Contacts of the helix formed by residues 201 - 215 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ARG* 4.8 16.2 - - - +
65B THR* 6.6 0.2 - - - -
189B MET* 5.9 0.6 - - - +
199B PHE 3.6 1.7 + - - +
200B THR* 1.3 91.6 + - - +
202B THR* 1.3 72.9 - - - +
203B ALA* 3.2 10.5 - - + +
204B GLU* 3.1 20.4 + - - +
205B ARG* 2.8 30.4 + - - +
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Residues in contact with THR 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU 5.8 0.2 - - - -
65B THR* 4.1 12.0 + - - -
66B LEU* 3.5 51.6 + - + +
68B TYR* 5.8 5.4 - - + -
201B THR* 1.3 77.8 - - - +
203B ALA* 1.3 66.6 + - - +
205B ARG* 3.1 37.6 + - + +
206B GLU* 3.2 10.8 + - + +
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Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ARG* 3.4 55.6 - - + +
62B GLY* 4.7 8.3 - - - +
64B LEU 5.2 3.4 + - - +
66B LEU* 4.6 3.5 - - - +
201B THR* 4.0 7.7 - - + +
202B THR* 1.3 82.9 - - - +
204B GLU* 1.3 64.7 + - - +
206B GLU* 3.1 14.0 + - - +
207B ILE* 3.5 3.6 + - - +
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Residues in contact with GLU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B SER 4.6 1.7 - - - +
199B PHE* 3.4 37.6 - - + +
200B THR* 2.9 24.8 + - - -
201B THR* 3.1 35.5 + - - +
203B ALA* 1.3 74.6 - - - +
205B ARG* 1.3 63.1 + - - +
206B GLU 3.1 1.3 - - - -
207B ILE* 2.9 32.2 + - + +
208B VAL* 2.9 17.2 + - - +
241B LEU* 6.1 1.8 - - + -
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Residues in contact with ARG 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B TYR* 3.8 19.2 - - - -
182B ARG* 3.3 55.2 + - - +
185B THR* 3.9 14.8 - - + +
186B ASP* 3.3 33.7 + - - -
189B MET* 3.8 24.4 - - - -
199B PHE* 5.5 1.1 - - - -
201B THR 2.8 13.4 + - - +
202B THR* 3.1 30.2 + - + +
204B GLU* 1.3 78.3 - - - +
206B GLU* 1.3 58.2 + - + +
208B VAL* 2.9 27.3 - - - +
209B ARG* 2.9 11.1 + - - +
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PRO* 4.9 1.2 - - - +
33B ILE* 3.9 7.2 - - - +
58B GLN* 2.4 39.7 + - - +
61B ARG* 4.4 8.8 + - - +
66B LEU* 3.5 22.7 - - + +
68B TYR* 2.7 36.1 + - + +
202B THR* 3.2 10.1 + - + +
203B ALA 3.1 10.7 + - - +
204B GLU 3.1 0.4 - - - -
205B ARG* 1.3 78.6 - - + +
207B ILE* 1.3 65.1 + - - +
209B ARG* 3.2 25.4 + - - +
210B ASP* 3.0 21.1 + - - +
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Residues in contact with ILE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ARG* 3.1 28.5 - - - +
199B PHE* 5.2 4.5 - - + -
203B ALA 3.5 1.5 + - - +
204B GLU* 2.9 30.0 + - + +
206B GLU* 1.3 73.5 - - - +
208B VAL* 1.3 62.7 + - - +
210B ASP* 3.0 19.4 + - + +
211B ILE* 3.0 16.0 + - + +
239B TYR* 4.4 19.1 - - + +
241B LEU* 4.2 27.6 - - + -
242B PRO* 3.7 30.7 - - + -
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B THR* 3.7 20.4 - - + +
188B LEU* 3.9 10.9 - - + +
189B MET* 4.3 17.9 - - + -
192B LEU* 4.0 16.6 - - + -
199B PHE* 3.3 39.3 - - + -
204B GLU 2.9 7.7 + - - +
205B ARG* 2.9 31.0 - - - +
207B ILE* 1.3 72.5 - - - +
209B ARG* 1.3 65.9 + - - +
211B ILE* 3.2 12.9 + - + +
212B LYS* 2.9 24.5 + - - +
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Residues in contact with ARG 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLY 6.1 0.4 - - - -
15B MET* 5.8 7.1 - - - +
31B PRO* 4.9 8.8 - - - +
58B GLN* 3.9 21.4 + - - +
68B TYR* 3.6 22.1 + - - -
156B ASP* 5.0 2.5 - - - -
185B THR* 4.1 21.8 - - + +
205B ARG 2.9 13.9 + - - +
206B GLU* 3.3 31.5 + - + +
208B VAL* 1.3 77.5 - - - +
210B ASP* 1.3 57.6 + - - +
212B LYS* 3.3 4.9 + - - +
213B GLU* 2.5 71.5 + - - +
401B ADP 3.7 27.6 + - - +
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Residues in contact with ASP 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B GLU 3.0 12.4 + - - +
207B ILE* 3.0 15.1 + - + +
209B ARG* 1.3 76.9 - - - +
211B ILE* 1.3 64.3 + - - +
213B GLU* 3.1 27.7 + - - +
214B LYS* 3.3 29.0 + - - +
239B TYR* 3.1 18.3 + - - +
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Residues in contact with ILE 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B LEU* 4.4 10.8 - - + -
192B LEU* 4.9 8.3 - - + -
199B PHE* 4.8 8.1 - - + -
207B ILE* 3.0 19.0 + - + +
208B VAL* 3.2 25.3 + - + +
210B ASP* 1.3 74.7 - - - +
212B LYS* 1.3 64.1 + - - +
214B LYS* 3.0 2.7 + - - -
215B LEU* 2.8 50.7 + - + +
216B CYS* 5.0 2.0 - - - -
239B TYR* 3.5 47.5 + - + -
241B LEU* 4.9 2.2 - - + -
247B ILE* 5.3 7.2 - - + -
249B ILE* 4.1 12.8 - - + -
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Residues in contact with LYS 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B GLY* 2.5 24.2 + - - -
184B LEU* 4.0 13.7 - - + -
185B THR* 2.5 35.0 + - - +
188B LEU* 3.8 7.9 - - + -
208B VAL 2.9 13.8 + - - +
209B ARG* 3.6 10.7 - - - +
211B ILE* 1.3 77.4 - - - +
213B GLU* 1.3 61.4 + - - +
214B LYS* 3.0 2.3 + - - -
216B CYS* 3.5 44.0 + - - +
256B CYS* 4.3 5.2 - - - -
305B TYR* 3.2 32.1 - - + +
401B ADP 2.6 32.5 + - - -
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Residues in contact with GLU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B MET* 5.9 1.4 - - - +
209B ARG* 2.5 55.8 + - - +
210B ASP* 3.1 23.1 + - - +
212B LYS* 1.3 75.4 - - - +
214B LYS* 1.3 56.4 + - - +
335B LYS* 5.3 1.9 + - - -
401B ADP 2.9 77.5 + - + +
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Residues in contact with LYS 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B ASP* 3.3 37.5 + - - +
211B ILE 3.0 4.8 + - - +
212B LYS 3.0 0.8 + - - -
213B GLU* 1.3 79.6 - - - +
215B LEU* 1.3 83.0 + - + +
216B CYS 3.3 10.5 + - - +
237B LYS* 5.8 0.9 + - - -
239B TYR* 3.4 32.3 - - - -
306B PRO* 5.2 5.9 - - - +
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Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B ILE* 2.8 23.8 + - + +
214B LYS* 1.3 92.1 - - + +
216B CYS* 1.3 54.2 + - - +
217B TYR* 4.0 1.9 - - - +
237B LYS* 3.8 36.4 + - + +
238B SER 4.7 3.1 - - - +
239B TYR* 3.7 35.9 - - + -
249B ILE* 3.5 37.5 - - + -
253B ARG* 2.7 36.6 + - + +
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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