 4.1 2.9 - - - -
209T SER* 4.4 2.2 - - - +
212T LEU* 3.4 33.0 - - + -
240T GLY* 2.4 31.6 + - - +
243T TYR* 1.3 71.4 - - - +
245T ALA* 1.3 62.7 + - - +
246T PRO* 3.5 1.6 - - - -
247T LYS* 3.5 15.3 + - - +
248T ARG* 3.5 10.2 + - - -
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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
------------------------------------------------------------
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