Contacts of the helix formed by residues 187 - 205 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A PHE* 3.3 21.2 - - + -
185A ARG 3.4 2.6 - - - +
186A ASN* 1.3 84.6 - - - +
188A GLN* 1.3 66.2 + - - +
189A GLU 3.2 2.7 - - - -
190A HIS* 2.9 41.5 + - + +
191A LEU 3.0 17.5 + - - -
249A VAL* 3.5 25.3 - - + +
250A ASP* 3.1 17.8 + - - -
343A HIS* 3.2 11.5 + - - +
346A ASP* 2.6 40.2 + - - -
404A UDP 2.7 54.7 + - - +
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Residues in contact with GLN 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 4.7 7.7 - - - +
184A PHE* 3.6 19.5 - - + -
186A ASN* 3.7 2.2 - - - +
187A ARG* 1.3 76.7 - - - +
189A GLU* 1.3 63.6 + - - +
191A LEU* 3.3 15.0 + - - +
192A LYS* 3.1 41.4 + - + +
387A TYR* 3.4 22.7 + - - -
389A GLN* 5.0 3.1 - - - +
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Residues in contact with GLU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ARG* 3.2 1.2 - - - -
188A GLN* 1.3 76.0 - - - +
190A HIS* 1.3 80.8 + - + +
192A LYS* 3.2 27.0 + - - +
193A TYR* 3.4 38.6 + - + -
341A ILE* 5.2 2.8 - - - +
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Residues in contact with HIS 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ARG* 2.9 49.5 + - + +
189A GLU* 1.3 90.7 + - + +
191A LEU* 1.3 63.8 + - - +
193A TYR* 3.1 6.7 + + - +
194A TRP* 2.9 20.6 + - - +
249A VAL* 3.9 19.3 - - + +
250A ASP* 3.7 6.4 - - + +
341A ILE* 3.5 42.6 - - + +
342A ARG 4.5 0.6 + - - -
343A HIS* 3.4 36.2 - + + +
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Residues in contact with LEU 191 (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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182A ILE* 4.2 15.9 - - + -
184A PHE* 4.0 12.3 - - + -
187A ARG 3.0 17.7 + - - +
188A GLN* 3.6 22.0 - - - +
189A GLU 3.1 0.2 - - - -
190A HIS* 1.3 77.6 - - - +
192A LYS* 1.3 57.8 + - - +
194A TRP* 3.1 5.9 + - + +
195A LEU* 2.8 47.8 + - + +
213A VAL* 3.9 24.0 - - + -
249A VAL* 3.7 16.8 - - + +
387A TYR* 3.9 34.8 - - + +
389A GLN* 5.1 0.7 - - - +
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Residues in contact with LYS 192 (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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149A VAL* 3.1 51.1 + - + +
151A LEU* 3.7 35.5 - - + +
188A GLN* 3.1 34.5 + - + +
189A GLU* 3.2 15.8 + - - +
191A LEU* 1.3 74.3 - - - +
193A TYR* 1.3 57.0 + - - +
195A LEU* 3.4 3.0 + - - +
196A TYR* 3.0 29.8 + - - +
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Residues in contact with TYR 193 (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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145A PHE* 2.8 55.8 + + + -
146A ASN 4.2 0.7 - - - -
147A MET* 2.5 39.1 + - + -
148A PRO* 4.8 0.2 - - - +
149A VAL* 3.7 19.3 - - + -
189A GLU* 3.4 44.1 + - + +
190A HIS* 3.1 6.8 + - - +
192A LYS* 1.3 74.5 - - + +
194A TRP* 1.3 67.0 + - - +
196A TYR* 3.4 3.6 + - - +
197A TYR* 2.9 41.9 + + + -
252A ILE* 4.3 1.1 - - + -
341A ILE* 4.0 25.4 - - + -
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Residues in contact with TRP 194 (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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180A ILE* 3.7 31.6 - - + -
182A ILE* 3.8 26.9 - - + +
190A HIS 2.9 12.7 + - - +
191A LEU* 3.1 14.6 + - + +
193A TYR* 1.3 78.4 - - - +
195A LEU* 1.3 73.5 + - + +
198A LEU* 2.9 67.3 + - + +
199A HIS* 5.4 2.0 - + - -
202A LEU* 4.4 4.3 - - + -
211A ILE* 4.0 27.4 - - + -
247A SER* 3.3 23.3 + - - -
248A ASP 3.9 1.7 + - - -
249A VAL* 3.3 26.9 - - + +
251A LEU 3.7 19.3 + - - -
252A ILE* 3.7 11.6 - - + +
260A TYR* 5.0 4.4 - + - -
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Residues in contact with LEU 195 (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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151A LEU* 3.8 27.1 - - + -
154A VAL* 4.2 3.9 - - - +
191A LEU* 2.8 34.5 + - + +
192A LYS 3.8 3.8 - - - +
194A TRP* 1.3 94.4 - - + +
196A TYR* 1.3 62.3 + - - +
199A HIS* 3.2 44.8 + - + +
211A ILE* 4.5 2.2 - - + -
386A LEU* 3.9 27.8 - - + +
387A TYR* 3.5 37.2 - - + -
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Residues in contact with TYR 196 (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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147A MET* 3.5 29.4 - - + +
149A VAL* 4.2 15.5 - - + -
154A VAL* 3.9 29.1 - - + +
157A GLN* 3.7 22.7 - - - -
158A ASN* 5.2 0.4 + - - -
192A LYS 3.0 18.0 + - - +
193A TYR* 3.6 4.3 - - - +
195A LEU* 1.3 77.5 - - - +
197A TYR* 1.3 90.8 + + - +
200A PRO* 3.1 23.9 - - - +
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Residues in contact with TYR 197 (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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142A LEU 4.0 8.7 - - - -
143A ILE* 3.8 25.6 - - + -
144A GLU* 2.4 53.2 + - - +
145A PHE* 3.8 17.7 - + - -
147A MET* 3.7 6.2 - - - +
193A TYR* 2.9 36.9 + + - +
194A TRP 4.3 0.9 - - - +
196A TYR* 1.3 100.7 - + - +
198A LEU* 1.3 65.5 + - + +
200A PRO* 3.5 7.8 - - - +
201A VAL* 3.4 20.7 - - + +
252A ILE* 3.5 28.3 - - + -
253A PRO* 6.3 0.2 - - - -
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Residues in contact with LEU 198 (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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194A TRP* 2.9 68.4 + - + +
197A TYR* 1.3 74.3 - - - +
199A HIS* 1.3 61.4 + - - +
201A VAL* 2.9 10.2 + - + +
202A LEU* 2.7 43.9 + - + +
251A LEU 4.3 0.4 - - - +
252A ILE* 3.8 18.4 - - + -
253A PRO* 3.7 35.4 - - + -
260A TYR* 3.8 28.5 - - + -
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Residues in contact with HIS 199 (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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154A VAL* 5.4 0.2 - - + -
158A ASN* 4.0 13.5 - - - +
161A VAL* 3.7 25.0 - - + +
165A GLY 4.3 1.8 - - - -
194A TRP* 5.4 1.3 - + - -
195A LEU* 3.2 39.0 + - + +
198A LEU* 1.3 80.5 - - + +
200A PRO* 1.4 68.8 - - + +
201A VAL 3.2 0.2 + - - -
202A LEU* 3.3 2.2 + - + +
203A GLN* 3.0 27.6 + - - +
209A TYR* 2.8 31.8 + + - -
211A ILE* 3.8 21.5 - - + +
386A LEU* 2.8 46.4 + - + +
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Residues in contact with PRO 200 (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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158A ASN* 3.7 18.1 - - - +
196A TYR* 3.1 26.0 - - + +
197A TYR 3.5 7.2 - - - +
199A HIS* 1.4 94.4 - - + +
201A VAL* 1.3 60.9 + - + +
203A GLN* 3.5 10.8 + - + +
204A ARG* 3.1 43.8 + - - +
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Residues in contact with VAL 201 (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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141A MET* 3.7 36.1 - - + -
197A TYR* 3.4 16.6 + - + +
198A LEU* 2.9 22.2 + - + +
200A PRO* 1.3 78.5 - - + +
202A LEU* 1.3 64.8 + - + +
204A ARG* 3.3 14.0 + - - +
205A GLN* 3.0 47.2 + - - +
253A PRO* 5.0 10.1 - - + -
256A ASP* 3.9 13.0 - - + -
260A TYR* 5.6 0.9 - - + -
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Residues in contact with LEU 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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180A ILE* 4.3 9.2 - - + -
194A TRP* 4.4 4.7 - - + -
198A LEU* 2.7 43.7 + - + +
199A HIS* 4.0 1.6 - - - +
201A VAL* 1.3 76.6 - - + +
203A GLN* 1.3 60.2 + - - +
205A GLN* 3.4 10.0 + - - +
206A GLN 3.4 8.1 + - - -
207A LEU* 3.7 26.6 + - + +
209A TYR* 3.5 43.0 - - + +
211A ILE* 3.8 17.3 - - + -
260A TYR* 3.7 40.2 - - + -
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Residues in contact with GLN 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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136A LEU* 4.4 4.1 - - - +
158A ASN* 3.1 26.4 + - - +
160A ASN* 4.0 14.9 + - - +
161A VAL* 3.6 23.4 + - - +
167A TYR* 3.5 56.2 + - + +
199A HIS 3.0 25.8 + - - +
200A PRO* 3.9 5.2 - - + +
202A LEU* 1.3 73.9 - - - +
204A ARG* 1.3 61.3 + - + +
206A GLN* 2.8 24.1 + - - +
209A TYR* 3.8 4.0 + - - +
408A SO4 4.8 0.6 + - - +
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Residues in contact with ARG 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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134A SER* 2.5 30.7 + - - -
136A LEU* 3.3 39.3 + - + +
137A LEU* 3.7 11.9 - - + +
138A VAL* 4.3 4.0 - - - +
141A MET* 3.3 29.5 - - - +
200A PRO* 3.1 34.2 + - - +
201A VAL* 3.8 17.1 - - - +
203A GLN* 1.3 75.6 - - + +
205A GLN* 1.3 55.5 + - - +
206A GLN* 3.3 1.9 + - - +
256A ASP* 2.9 28.1 + - - +
142C LEU* 3.6 36.6 - - - +
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Residues in contact with GLN 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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134A SER* 4.2 7.5 - - - -
137A LEU* 3.9 11.2 - - + -
176A HIS* 5.2 2.6 - - - -
201A VAL* 3.0 37.5 + - + +
202A LEU* 3.8 6.7 - - - +
203A GLN 3.1 0.8 - - - -
204A ARG* 1.3 74.2 - - - +
206A GLN* 1.3 71.9 + - - +
207A LEU* 3.3 23.5 + - + +
256A ASP* 3.1 24.8 + - - +
258A ASN 2.8 27.4 + - - -
259A ALA* 3.6 5.7 - - - +
260A TYR* 2.9 34.4 + - - +
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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
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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