Contacts of the helix formed by residues 184 - 197 (chain A) in PDB entry 2IUK
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 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ILE* 4.5 9.6 - - + -
72A SER 4.3 13.0 - - - +
73A ALA* 4.0 25.1 - - + +
121A GLY* 4.0 31.4 - - - +
122A ALA* 4.4 10.3 - - + -
170A PHE* 4.4 15.5 - - + -
171A VAL* 4.9 3.4 - - + -
175A TYR* 4.6 13.2 - - + +
180A THR* 3.9 9.4 - - + -
181A PRO* 3.0 26.3 + - + +
183A PRO* 1.3 76.2 - - - +
185A LEU* 1.3 52.8 + - - +
186A LYS 3.5 1.8 - - - -
187A TYR* 3.6 6.5 - - + +
188A ARG* 2.7 34.4 + - - +
547A LEU* 5.3 1.6 - - + -
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Residues in contact with LEU 185 (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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177A PRO* 4.3 9.6 - - + +
178A SER* 5.9 1.3 - - - +
180A THR* 4.0 33.7 - - + +
181A PRO 3.2 6.3 + - - +
182A ALA* 3.5 16.4 + - - +
183A PRO 3.4 1.8 - - - -
184A LEU* 1.3 75.9 - - - +
186A LYS* 1.3 68.7 + - - +
188A ARG* 4.2 9.2 - - + +
189A LYS* 3.0 40.9 + - + +
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Residues in contact with LYS 186 (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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81A ASN* 3.2 45.6 + - + +
182A ALA 4.8 1.2 + - - -
183A PRO 4.5 0.8 + - - +
184A LEU 3.5 0.2 - - - -
185A LEU* 1.3 79.9 + - - +
187A TYR* 1.3 71.4 - - + +
189A LYS* 4.2 3.8 - - - +
190A GLU* 2.8 62.8 + - - +
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Residues in contact with TYR 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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71A ILE* 3.9 27.4 - - + -
77A ASP* 5.1 1.7 + - - -
81A ASN* 4.1 15.8 - - + +
82A GLY* 2.8 33.2 + - - -
84A VAL* 3.9 10.0 - - + +
124A TYR* 3.1 31.1 + + - -
168A ILE* 3.9 15.7 - - + +
170A PHE* 3.8 18.4 - - + -
183A PRO 3.0 28.5 - - - -
184A LEU* 3.6 10.3 - - + +
186A LYS* 1.3 83.3 - - + +
188A ARG* 1.3 63.9 + - - +
190A GLU* 4.0 7.4 - - - -
191A GLU* 3.2 21.7 + - - +
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Residues in contact with ARG 188 (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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170A PHE* 3.7 12.2 - - - -
175A TYR* 2.9 31.9 + - - +
176A LEU 3.4 2.0 + - - -
177A PRO* 3.2 18.2 - - - +
180A THR* 2.9 34.6 + - + -
184A LEU 2.7 23.0 + - - +
185A LEU* 4.1 9.2 - - + +
186A LYS 3.4 0.2 - - - -
187A TYR* 1.3 71.5 - - - +
189A LYS* 1.3 65.5 + - - +
191A GLU* 3.7 7.4 + - - +
192A PHE* 3.8 10.2 + - - -
545A SER* 3.7 24.0 + - - +
547A LEU* 3.2 33.8 - - + +
548A HIS* 3.5 13.5 - - - +
670A GLU* 2.9 36.1 + - - +
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Residues in contact with LYS 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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177A PRO* 4.7 6.3 - - - +
185A LEU* 3.0 30.8 + - + +
186A LYS* 4.2 4.9 - - - +
188A ARG* 1.3 81.4 - - - +
190A GLU* 1.3 61.1 + - - +
192A PHE* 3.4 34.7 - - + +
193A GLU* 3.9 12.7 + - - +
196A ARG* 4.8 7.2 + - - +
669A THR* 4.2 10.9 + - - -
670A GLU* 3.2 37.1 + - - +
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Residues in contact with GLU 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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124A TYR* 4.8 9.4 + - - -
165A LYS* 3.3 33.6 + - + +
168A ILE* 5.5 5.0 - - + +
186A LYS* 2.8 49.7 + - + +
187A TYR* 4.1 7.7 - - - +
189A LYS* 1.3 70.1 - - - +
191A GLU* 1.4 63.5 + - - +
192A PHE 3.2 1.8 - - - -
193A GLU* 3.1 35.7 + - - +
194A VAL* 3.4 8.2 + - - +
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Residues in contact with GLU 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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166A ASN 4.9 3.8 - - - +
167A ARG* 5.3 0.7 + - - -
168A ILE* 4.0 39.5 + - + +
170A PHE* 4.5 16.2 - - + -
187A TYR 3.2 16.1 + - - +
188A ARG 3.7 4.7 + - - +
190A GLU* 1.4 74.6 - - - +
192A PHE* 1.3 63.8 + - + +
194A VAL* 3.1 25.9 - - - +
195A LEU* 3.0 27.3 - - + +
208A ARG* 3.0 38.3 + - - -
545A SER* 5.5 3.6 - - - +
546A VAL* 6.0 6.6 - - + +
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Residues in contact with PHE 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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188A ARG 3.8 4.9 + - - -
189A LYS* 3.4 33.3 + - + +
190A GLU 3.2 0.2 - - - -
191A GLU* 1.3 75.9 - - + +
193A GLU* 1.3 65.3 + - - +
195A LEU* 3.0 16.7 + - + +
196A ARG* 3.0 49.2 + - - +
541A ASN 4.5 2.9 - - - -
542A ARG 3.9 10.1 - - - -
543A HIS* 3.4 16.2 - - - -
544A LEU 3.2 15.5 - - - -
545A SER* 2.9 49.1 - - - -
670A GLU* 3.2 25.4 - - + -
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Residues in contact with GLU 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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165A LYS* 5.9 0.2 + - - -
189A LYS* 4.0 13.3 - - - +
190A GLU* 3.1 26.4 + - + +
192A PHE* 1.3 78.6 - - - +
194A VAL* 1.3 65.0 + - + +
196A ARG* 3.5 25.5 + - - +
197A GLY* 3.2 20.8 + - - +
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Residues in contact with VAL 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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164A LYS* 3.7 31.2 - - + +
165A LYS* 4.0 32.3 - - + +
166A ASN 6.0 1.3 - - - +
190A GLU 3.6 12.8 - - - +
191A GLU* 3.1 23.3 - - - +
193A GLU* 1.3 78.6 - - + +
195A LEU* 1.3 59.3 + - - +
197A GLY* 3.4 7.6 + - - -
208A ARG* 3.6 27.9 - - - +
209A ILE* 3.9 12.8 - - - +
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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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191A GLU* 3.0 50.2 + - + +
192A PHE* 3.0 17.2 + - + +
194A VAL* 1.3 75.9 - - - +
196A ARG* 1.3 57.1 + - - +
208A ARG* 3.7 40.8 - - + +
209A ILE* 3.3 2.9 - - - -
210A TYR* 2.9 47.2 + - + +
541A ASN* 3.3 32.5 - - + +
542A ARG* 4.6 1.1 - - - -
546A VAL* 6.2 3.8 - - + -
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Residues in contact with ARG 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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189A LYS* 4.8 7.5 + - - +
192A PHE* 3.0 38.3 + - - +
193A GLU* 3.9 27.0 - - - +
194A VAL 3.4 0.2 + - - -
195A LEU* 1.3 76.0 - - - +
197A GLY* 1.3 66.8 + - - +
198A ASP 3.8 0.2 + - - -
209A ILE* 3.4 10.5 - - - +
210A TYR 3.9 1.8 - - - -
211A ASP* 4.0 2.8 - - - +
542A ARG* 2.8 82.8 + - + +
543A HIS* 3.5 29.4 + - - -
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Residues in contact with GLY 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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193A GLU 3.2 14.6 + - - +
194A VAL 3.4 5.9 + - - -
195A LEU 3.5 0.2 - - - -
196A ARG* 1.3 85.1 - - - +
198A ASP* 1.3 59.3 + - - -
203A ARG* 6.2 0.4 - - - -
209A ILE* 3.6 22.7 - - - -
542A ARG* 5.1 0.3 + - - -
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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