Contacts of the helix formed by residues 197 - 211 (chain A) in PDB entry 1JPM
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 ARG 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A TRP* 1.3 76.3 - - - +
198A PRO* 1.3 65.9 - - + +
199A LYS* 3.4 4.4 - - + +
200A GLU* 3.0 49.5 + - + +
201A ALA* 2.7 31.4 + - - +
222A VAL* 3.9 1.1 - - - -
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Residues in contact with PRO 198 (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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197A ARG* 1.3 85.5 - - + +
199A LYS* 1.3 63.3 + - + +
201A ALA* 3.1 3.1 + - - +
202A VAL* 3.0 29.3 + - - +
222A VAL* 3.5 19.9 - - + -
226A ASP* 3.9 19.1 - - - +
229A GLY* 3.7 25.6 - - - +
232A LYS* 3.8 18.4 - - + -
233A VAL* 3.7 3.7 - - + +
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Residues in contact with LYS 199 (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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197A ARG* 3.4 4.4 - - + +
198A PRO* 1.3 81.1 - - + +
200A GLU* 1.3 61.3 + - - +
202A VAL* 3.5 6.0 + - - +
203A THR* 3.1 29.5 + - - +
232A LYS* 4.2 21.9 - - - +
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Residues in contact with GLU 200 (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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168A ILE* 3.9 18.5 - - + +
195A GLY 4.3 3.3 - - - +
196A TRP* 3.5 29.4 - - + -
197A ARG* 3.0 62.3 + - + +
199A LYS* 1.3 77.1 - - - +
201A ALA* 1.3 59.6 + - - +
203A THR* 3.3 7.5 + - - -
204A ALA* 3.0 27.0 + - - +
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Residues in contact with ALA 201 (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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196A TRP* 3.6 33.2 - - + -
197A ARG 2.7 20.5 + - - +
198A PRO* 3.5 4.9 - - + +
200A GLU* 1.3 71.9 - - - +
202A VAL* 1.3 60.8 + - - +
204A ALA* 3.6 0.5 - - - +
205A ILE* 2.8 37.0 + - + +
221A PRO* 3.9 11.4 - - + -
222A VAL* 4.5 0.7 - - + -
233A VAL* 3.8 17.9 - - + -
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Residues in contact with VAL 202 (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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198A PRO 3.0 20.3 + - - +
199A LYS* 3.7 9.9 - - - +
200A GLU 3.3 0.2 - - - -
201A ALA* 1.3 75.2 - - - +
203A THR* 1.3 60.4 + - - +
205A ILE* 3.8 0.7 - - - +
206A ARG* 2.9 67.1 + - + +
232A LYS* 4.4 9.4 - - + +
233A VAL* 3.9 19.7 - - + +
236A ALA* 3.8 25.1 - - + +
237A THR* 4.4 7.8 - - + +
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Residues in contact with THR 203 (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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168A ILE* 5.0 6.5 - - + -
199A LYS* 3.1 15.9 + - - +
200A GLU* 3.6 10.0 - - - -
201A ALA 3.2 0.4 - - - -
202A VAL* 1.3 81.3 - - - +
204A ALA* 1.3 57.6 + - - +
206A ARG* 3.9 4.9 - - - +
207A LYS* 2.9 62.2 + - + +
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Residues in contact with ALA 204 (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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168A ILE* 3.6 36.1 - - + +
172A ILE* 4.6 1.0 - - - +
196A TRP* 3.8 27.8 - - + -
200A GLU 3.0 16.5 + - - +
201A ALA 3.2 4.0 + - - +
203A THR* 1.3 77.2 - - - +
205A ILE* 1.3 62.1 + - - +
207A LYS* 3.3 4.5 + - - +
208A MET* 3.1 29.6 + - + +
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Residues in contact with ILE 205 (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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196A TRP* 4.1 15.5 - - + -
201A ALA 2.8 22.1 + - - +
204A ALA* 1.3 72.3 - - - +
206A ARG* 1.3 62.1 + - - +
208A MET* 3.3 12.6 + - + +
209A GLU* 3.2 20.8 + - - +
215A ILE* 6.3 1.1 - - + -
218A VAL* 4.0 21.8 - - + -
221A PRO* 4.8 2.0 - - + -
233A VAL* 3.7 18.8 - - + -
237A THR* 3.6 21.8 - - + -
239A THR* 3.6 29.5 + - + +
241A ILE* 3.7 28.0 - - + -
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Residues in contact with ARG 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A VAL* 2.9 38.3 + - + +
203A THR* 3.9 4.9 - - - +
205A ILE* 1.3 73.8 - - - +
207A LYS* 1.3 60.8 + - + +
209A GLU* 3.2 20.5 - - + +
210A ASP* 2.9 41.3 + - - +
236A ALA* 3.0 42.4 + - - +
237A THR* 4.6 2.9 - - + -
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Residues in contact with LYS 207 (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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168A ILE* 4.8 12.4 - - + +
172A ILE* 3.7 23.4 - - + +
203A THR* 2.9 43.5 + - + +
204A ALA 3.7 4.7 - - - +
206A ARG* 1.3 76.7 - - + +
208A MET* 1.3 62.5 + - - +
210A ASP* 3.5 9.3 + - - +
211A ALA* 3.2 22.7 + - - +
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Residues in contact with MET 208 (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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163A VAL* 5.3 0.4 - - + -
168A ILE* 5.1 0.9 - - + -
171A ASP* 4.8 8.5 - - + -
172A ILE* 3.9 17.3 - - + -
175A ILE* 3.9 12.3 - - + -
190A LEU* 3.4 30.5 - - + -
196A TRP* 3.7 33.4 - - + -
204A ALA* 3.1 23.1 + - + +
205A ILE* 3.5 15.5 - - + +
206A ARG 3.1 0.2 - - - -
207A LYS* 1.3 79.9 - - - +
209A GLU* 1.3 61.7 + - - +
211A ALA 3.1 6.4 + - - -
213A LEU* 3.1 49.4 + - + +
214A GLY 5.4 0.2 - - - -
215A ILE* 4.0 15.7 - - + -
218A VAL* 5.7 0.9 - - + -
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Residues in contact with GLU 209 (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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205A ILE 3.2 12.1 + - - +
206A ARG* 3.2 29.3 - - + +
208A MET* 1.3 74.9 - - - +
210A ASP* 1.3 65.5 + - - +
211A ALA 3.1 2.0 - - - -
212A GLY* 3.0 17.9 + - - +
213A LEU 4.6 2.7 - - - +
214A GLY* 5.2 4.5 - - - +
215A ILE* 6.1 1.3 - - - +
237A THR* 4.2 7.3 - - - -
238A ASP* 3.4 42.1 + - - +
239A THR* 3.9 15.0 + - - +
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Residues in contact with ASP 210 (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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206A ARG* 2.9 28.5 + - - +
207A LYS* 3.8 8.8 - - - +
208A MET 3.2 0.2 - - - -
209A GLU* 1.3 83.0 - - - +
211A ALA* 1.3 56.8 + - - +
212A GLY 3.2 1.6 + - - -
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Residues in contact with ALA 211 (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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172A ILE* 5.1 4.5 - - + -
176A GLN* 4.6 12.6 - - + +
207A LYS 3.2 16.1 + - - +
208A MET 3.1 7.3 + - - +
209A GLU 3.1 0.4 - - - -
210A ASP* 1.3 77.0 - - - +
212A GLY* 1.3 63.2 + - - +
213A LEU* 3.2 20.7 + - + +
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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