Contacts of the helix formed by residues 208 - 221 (chain L) in PDB entry 1JH0
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 208 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67H PRO* 4.3 22.7 - - + -
68H HIS* 4.5 7.4 - - - +
123H LEU 4.9 5.6 - - - +
124H ASP 4.6 2.5 - - - +
125H GLY* 3.7 15.0 - - - +
206L MET 4.6 0.4 - - - +
207L ARG* 1.3 80.8 - - - +
209L PRO* 1.3 66.0 - - - +
210L ASP* 2.6 35.4 + - - +
211L HIS* 2.6 39.1 + - + +
212L GLU* 3.3 6.4 + - - +
235M LEU* 4.0 4.9 - - - -
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Residues in contact with PRO 209 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H GLU* 4.7 11.2 - - - +
123H LEU 5.8 2.2 - - - +
130H LYS* 4.1 19.3 - - + +
172H PRO* 6.0 0.4 - - + -
173H GLU* 4.2 15.5 - - + +
208L THR* 1.3 86.8 - - - +
210L ASP* 1.3 68.5 + - - +
211L HIS 3.3 0.2 - - - -
212L GLU* 3.3 24.9 - - - +
213L ASP* 3.1 30.6 + - - +
226L THR* 4.5 10.3 - - + +
235M LEU* 3.8 16.0 - - + -
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Residues in contact with ASP 210 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H ASP* 3.7 10.4 - - - +
125H GLY* 3.0 32.6 + - - +
126H HIS* 5.2 5.0 + - - -
130H LYS* 4.8 0.2 + - - -
172H PRO* 3.1 31.9 - - - +
208L THR* 2.6 20.6 + - - +
209L PRO* 1.3 82.1 - - - +
211L HIS* 1.3 50.6 + - - +
213L ASP* 3.6 5.7 + - - +
214L THR* 2.7 37.3 + - - -
17M ASP* 4.8 6.1 - - - +
20M MET* 4.1 11.7 - - + +
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Residues in contact with HIS 211 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H GLY* 4.9 2.0 - - - -
207L ARG* 3.2 37.2 + - + +
208L THR* 2.6 51.1 + - + +
210L ASP* 1.3 70.1 - - - +
212L GLU* 1.3 59.0 + - - +
214L THR* 3.5 8.3 - - - -
215L PHE* 2.8 30.8 + - - +
20M MET* 3.4 31.9 - - + +
22M GLU* 3.1 28.6 + - + -
140M LEU* 3.8 19.9 - - + +
142M MET* 3.3 10.4 - - + +
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Residues in contact with GLU 212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193L LEU* 3.6 29.9 - - + +
194L VAL* 3.4 37.0 + - - +
197L ALA* 3.9 18.6 - - + -
208L THR 3.3 1.1 + - - +
209L PRO* 3.3 29.2 - - + +
210L ASP 3.2 0.4 - - - -
211L HIS* 1.3 81.0 - - - +
213L ASP* 1.3 71.4 + - - +
215L PHE* 2.8 14.9 + - - +
216L PHE* 3.3 6.2 + - - +
226L THR* 4.3 14.2 - - + +
142M MET* 3.7 8.3 - - + -
235M LEU* 3.3 18.2 - - - +
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Residues in contact with ASP 213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H PRO* 4.4 7.3 - - - +
173H GLU* 3.9 23.4 - - - +
209L PRO* 3.1 17.3 + - - +
210L ASP* 3.9 5.7 - - - +
212L GLU* 1.3 79.9 - - - +
214L THR* 1.3 65.9 + - - +
216L PHE* 3.4 1.4 + - - -
217L ARG* 3.1 40.1 + - - +
223L SER* 2.4 38.8 + - - +
225L GLY* 3.9 8.9 - - - -
226L THR* 4.8 4.8 + - - +
44M ASN* 3.7 14.1 + - - -
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Residues in contact with THR 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210L ASP* 2.7 24.8 + - - +
211L HIS* 3.5 9.2 - - - -
212L GLU 2.8 3.0 + - - -
213L ASP* 1.3 71.7 - - - +
215L PHE* 1.3 67.3 + - - +
217L ARG* 2.8 24.5 + - - +
218L ASP* 3.0 16.9 + - - +
19M GLY* 3.7 9.8 - - - -
20M MET* 3.1 26.4 + - - +
29M ARG* 3.4 29.8 - - - +
140M LEU* 3.7 16.6 - - + -
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Residues in contact with PHE 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193L LEU* 3.6 20.4 - - + -
196L SER* 5.6 1.6 - - - -
211L HIS 2.8 21.7 + - - +
212L GLU 2.8 4.8 + - - +
214L THR* 1.3 71.5 - - - +
216L PHE* 1.3 75.7 + + - +
218L ASP* 3.6 5.3 + - - +
219L LEU* 3.2 42.9 + - + +
133M THR* 4.2 8.7 - - - -
136M ARG* 3.9 12.7 - - + +
137M ALA* 3.8 36.6 - - + -
140M LEU* 3.3 22.4 - - + -
142M MET* 3.9 11.7 - - + -
146M THR* 3.9 31.4 - - + -
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Residues in contact with PHE 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189L LEU* 3.8 37.9 - - + -
193L LEU* 4.1 28.3 - - + -
212L GLU 3.3 4.4 + - - +
213L ASP 4.0 5.4 - - - +
214L THR 2.9 2.2 + - - -
215L PHE* 1.3 100.2 - + - +
217L ARG* 1.3 59.9 + - - +
218L ASP 3.1 1.6 - - - -
219L LEU* 4.1 10.1 - - + -
220L VAL* 2.7 56.3 + - + +
221L GLY 3.3 2.6 + - - -
222L TYR 3.5 13.5 - - - +
223L SER* 4.3 9.0 - - - +
146M THR* 5.4 1.1 - - - -
854M BPH 3.7 23.6 - - - -
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Residues in contact with ARG 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H PRO 5.2 5.7 + - - -
213L ASP* 3.1 34.9 + - - +
214L THR* 2.8 15.7 + - - +
216L PHE* 1.3 72.6 - - - +
218L ASP* 1.3 61.1 + - - +
221L GLY* 2.8 20.1 + - - -
222L TYR* 3.6 22.9 - - - +
223L SER* 4.2 5.5 - - - +
17M ASP* 3.9 31.0 + - - +
19M GLY* 5.4 2.8 - - - +
44M ASN* 4.0 28.3 - - - +
46M GLN* 4.0 36.6 + - - +
48M GLY 3.8 15.3 + - - +
49M PRO* 2.9 32.1 - - + +
50M ILE* 3.2 3.8 - - - -
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Residues in contact with ASP 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214L THR* 3.0 20.9 + - - +
215L PHE* 3.7 8.5 - - - +
217L ARG* 1.3 79.3 - - - +
219L LEU* 1.3 50.3 + - - +
24M VAL* 4.6 5.7 - - - +
29M ARG* 3.1 44.6 + - - +
49M PRO* 4.9 3.1 - - - +
50M ILE* 3.5 1.6 - - - +
51M TYR* 3.2 40.8 + - + +
132M ARG* 2.7 29.3 + - - -
136M ARG* 4.6 15.0 + - + +
140M LEU* 4.3 6.4 - - - +
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Residues in contact with LEU 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215L PHE* 3.2 39.3 + - + +
216L PHE* 3.1 13.6 + - + +
218L ASP* 1.3 80.6 - - - +
220L VAL* 1.3 69.2 + - + +
221L GLY 3.7 0.2 - - - -
50M ILE* 4.6 0.9 - - - +
129M TRP* 3.4 14.4 - - + -
132M ARG* 2.5 50.7 + - + +
133M THR* 3.6 40.4 - - + +
136M ARG* 4.3 10.3 - - + +
146M THR* 5.0 3.8 - - + -
854M BPH 4.0 22.0 - - - +
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Residues in contact with VAL 220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216L PHE* 2.7 31.5 + - + +
219L LEU* 1.3 92.5 - - + +
221L GLY* 1.3 58.4 + - - +
222L TYR* 3.5 22.2 - - + +
50M ILE* 4.4 4.7 - - - -
129M TRP* 4.3 11.2 - - + -
854M BPH 3.9 22.0 - - - -
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Residues in contact with GLY 221 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216L PHE 3.3 0.2 + - - -
217L ARG* 2.8 25.6 + - - -
219L LEU 3.7 0.6 - - - -
220L VAL* 1.3 76.4 - - - +
222L TYR* 1.3 65.2 + - - +
47M LEU* 3.9 2.9 - - - +
48M GLY* 2.8 27.3 + - - -
49M PRO 4.0 2.2 - - - -
50M ILE* 3.8 17.3 - - - +
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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