Contacts of the helix formed by residues 187 - 205 (chain C) in PDB entry 4EE5
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 187 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C PHE* 3.4 20.9 - - + -
185C ARG 3.4 0.8 - - - +
186C ASN* 1.3 81.3 - - - +
188C GLN* 1.3 65.6 + - - +
189C GLU 3.1 4.2 + - - -
190C HIS* 2.9 41.7 + - + +
191C LEU 3.0 18.2 + - - -
249C VAL* 3.7 21.2 - - + +
250C ASP* 3.2 16.0 + - - -
343C HIS* 3.2 13.3 + - - +
346C ASP* 2.8 38.7 + - - -
404C UDP 3.0 55.2 + - + +
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Residues in contact with GLN 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C LEU* 4.6 8.9 - - - +
184C PHE* 3.7 19.4 - - + -
186C ASN* 3.7 5.1 + - - +
187C ARG* 1.3 78.1 - - - +
189C GLU* 1.3 63.5 + - - +
191C LEU* 3.3 14.4 + - - +
192C LYS* 3.1 41.7 + - + +
387C TYR* 3.6 20.6 + - - -
389C GLN* 4.7 3.1 - - - +
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Residues in contact with GLU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C ARG 3.1 1.0 - - - -
188C GLN* 1.3 78.8 - - - +
190C HIS* 1.3 77.0 + - + +
192C LYS* 3.2 29.3 + - - +
193C TYR* 3.5 35.3 + - + -
341C ILE* 5.8 1.0 - - - +
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Residues in contact with HIS 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C ARG* 2.9 50.3 + - - +
189C GLU* 1.3 90.0 + - + +
191C LEU* 1.3 57.7 + - - +
193C TYR* 3.0 8.9 + + - +
194C TRP* 2.9 24.8 + - - +
249C VAL* 3.9 21.6 - - + +
250C ASP* 3.5 7.3 - - + +
341C ILE* 3.7 36.2 - - + +
342C ARG 4.3 1.0 + - - -
343C HIS* 3.6 35.4 - + + +
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Residues in contact with LEU 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C ILE* 4.1 12.6 - - + -
184C PHE* 4.0 12.8 - - + -
187C ARG 3.0 11.8 + - - +
188C GLN* 3.6 21.8 - - - +
190C HIS* 1.3 76.2 - - - +
192C LYS* 1.3 62.8 + - - +
194C TRP* 3.7 4.0 - - + +
195C LEU* 3.0 40.9 + - + +
213C VAL* 3.6 25.6 - - + -
249C VAL* 3.6 21.4 - - + +
387C TYR* 3.5 42.2 - - + +
389C GLN* 5.1 0.2 - - - +
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Residues in contact with LYS 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C PRO* 5.9 1.0 - - - +
149C VAL* 3.0 49.9 + - + +
151C LEU* 4.1 32.9 - - + +
188C GLN* 3.1 30.0 + - + +
189C GLU* 3.5 21.7 - - - +
190C HIS 3.1 1.4 + - - -
191C LEU* 1.3 77.1 - - - +
193C TYR* 1.3 61.7 + - + +
195C LEU* 4.1 2.4 - - - +
196C TYR* 3.2 22.3 + - - +
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Residues in contact with TYR 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C GLU 4.4 3.8 - - - -
145C PHE* 2.8 56.1 + + + -
146C ASN 4.2 0.5 - - - -
147C MET* 2.5 41.5 + - + -
148C PRO* 4.7 1.2 - - + +
149C VAL* 3.6 20.9 - - + -
189C GLU* 3.5 41.7 + - + -
190C HIS* 3.0 6.5 + + - +
192C LYS* 1.3 75.2 - - + +
194C TRP* 1.3 65.6 + - - +
195C LEU 3.1 0.4 - - - -
196C TYR* 3.2 3.3 + - - +
197C TYR* 3.1 32.8 + + + +
252C ILE* 4.2 2.0 - - + -
341C ILE* 4.1 28.0 - - + -
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Residues in contact with TRP 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ILE* 3.6 33.0 - - + -
182C ILE* 3.7 20.6 - - + +
190C HIS 2.9 7.9 + - - +
191C LEU* 3.2 11.6 + - + +
193C TYR* 1.3 76.2 - - - +
195C LEU* 1.3 73.1 + - + +
198C LEU* 2.7 70.0 + - + +
199C HIS* 5.5 1.6 - - - -
202C LEU* 4.5 2.7 - - + -
211C ILE* 3.8 34.5 - - + -
247C SER* 3.2 23.1 + - - -
248C ASP 3.8 6.7 + - - -
249C VAL* 3.6 28.3 - - + +
251C LEU 3.6 18.8 + - - -
252C ILE* 3.6 9.8 - - + +
260C TYR* 4.8 5.3 - + - -
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Residues in contact with LEU 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C LEU* 4.1 24.7 - - + -
154C VAL* 4.2 4.0 - - - +
191C LEU* 3.0 36.7 + - + +
192C LYS 4.1 2.9 - - - +
194C TRP* 1.3 93.1 - - + +
196C TYR* 1.3 66.0 + - - +
198C LEU 4.5 0.2 - - - +
199C HIS* 3.3 42.8 + - + +
211C ILE* 4.3 3.1 - - + -
386C LEU* 3.4 30.5 - - + +
387C TYR* 3.6 34.8 - - + -
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Residues in contact with TYR 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C MET* 3.5 29.4 - - + +
149C VAL* 4.3 10.1 - - + -
154C VAL* 3.8 33.6 - - + +
157C GLN* 3.8 20.4 + - - -
158C ASN* 5.1 0.6 + - - -
192C LYS 3.2 16.1 + - - +
193C TYR* 3.2 6.4 + - - +
195C LEU* 1.3 79.5 - - - +
197C TYR* 1.3 91.5 - + - +
200C PRO* 3.2 24.0 - - + +
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Residues in contact with TYR 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C MET* 6.4 1.1 - - - -
142C LEU 4.0 15.3 - - - -
143C ILE* 3.9 13.7 - - + -
144C GLU* 2.8 54.9 + - - +
145C PHE* 4.0 17.5 - + - -
147C MET* 3.8 5.5 - - - +
193C TYR* 3.1 29.1 + + - +
194C TRP 4.1 0.9 - - - +
196C TYR* 1.3 106.6 - + - +
198C LEU* 1.3 64.7 + - - +
199C HIS 3.4 0.2 - - - -
200C PRO* 3.2 11.1 - - - +
201C VAL* 3.4 18.7 - - + +
252C ILE* 3.7 31.6 - - + -
253C PRO* 6.0 0.2 - - - -
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Residues in contact with LEU 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C TRP* 2.7 79.5 + - + +
197C TYR* 1.3 72.5 - - - +
199C HIS* 1.3 66.8 + - - +
201C VAL* 3.0 12.9 + - + +
202C LEU* 2.8 35.9 + - + +
251C LEU 4.2 1.6 - - - +
252C ILE* 4.0 10.1 - - + -
253C PRO* 3.7 40.8 - - + -
260C TYR* 3.8 20.6 - - + +
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Residues in contact with HIS 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C VAL* 5.3 0.4 - - + -
158C ASN* 4.0 14.4 - - - +
161C VAL* 3.6 25.6 - - + +
165C GLY* 4.4 1.3 - - - -
194C TRP* 5.7 0.7 - + - -
195C LEU* 3.3 39.5 + - + +
198C LEU* 1.3 77.2 - - - +
200C PRO* 1.4 67.0 - - + +
202C LEU* 4.4 2.0 - - + -
203C GLN* 2.8 30.7 + - - +
209C TYR* 2.8 31.8 + + - -
211C ILE* 3.6 24.8 - - + +
386C LEU* 2.9 42.2 + - + +
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Residues in contact with PRO 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C ASN* 4.0 15.3 - - - +
196C TYR* 3.2 26.2 - - + +
197C TYR* 3.2 10.8 - - - +
199C HIS* 1.4 92.5 - - + +
201C VAL* 1.3 60.8 + - + +
203C GLN* 3.6 9.6 + - + +
204C ARG* 3.1 46.1 + - - +
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Residues in contact with VAL 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C MET* 3.8 35.2 - - + -
197C TYR* 3.4 16.8 - - + +
198C LEU* 3.0 21.3 + - + +
200C PRO* 1.3 75.5 - - + +
202C LEU* 1.3 62.3 + - + +
204C ARG* 2.9 28.0 + - - +
205C GLN* 2.9 37.0 + - - +
253C PRO* 5.0 9.2 - - + +
256C ASP* 3.8 13.5 - - + -
260C TYR* 5.8 1.6 - - + -
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Residues in contact with LEU 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ILE* 3.8 21.1 - - + -
194C TRP* 4.5 1.8 - - + -
198C LEU* 2.8 43.3 + - + +
199C HIS* 4.4 0.9 - - - +
201C VAL* 1.3 73.5 - - + +
203C GLN* 1.3 62.6 + - - +
205C GLN* 3.3 14.7 + - - +
206C GLN 3.5 6.6 + - - -
207C LEU* 3.6 25.1 + - + +
209C TYR* 3.5 38.7 - - + -
211C ILE* 3.9 10.1 - - + -
260C TYR* 3.7 37.7 - - + -
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Residues in contact with GLN 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C LEU* 4.6 3.9 - - - +
158C ASN* 2.8 30.6 + - - +
159C PRO* 6.0 0.2 - - - +
160C ASN* 3.9 19.4 + - - +
161C VAL* 3.8 18.7 + - - +
167C TYR* 3.8 46.3 + - + +
199C HIS 2.8 24.5 + - - +
200C PRO* 3.8 6.7 - - + +
202C LEU* 1.3 75.3 - - - +
204C ARG* 1.3 59.8 + - + +
206C GLN* 2.9 22.9 + - - +
209C TYR* 3.6 10.1 - - - +
408C SO4 5.2 0.7 + - - -
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Residues in contact with ARG 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LEU* 3.8 33.6 - - - +
134C SER* 2.6 30.0 + - - -
136C LEU* 3.5 37.2 + - + +
137C LEU* 3.8 12.3 - - + +
138C VAL* 4.0 9.3 - - - +
141C MET* 3.2 29.5 - - - +
200C PRO* 3.1 36.4 + - - +
201C VAL* 2.9 18.3 + - - +
203C GLN* 1.3 78.5 - - + +
205C GLN* 1.3 52.8 + - - +
206C GLN* 3.1 3.5 + - - +
256C ASP* 3.0 25.8 + - - +
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Residues in contact with GLN 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C SER* 4.3 7.8 + - - -
137C LEU* 4.0 11.9 - - + -
176C HIS* 5.4 2.4 - - - -
201C VAL* 2.9 30.3 + - + +
202C LEU* 3.5 10.8 - - - +
203C GLN 3.0 0.4 - - - -
204C ARG* 1.3 75.5 - - - +
206C GLN* 1.3 69.6 + - - +
207C LEU* 3.3 30.5 + - + +
256C ASP 3.0 25.4 + - - +
257C HIS 4.7 0.2 - - - -
258C ASN 2.9 25.7 + - - -
259C ALA* 3.8 5.9 - - - +
260C TYR* 3.0 25.2 + - - +
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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