Contacts of the helix formed by residues 187 - 205 (chain B) in PDB entry 4EEM
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B PHE* 3.2 27.4 - - + -
185B ARG 3.3 4.7 - - - +
186B ASN* 1.3 83.7 - - - +
188B GLN* 1.3 65.1 + - - +
189B GLU 3.2 3.1 - - - -
190B HIS* 3.0 36.0 + - + -
191B LEU 3.0 17.0 + - - -
249B VAL* 3.7 12.3 - - + +
250B ASP* 2.8 24.4 + - - -
343B HIS* 3.3 13.1 + - - +
346B ASP* 2.7 41.8 + - - -
403B UDP 2.8 56.2 + - - +
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Residues in contact with GLN 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 4.3 8.5 - - - +
184B PHE* 3.5 19.8 - - + -
186B ASN* 3.7 2.7 - - - -
187B ARG* 1.3 75.9 - - - +
189B GLU* 1.3 63.1 + - - +
191B LEU* 3.1 14.0 + - - +
192B LYS* 3.0 48.1 + - + +
387B TYR* 3.6 21.5 + - - -
389B GLN* 4.7 2.8 - - - +
410B SO4 4.8 4.8 + - - -
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PHE 5.5 0.2 - - - +
187B ARG 3.2 0.6 - - - -
188B GLN* 1.3 79.6 - - - +
190B HIS* 1.3 72.4 + - + +
192B LYS* 3.3 24.8 + - - +
193B TYR* 3.4 38.7 + - + -
407B SO4 4.7 10.6 + - - -
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Residues in contact with HIS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ARG* 3.0 50.2 + - - +
189B GLU* 1.3 88.1 + - + +
191B LEU* 1.3 65.8 + - - +
193B TYR* 3.0 7.6 + + - +
194B TRP* 2.9 21.3 + - - +
249B VAL* 3.9 22.4 - - + +
250B ASP* 3.8 3.6 - - + +
341B ILE* 3.7 38.2 - - + +
342B ARG 4.5 1.0 + - - -
343B HIS* 3.6 35.3 - + + +
407B SO4 4.7 7.9 + - - -
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Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ILE* 4.0 20.2 - - + -
184B PHE* 3.9 12.3 - - + -
187B ARG 3.0 12.9 + - - +
188B GLN* 3.1 24.7 + - - +
190B HIS* 1.3 77.3 - - - +
192B LYS* 1.3 64.2 + - - +
194B TRP* 3.1 4.2 + - + +
195B LEU* 2.9 48.7 + - + +
213B VAL* 3.9 25.1 - - + -
249B VAL* 3.5 16.5 - - + +
387B TYR* 3.9 33.0 - - + +
389B GLN* 4.7 0.9 - - - +
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Residues in contact with LYS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B PRO* 6.2 0.4 - - - +
149B VAL* 3.3 44.4 + - + +
151B LEU* 3.8 27.9 - - + +
188B GLN* 3.0 33.3 + - + +
189B GLU* 3.7 19.2 - - - +
190B HIS 3.1 0.4 - - - -
191B LEU* 1.3 78.7 - - - +
193B TYR* 1.3 60.7 + - - +
195B LEU* 4.0 1.6 - - - +
196B TYR* 3.1 24.3 + - - +
410B SO4 3.7 29.2 + - - +
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Residues in contact with TYR 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLU 4.3 0.4 - - - -
145B PHE* 2.8 55.9 + + + -
146B ASN 4.0 0.7 - - - -
147B MET* 2.5 48.7 + - + -
148B PRO* 4.7 0.2 - - - +
149B VAL* 3.6 19.3 - - + -
189B GLU* 3.4 44.1 + - + -
190B HIS* 3.0 7.9 + + - +
192B LYS* 1.3 77.6 - - - +
194B TRP* 1.3 65.5 + - - +
196B TYR* 3.4 2.9 + - - +
197B TYR* 3.1 34.0 + + + -
252B ILE* 4.4 0.7 - - - -
341B ILE* 3.9 27.8 - - + -
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Residues in contact with TRP 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ILE* 3.7 33.4 - - + -
182B ILE* 3.7 27.8 - - + -
190B HIS 2.9 12.4 + - - +
191B LEU* 3.1 12.1 + - - +
193B TYR* 1.3 79.2 - - - +
195B LEU* 1.3 70.3 + - + +
198B LEU* 2.7 68.8 + - + +
199B HIS* 5.5 1.3 - + - -
202B LEU* 4.4 3.4 - - + -
211B ILE* 3.8 28.7 - - + -
247B SER* 3.2 23.1 + - - -
248B ASP 3.7 6.6 + - - -
249B VAL* 3.5 22.9 - - + +
251B LEU 3.5 21.4 + - - -
252B ILE* 3.7 11.3 - - + +
260B TYR* 5.0 2.8 - + - -
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Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 3.9 24.9 - - + -
154B VAL* 4.2 3.5 - - - +
191B LEU* 2.9 34.3 + - + +
192B LYS 4.0 2.7 - - - +
194B TRP* 1.3 94.2 - - + +
196B TYR* 1.3 64.6 + - - +
199B HIS* 3.1 43.5 + - + +
211B ILE* 4.3 7.6 - - + -
386B LEU* 3.6 29.8 - - + +
387B TYR* 3.5 33.9 - - + -
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Residues in contact with TYR 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B MET* 3.6 26.7 - - + +
149B VAL* 4.3 9.6 - - + -
154B VAL* 3.9 33.7 - - + +
157B GLN* 3.7 23.2 + - - -
158B ASN* 6.1 0.4 - - - -
192B LYS 3.1 18.4 + - - +
193B TYR* 3.5 4.7 - - - +
195B LEU* 1.3 77.1 - - - +
197B TYR* 1.3 91.3 + + - +
200B PRO* 3.2 22.7 - - + +
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Residues in contact with TYR 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B MET* 6.5 0.7 - - - -
142B LEU 3.9 9.7 + - - -
143B ILE* 3.7 24.8 - - + -
144B GLU* 2.7 53.2 + - - +
145B PHE* 3.9 18.6 - + - -
147B MET* 3.9 3.7 - - + +
193B TYR* 3.1 26.0 + + - +
194B TRP 4.0 1.3 - - - +
196B TYR* 1.3 105.9 - + - +
198B LEU* 1.3 65.9 + - + +
200B PRO* 3.3 11.3 - - - +
201B VAL* 3.5 19.1 - - + +
252B ILE* 3.6 29.2 - - + -
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B TRP* 2.7 67.0 + - + +
197B TYR* 1.3 75.4 - - + +
199B HIS* 1.3 66.0 + - - +
201B VAL* 2.9 10.0 + - + +
202B LEU* 2.8 36.7 + - + +
252B ILE* 3.8 20.0 - - + -
253B PRO* 3.6 42.0 - - + -
260B TYR* 3.8 23.3 - - + +
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Residues in contact with HIS 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B VAL* 5.4 0.2 - - + -
158B ASN* 4.0 14.6 - - - +
161B VAL* 3.8 24.4 - - + +
165B GLY 4.3 2.0 - - - -
194B TRP* 5.5 1.1 - + - -
195B LEU* 3.1 41.1 + - + +
198B LEU* 1.3 78.7 - - - +
200B PRO* 1.4 68.5 - - + +
202B LEU* 3.3 2.4 + - + +
203B GLN* 2.9 31.8 + - - +
209B TYR* 2.8 40.4 + + - -
211B ILE* 3.7 9.3 - - + +
386B LEU* 2.9 44.9 + - + +
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Residues in contact with PRO 200 (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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157B GLN* 6.5 0.4 - - + -
158B ASN* 3.8 18.2 - - - +
195B LEU 4.1 0.2 - - - +
196B TYR* 3.2 25.6 - - + +
197B TYR 3.3 7.4 - - - +
199B HIS* 1.4 96.0 - - + +
201B VAL* 1.3 57.4 + - + +
203B GLN* 3.5 10.1 + - + +
204B ARG* 3.0 48.8 + - - +
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Residues in contact with VAL 201 (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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141B MET* 3.7 35.2 - - + -
197B TYR* 3.5 16.4 - - + +
198B LEU* 2.9 23.8 + - + +
200B PRO* 1.3 76.5 - - + +
202B LEU* 1.3 68.1 + - + +
204B ARG* 3.2 14.1 + - - +
205B GLN* 3.0 46.2 + - - +
253B PRO* 4.8 9.0 - - + -
256B ASP* 4.0 11.4 - - + -
260B TYR* 5.5 1.1 - - + -
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Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ILE* 3.7 26.2 - - + -
194B TRP* 4.4 2.0 - - + -
198B LEU* 2.8 43.9 + - + +
199B HIS* 4.6 1.6 - - - +
201B VAL* 1.3 74.3 - - + +
203B GLN* 1.3 61.2 + - - +
205B GLN* 3.3 9.9 + - - +
206B GLN 3.4 7.6 + - - -
207B LEU* 3.6 27.5 + - + +
209B TYR* 3.5 39.8 - - + +
211B ILE* 3.9 9.6 - - + -
260B TYR* 3.6 37.9 - - + -
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Residues in contact with GLN 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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136B LEU* 4.7 3.5 - - - +
158B ASN* 2.7 34.2 + - - +
159B PRO* 5.9 0.2 - - - +
160B ASN* 4.1 15.4 + - - +
161B VAL* 3.7 19.1 + - - +
167B TYR* 3.6 50.0 + - + +
199B HIS 2.9 22.8 + - - +
200B PRO* 3.7 6.2 - - + +
202B LEU* 1.3 74.3 - - - +
204B ARG* 1.3 65.4 + - + +
205B GLN 3.1 0.2 - - - -
206B GLN* 3.0 18.5 + - - +
209B TYR* 3.6 10.3 - - - +
405B SO4 4.9 1.3 + - - +
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Residues in contact with ARG 204 (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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142A LEU* 3.9 33.3 - - - +
134B SER* 2.6 29.5 + - - -
136B LEU* 3.4 37.2 - - + +
137B LEU* 3.7 13.2 - - + +
138B VAL* 4.0 10.4 - - - +
141B MET* 3.2 28.9 - - - +
200B PRO* 3.0 37.5 + - - +
201B VAL* 3.2 16.8 + - - +
203B GLN* 1.3 75.9 - - + +
205B GLN* 1.3 53.1 + - - +
206B GLN* 3.3 3.3 + - - +
256B ASP* 2.9 28.8 + - - +
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Residues in contact with GLN 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B SER* 4.1 11.7 - - - -
137B LEU* 3.9 8.7 - - + -
176B HIS* 5.2 2.4 - - - -
201B VAL* 3.0 36.5 + - + +
202B LEU* 3.8 6.3 - - - +
203B GLN 3.1 1.0 - - - -
204B ARG* 1.3 73.8 - - - +
206B GLN* 1.3 70.2 + - - +
207B LEU* 3.3 27.2 + - + +
256B ASP* 2.9 31.5 + - + +
258B ASN 2.9 20.8 + - - -
259B ALA* 3.6 7.0 - - + +
260B TYR* 2.8 29.7 + - - +
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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
------------------------------------------------------------
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