Contacts of the helix formed by residues 201 - 215 (chain A) in PDB entry 5JLH
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 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ARG* 4.8 0.9 - - - +
189A MET* 5.3 0.4 - - - +
199A PHE 3.5 0.9 - - - +
200A THR* 1.3 91.7 + - - +
202A THR* 1.3 72.0 + - - +
203A ALA* 3.2 9.0 - - + +
204A GLU* 3.0 21.1 + - - +
205A ARG* 2.8 30.9 + - - +
285B ASP* 4.7 10.3 - - - +
268D MET* 6.0 0.9 - - - +
269D GLU* 3.3 43.3 + - + +
270D SER* 4.6 5.4 + - - -
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Residues in contact with THR 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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65A THR* 4.1 3.0 + - - -
66A LEU* 3.5 49.8 + - + +
68A TYR* 5.8 5.4 - - + -
201A THR* 1.3 75.5 - - - +
203A ALA* 1.3 67.6 + - - +
205A ARG* 3.1 38.8 + - + +
206A GLU* 3.2 10.5 + - + +
269D GLU* 3.1 18.2 + - - -
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Residues in contact with ALA 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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61A ARG* 3.4 56.7 - - + +
62A GLY* 4.7 6.3 - - - +
64A LEU 5.2 3.0 + - - +
66A LEU* 4.6 3.9 - - - +
201A THR* 4.0 7.6 - - + +
202A THR* 1.3 83.3 - - - +
204A GLU* 1.3 63.9 + - - +
206A GLU* 3.1 13.5 + - - +
207A ILE* 3.5 4.2 + - - +
285B ASP* 4.8 8.1 - - + +
286B VAL* 5.5 2.9 - - + -
287B ASP* 4.9 7.0 - - + -
269D GLU* 5.2 1.0 + - - +
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Residues in contact with GLU 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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198A SER 4.6 1.9 - - - +
199A PHE* 3.4 36.9 - - + +
200A THR* 2.9 26.0 + - - -
201A THR* 3.0 33.3 + - - +
203A ALA* 1.3 74.4 - - - +
205A ARG* 1.3 62.0 + - - +
206A GLU 3.1 1.8 - - - -
207A ILE* 2.8 30.0 + - + +
208A VAL* 2.9 16.0 + - - +
241A LEU* 6.1 0.2 - - + -
285B ASP* 6.0 1.6 - - - +
286B VAL* 3.9 30.5 + - + +
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Residues in contact with ARG 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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68A TYR* 3.8 19.4 - - - -
182A ARG* 3.3 55.9 + - - +
185A THR* 3.9 15.3 - - + +
186A ASP* 3.3 32.1 + - - -
189A MET* 3.8 24.7 - - - -
199A PHE* 5.5 1.1 - - - -
201A THR 2.8 14.7 + - - +
202A THR* 3.1 29.3 - - + +
204A GLU* 1.3 77.1 - - - +
206A GLU* 1.3 57.2 + - + +
208A VAL* 2.9 26.9 - - - +
209A ARG* 2.9 11.4 + - - +
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Residues in contact with GLU 206 (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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31A PRO* 4.9 1.2 - - - +
33A ILE* 3.9 7.1 - - - +
58A GLN* 2.3 42.3 + - - +
61A ARG* 4.4 9.6 + - - +
66A LEU* 3.6 22.9 - - + +
68A TYR* 2.7 36.1 + - + +
202A THR* 3.2 10.7 + - + +
203A ALA 3.1 10.6 + - - +
204A GLU 3.1 0.4 - - - -
205A ARG* 1.3 78.9 - - + +
207A ILE* 1.3 64.9 + - - +
209A ARG* 3.2 21.9 + - - +
210A ASP* 3.0 21.5 + - - +
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Residues in contact with ILE 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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61A ARG* 3.1 29.2 - - - +
199A PHE* 5.1 4.9 - - + -
203A ALA 4.1 1.3 - - - +
204A GLU* 2.8 29.8 + - + +
206A GLU* 1.3 75.1 - - - +
208A VAL* 1.3 63.4 + - - +
210A ASP* 3.0 10.7 + - + +
211A ILE* 3.0 23.4 + - + +
239A TYR* 4.3 18.4 - - + +
241A LEU* 4.1 27.6 - - + -
242A PRO* 3.7 28.9 - - + -
286B VAL* 5.0 4.9 - - + -
287B ASP* 5.3 1.3 - - + +
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Residues in contact with VAL 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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185A THR* 3.7 20.6 - - + +
188A LEU* 3.9 13.9 - - + +
189A MET* 4.3 20.4 - - + -
192A LEU* 4.1 12.6 - - + -
199A PHE* 3.3 38.8 - - + -
204A GLU 2.9 7.9 + - - +
205A ARG* 2.9 31.4 - - + +
207A ILE* 1.3 73.0 - - - +
209A ARG* 1.3 65.8 + - - +
211A ILE* 3.1 12.0 + - + +
212A LYS* 2.9 24.1 + - - +
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Residues in contact with ARG 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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15A MET* 5.8 7.3 - - - +
31A PRO* 4.9 9.0 - - - +
58A GLN* 3.9 20.4 + - - +
68A TYR* 3.6 22.3 + - - -
156A ASP* 4.9 3.1 - - - -
185A THR* 4.2 21.3 - - + +
205A ARG 2.9 12.5 + - - +
206A GLU* 3.3 32.1 + - - +
208A VAL* 1.3 77.6 - - - +
210A ASP* 1.3 57.6 + - - +
212A LYS* 3.3 5.0 + - - +
213A GLU* 2.5 73.0 + - - +
401A ADP 3.7 28.0 + - - +
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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 GLU 3.0 12.4 + - - +
207A ILE* 3.0 15.1 + - + +
209A ARG* 1.3 76.3 - - - +
211A ILE* 1.3 69.4 + - - +
213A GLU* 3.2 27.3 + - - +
214A LYS* 3.3 27.4 + - - +
239A TYR* 3.0 18.5 + - - +
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Residues in contact with ILE 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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188A LEU* 4.4 10.5 - - + -
192A LEU* 4.9 8.1 - - + -
199A PHE* 4.8 8.1 - - + -
207A ILE* 3.0 19.8 + - + +
208A VAL* 3.3 24.5 - - + +
210A ASP* 1.3 76.9 - - - +
212A LYS* 1.3 64.6 + - - +
214A LYS* 2.8 4.5 + - - +
215A LEU* 2.8 47.3 + - + -
216A CYS* 5.0 2.2 - - - -
239A TYR* 3.5 47.1 - - + -
241A LEU* 4.9 2.2 - - + -
247A ILE* 5.3 6.7 - - + -
249A ILE* 4.1 16.8 - - + -
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Residues in contact with LYS 212 (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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156A ASP* 5.1 0.2 + - - -
181A GLY* 2.5 24.2 + - - -
184A LEU* 4.0 14.6 - - + -
185A THR* 2.5 35.5 + - - +
188A LEU* 3.8 7.6 - - + -
208A VAL 2.9 13.3 + - - +
209A ARG* 3.6 10.0 - - - +
211A ILE* 1.3 76.6 - - - +
213A GLU* 1.3 60.8 + - - +
214A LYS* 3.0 2.8 + - - -
216A CYS* 3.5 44.2 + - - +
256A CYS* 4.4 4.5 - - - -
305A TYR* 3.2 33.4 - - + +
401A ADP 2.7 30.8 + - - -
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Residues in contact with GLU 213 (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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15A MET* 6.0 1.2 - - - +
209A ARG* 2.5 57.0 + - - +
210A ASP* 3.2 22.2 + - - +
212A LYS* 1.3 75.0 - - - +
214A LYS* 1.3 58.6 + - - +
335A LYS* 5.3 2.0 + - - -
401A ADP 2.9 78.4 + - + +
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Residues in contact with LYS 214 (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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210A ASP* 3.3 29.5 + - - +
211A ILE 2.8 10.8 + - - +
212A LYS 3.8 0.4 - - - -
213A GLU* 1.3 79.4 - - - +
215A LEU* 1.3 83.6 + - + +
216A CYS 3.3 10.9 + - - +
237A LYS* 5.8 0.9 + - - -
239A TYR* 3.4 35.7 + - - -
306A PRO* 5.2 5.7 - - - +
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Residues in contact with LEU 215 (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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211A ILE* 2.8 21.4 + - + +
214A LYS* 1.3 92.0 - - + +
216A CYS* 1.3 54.3 + - - +
217A TYR* 4.1 1.6 - - - +
237A LYS* 3.8 37.1 + - + +
238A SER 4.7 3.1 - - - +
239A TYR* 3.7 35.2 - - + -
249A ILE* 3.5 37.5 - - + -
253A ARG* 2.7 34.8 + - + +
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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