Contacts of the helix formed by residues 186 - 203 (chain A) in PDB entry 4IQJ
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 LEU 186 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 3.9 20.2 - - + -
183A ASN* 5.9 0.5 + - - -
184A HIS* 3.0 22.5 + - + +
185A GLY* 1.3 80.1 - - - +
187A PRO* 1.3 70.2 - - + +
188A GLU* 3.9 13.7 - - - +
189A GLN* 3.3 45.2 + - + +
190A LYS* 3.9 10.6 + - - +
245A PRO* 3.6 39.9 - - + +
246A CYS* 4.4 6.3 - - + -
249A PHE* 5.2 1.6 - - + -
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Residues in contact with PRO 187 (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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185A GLY 4.2 4.5 - - - +
186A LEU* 1.3 84.2 - - + +
188A GLU* 1.3 81.3 + - + +
189A GLN 3.3 0.2 - - - -
190A LYS* 3.5 24.5 + - + +
191A LYS* 3.8 7.1 + - - +
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Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 4.3 17.7 - - + -
155A LEU* 3.8 25.8 - - + +
186A LEU* 3.2 12.8 - - - +
187A PRO* 1.3 99.2 - - + +
189A GLN* 1.3 63.6 + - - +
191A LYS* 3.5 5.3 + - - +
192A VAL* 3.2 28.4 + - - +
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Residues in contact with GLN 189 (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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146A LEU* 4.0 26.1 - - + +
182A GLN* 3.3 33.3 + - + +
183A ASN* 3.5 6.1 - - - +
184A HIS* 2.7 56.7 + - - +
186A LEU* 3.3 26.3 + - + +
187A PRO 3.3 0.8 - - - -
188A GLU* 1.3 77.3 - - - +
190A LYS* 1.3 55.7 + - - +
192A VAL* 4.5 2.5 - - - -
193A ASN* 2.7 51.8 + - - +
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Residues in contact with LYS 190 (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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183A ASN* 5.2 13.1 - - - +
186A LEU 3.9 11.5 + - - +
187A PRO* 3.5 14.4 + - + +
188A GLU 3.3 0.6 - - - -
189A GLN* 1.3 78.1 - - - +
191A LYS* 1.3 61.1 + - - +
193A ASN* 4.7 2.2 - - - +
194A GLN* 3.2 29.1 + - - +
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Residues in contact with LYS 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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154A ILE* 3.6 27.2 + - + +
155A LEU* 4.5 15.6 + - + +
157A ASP* 2.6 32.2 + - - -
159A LEU* 6.2 2.5 - - - -
187A PRO 3.8 6.7 + - - +
188A GLU* 3.5 8.8 + - - +
189A GLN 3.4 0.4 - - - -
190A LYS* 1.3 76.2 - - - +
192A VAL* 1.3 64.4 + - + +
194A GLN* 3.7 10.1 + - - +
195A VAL* 3.1 36.4 + - + +
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 4.2 11.2 - - + -
151A PRO* 3.6 42.8 - - + +
154A ILE* 4.2 12.3 - - + -
155A LEU* 3.7 17.9 - - + -
188A GLU 3.2 18.2 + - - +
189A GLN* 4.1 4.9 - - - +
191A LYS* 1.3 74.9 - - - +
193A ASN* 1.3 59.4 + - - +
195A VAL* 2.9 5.4 + - - +
196A LEU* 2.7 60.3 + - + +
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Residues in contact with ASN 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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180A GLU 4.8 0.3 - - - +
181A ILE* 3.9 21.0 - - - +
182A GLN* 3.2 31.5 + - - +
183A ASN* 4.3 12.9 - - - +
189A GLN* 2.7 32.5 + - - +
190A LYS* 4.7 2.0 - - - +
192A VAL* 1.3 74.2 - - - +
194A GLN* 1.3 55.9 + - - +
196A LEU* 3.8 17.9 - - - +
197A LYS* 2.9 28.9 + - - +
266A TRP* 3.8 26.2 - - + -
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Residues in contact with GLN 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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190A LYS 3.2 22.4 + - - +
191A LYS* 3.7 11.5 - - - +
192A VAL 3.1 0.2 - - - -
193A ASN* 1.3 76.1 - - - +
195A VAL* 1.3 65.1 + - - +
197A LYS* 3.4 24.9 + - - +
198A GLU* 3.4 29.0 + - - +
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Residues in contact with VAL 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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154A ILE* 3.5 31.2 - - + -
159A LEU* 4.3 22.0 - - + -
191A LYS* 3.1 22.4 - - + +
192A VAL 2.9 3.1 + - - +
194A GLN* 1.3 79.3 - - + +
196A LEU* 1.3 59.2 + - - +
198A GLU* 3.5 17.9 + - + +
199A PHE* 3.2 51.0 + - + -
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Residues in contact with LEU 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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143A SER* 4.4 12.6 - - - +
144A GLY 5.7 0.7 - - - +
150A ILE* 3.8 28.5 - - + -
151A PRO* 4.8 7.2 - - + -
154A ILE* 4.2 4.3 - - + -
179A ILE* 3.7 28.5 - - + +
180A GLU 4.0 20.9 - - - +
181A ILE* 5.3 4.3 - - + -
192A VAL* 2.7 45.0 + - + +
193A ASN* 3.9 13.7 - - - +
195A VAL* 1.3 71.7 - - - +
197A LYS* 1.3 54.8 + - - +
199A PHE* 3.9 7.3 - - + +
200A ALA* 2.7 36.8 + - - +
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Residues in contact with LYS 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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181A ILE* 5.7 0.7 - - - -
193A ASN 2.9 18.2 + - - +
194A GLN* 3.4 16.2 - - - +
195A VAL 3.3 0.2 - - - -
196A LEU* 1.3 78.5 - - - +
198A GLU* 1.3 56.4 + - + +
200A ALA* 3.7 6.1 - - - +
201A ARG* 3.1 74.2 + - - +
207A MET* 4.6 9.4 - - + -
265A GLU* 2.6 35.4 + - - +
266A TRP* 3.7 28.2 - - + -
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Residues in contact with GLU 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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159A LEU* 5.9 2.4 - - - +
194A GLN* 3.4 31.4 + - - +
195A VAL* 3.6 18.6 - - + +
196A LEU 3.3 0.2 - - - -
197A LYS* 1.3 75.9 - - + +
199A PHE* 1.3 56.2 + - + +
201A ARG* 3.1 8.6 + - - +
202A LYS* 2.8 37.5 + - - +
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Residues in contact with PHE 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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150A ILE* 4.6 7.9 - - + -
154A ILE* 4.3 5.8 - - + -
159A LEU* 3.9 18.6 - - + -
162A ALA* 4.1 17.0 - - + -
163A GLU* 3.4 48.2 - - + -
166A LEU* 3.7 28.9 - - + -
179A ILE* 5.3 2.9 - - + -
195A VAL* 3.2 42.9 + - + +
196A LEU* 3.9 10.5 - - + +
198A GLU* 1.3 76.3 - - + +
200A ALA* 1.3 66.9 + - - +
202A LYS* 3.2 17.0 + - + -
203A TYR* 3.4 22.1 + + - +
205A LEU* 4.3 3.1 - - - +
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Residues in contact with ALA 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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179A ILE* 3.7 21.0 - - + +
196A LEU 2.7 23.4 + - - +
197A LYS 3.7 6.1 - - - +
199A PHE* 1.3 75.2 - - - +
201A ARG* 1.3 60.9 + - - +
204A GLY* 4.0 1.4 + - - -
205A LEU* 3.5 25.4 + - - +
206A GLY* 4.2 4.9 + - - +
207A MET* 3.5 35.9 - - + -
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Residues in contact with ARG 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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197A LYS* 3.1 58.8 + - - +
198A GLU* 3.1 7.6 + - - +
200A ALA* 1.3 78.6 - - + +
202A LYS* 1.3 62.2 + - - +
203A TYR 3.6 0.2 + - - -
204A GLY* 4.2 5.2 + - - -
207A MET* 5.5 6.7 - - - +
265A GLU 4.7 6.7 + - - -
266A TRP* 5.6 3.2 + - - +
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Residues in contact with LYS 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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163A GLU* 2.8 33.3 + - - +
198A GLU 2.8 20.2 + - - +
199A PHE* 3.2 7.1 + - + +
201A ARG* 1.3 74.6 - - - +
203A TYR* 1.3 81.6 + - + +
204A GLY 3.6 0.6 + - - -
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Residues in contact with TYR 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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163A GLU* 2.6 43.2 + - + +
166A LEU* 4.0 13.7 - - + -
167A ASN* 3.2 32.5 + - - -
170A LEU* 4.2 10.9 - - + +
199A PHE* 3.4 13.0 + + - +
202A LYS* 1.3 103.7 - - + +
204A GLY* 1.3 62.5 + - - +
205A LEU* 3.3 30.8 - - + +
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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