Contacts of the helix formed by residues 209 - 228 (chain J) in PDB entry 5U0A
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 VAL 209 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198J ASP* 3.7 26.5 - - + +
201J ARG* 3.5 36.1 - - + +
202J TRP* 3.1 35.4 - - + -
205J THR* 3.6 11.7 - - - +
208J HIS* 1.3 77.1 - - - +
210J ALA* 1.3 63.2 + - - +
211J ARG 3.2 1.8 - - - -
212J GLU* 2.8 28.5 + - - +
213J TRP* 3.0 20.1 + - + +
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Residues in contact with ALA 210 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165J ALA* 3.9 26.7 - - + +
202J TRP* 3.2 30.9 - - + -
207J ARG* 3.4 9.1 + - - +
209J VAL* 1.3 82.0 - - - +
211J ARG* 1.3 64.4 + - - +
213J TRP* 3.0 16.7 + - + +
214J VAL* 2.9 26.3 + - - +
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Residues in contact with ARG 211 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513C ASP* 4.8 9.9 + - - +
516C THR* 5.2 3.2 - - - +
517C GLY* 5.6 4.0 - - - -
520C CYS* 2.9 52.2 + - - +
529C VAL* 5.0 4.0 - - - +
530C GLU* 3.0 17.6 + - - -
533C ARG* 5.0 0.2 - - - +
162J HIS* 5.9 0.2 - - - -
207J ARG* 2.9 64.2 + - + +
208J HIS* 4.5 5.4 - - - +
210J ALA* 1.3 75.5 - - - +
212J GLU* 1.3 58.5 + - + +
214J VAL* 4.0 11.8 - - - +
215J GLN* 2.9 57.0 + - - +
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Residues in contact with GLU 212 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138J ASN* 4.4 8.6 + - - +
198J ASP* 4.8 0.5 - - - +
201J ARG* 3.7 24.5 + - - -
208J HIS* 3.2 31.4 + - + +
209J VAL* 2.8 12.5 + - - +
211J ARG* 1.3 76.2 - - + +
213J TRP* 1.3 57.8 - - + +
215J GLN* 4.0 10.3 - - - +
216J ASP* 3.0 44.6 + - - +
33O T 4.0 25.8 + - - +
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Residues in contact with TRP 213 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138J ASN* 3.9 24.0 - - + +
139J LEU* 3.8 31.4 - - + +
140J GLY* 3.7 13.5 - - - +
161J LEU* 4.2 22.3 - - + +
164J ILE* 4.1 24.9 - - + -
165J ALA* 6.3 1.3 - - - -
172J VAL* 5.4 3.1 - - + -
176J LEU* 4.4 11.0 - - + -
179J LEU* 6.1 0.2 - - + -
195J LEU* 3.7 30.7 - - + -
198J ASP* 3.3 32.9 + - + +
199J LEU* 4.9 9.4 - - + -
209J VAL* 3.0 20.5 + - + +
210J ALA* 3.0 17.2 + - + +
212J GLU* 1.3 76.2 - - + +
214J VAL* 1.3 62.8 + - + +
216J ASP* 4.2 0.5 - - - -
217J TYR* 3.2 22.7 + - - +
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Residues in contact with VAL 214 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526C ALA* 5.2 0.4 - - + -
530C GLU* 4.8 4.7 - - + +
161J LEU* 4.1 22.7 - - + -
162J HIS* 3.4 32.1 - - + +
165J ALA* 4.0 23.8 - - + -
207J ARG* 4.2 7.6 - - - +
210J ALA 2.9 18.4 + - - +
211J ARG* 4.0 17.9 - - - +
213J TRP* 1.3 73.9 - - + +
215J GLN* 1.3 67.6 + - - +
217J TYR* 3.1 2.6 + - - +
218J HIS* 3.0 39.3 + - + +
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Residues in contact with GLN 215 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513C ASP* 3.9 9.1 + - - -
530C GLU* 3.1 32.8 - - - +
533C ARG* 3.1 43.6 + - - +
537C PHE* 5.7 1.8 - - + -
211J ARG* 2.9 50.2 + - - +
212J GLU* 4.0 9.2 - - - +
214J VAL* 1.3 75.3 - - - +
216J ASP* 1.3 65.9 + - - +
218J HIS* 3.4 1.6 + - - +
219J ARG* 2.9 27.1 + - - +
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Residues in contact with ASP 216 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138J ASN* 2.8 26.4 + - - +
141J VAL* 4.0 21.7 - - + +
212J GLU* 3.0 23.7 + - - +
213J TRP* 4.3 2.2 - - - +
215J GLN* 1.3 78.2 - - - +
217J TYR* 1.3 58.8 + - - +
219J ARG* 2.6 38.5 + - - +
220J THR* 2.8 36.2 + - - +
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Residues in contact with TYR 217 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140J GLY* 3.2 30.2 - - - +
143J LEU* 3.4 21.5 - - + -
144J ALA* 3.3 30.7 - - + +
147J VAL* 3.4 21.8 - - + +
154J ALA* 4.7 1.6 + - - +
157J THR* 3.6 13.7 - - + +
158J GLU* 4.2 27.3 - - + +
161J LEU* 3.9 19.5 - - + -
213J TRP 3.2 18.7 + - - +
214J VAL 3.1 4.3 + - - +
216J ASP* 1.3 75.1 - - - +
218J HIS* 1.3 83.1 + + - +
221J LEU* 2.9 42.4 + - + +
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Residues in contact with HIS 218 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527C LYS* 4.0 31.8 + - + +
530C GLU* 3.7 32.3 - - + -
158J GLU* 3.3 25.7 + - + -
162J HIS* 2.8 36.7 + - - -
214J VAL* 3.0 37.8 + - + +
215J GLN 4.0 0.7 - - - +
217J TYR* 1.3 90.5 - + - +
219J ARG* 1.3 64.5 + - - +
221J LEU* 3.2 6.8 + - - +
222J GLU* 2.9 24.3 + - - +
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Residues in contact with ARG 219 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530C GLU* 5.6 0.8 - - + +
534C SER* 4.9 8.3 - - - -
537C PHE* 3.0 49.8 - - + -
215J GLN* 2.9 18.0 + - - +
216J ASP* 2.6 34.4 + - - +
218J HIS* 1.3 78.0 - - - +
220J THR* 1.3 61.2 + - - +
222J GLU* 2.9 42.2 - - - +
223J THR* 2.9 19.6 + - + +
31O C 5.0 17.9 + - - -
32O A 4.9 6.9 + - - -
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Residues in contact with THR 220 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141J VAL* 3.9 32.6 - - + +
144J ALA* 3.9 16.4 - - + -
145J GLN* 5.2 2.7 - - - +
216J ASP* 2.8 28.2 + - - +
217J TYR* 3.9 2.2 - - - -
219J ARG* 1.3 79.2 + - - +
221J LEU* 1.3 58.0 + - - +
223J THR* 2.9 10.2 + - - +
224J LEU* 2.9 43.9 + - + +
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Residues in contact with LEU 221 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527C LYS* 5.4 13.7 - - - +
144J ALA* 3.9 20.8 - - + +
147J VAL* 4.3 23.8 - - + -
148J PHE* 4.5 13.5 - - + -
154J ALA* 6.0 3.1 - - + -
158J GLU* 6.1 0.7 - - - +
217J TYR* 2.9 38.4 + - + +
218J HIS* 3.6 6.7 - - - +
220J THR* 1.3 77.2 - - - +
222J GLU* 1.3 63.6 + - - +
224J LEU* 3.3 2.3 + - - +
225J THR* 3.0 39.3 + - + +
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Residues in contact with GLU 222 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531C ARG* 6.1 9.0 - - + +
534C SER* 4.9 12.3 + - - +
218J HIS 2.9 16.6 + - - +
219J ARG* 2.9 30.0 - - + +
221J LEU* 1.3 77.5 - - - +
223J THR* 1.3 84.5 + - - +
225J THR* 2.5 22.7 + - - +
226J ARG* 2.9 52.7 + - - +
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Residues in contact with THR 223 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219J ARG* 2.9 15.7 + - + +
220J THR* 2.9 17.3 + - - +
222J GLU* 1.3 100.4 - - - +
224J LEU* 1.3 63.7 + - - +
226J ARG* 3.7 4.8 - - - +
227J GLN* 2.9 44.5 + - - +
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Residues in contact with LEU 224 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144J ALA* 4.1 10.5 - - + +
145J GLN* 3.6 33.4 - - - +
148J PHE* 3.8 48.7 - - + -
220J THR* 2.9 41.5 + - + +
221J LEU* 3.8 4.5 - - - +
223J THR* 1.3 81.2 + - - +
225J THR* 1.3 62.3 + - - +
227J GLN* 3.7 9.0 + - + +
228J ALA 3.6 13.2 + - - -
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Residues in contact with THR 225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148J PHE* 4.7 15.5 - - + -
221J LEU* 3.0 30.2 + - + +
222J GLU* 2.5 26.2 + - - -
224J LEU* 1.3 78.5 - - - +
226J ARG* 1.3 63.0 + - - +
228J ALA* 3.3 19.6 + - - +
229J GLU* 4.2 2.3 + - - +
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Residues in contact with ARG 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531C ARG* 4.9 18.4 - - - +
222J GLU* 2.9 44.6 + - - +
223J THR* 4.0 5.2 - - - +
225J THR* 1.3 79.0 - - - +
227J GLN* 1.3 64.1 + - - +
229J GLU* 2.7 36.8 - - + +
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Residues in contact with GLN 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223J THR* 2.9 29.2 + - - +
224J LEU* 4.1 11.0 - - + +
225J THR 3.2 0.4 - - - -
226J ARG* 1.3 78.5 - - - +
228J ALA* 1.3 57.8 + - - +
229J GLU* 3.0 18.4 + - - +
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Residues in contact with ALA 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148J PHE* 4.2 19.3 - - + -
224J LEU 3.6 10.6 + - - +
225J THR* 3.3 12.1 + - - +
226J ARG 3.3 0.8 - - - -
227J GLN* 1.3 77.6 - - - +
229J GLU* 1.3 58.4 + - - +
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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
------------------------------------------------------------
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