Contacts of the helix formed by residues 204 - 215 (chain A) in PDB entry 2IK8
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 GLN 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLY* 3.6 10.1 - - - +
43A GLU* 4.8 2.6 + - - +
178A ARG* 3.7 10.3 - - - +
180A LYS* 4.1 7.0 - - + +
181A THR 4.1 5.9 - - - +
202A GLY 3.5 1.0 - - - -
203A GLY* 1.3 87.7 + - - +
205A ARG* 1.3 66.9 + - - +
206A SER* 3.3 4.7 - - - +
207A GLU* 3.0 14.2 + - + +
208A ARG* 3.4 8.1 + - - +
235A ALA* 6.2 3.2 - - + +
236A GLU* 3.8 25.8 - - + +
355A ALF 2.6 35.3 - - - -
131B ASN* 2.8 47.5 + - - +
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Residues in contact with ARG 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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203A GLY 3.7 0.4 + - - -
204A GLN* 1.3 72.5 - - - +
206A SER* 1.3 62.5 + - - +
208A ARG* 3.2 44.0 + - - +
209A LYS* 4.4 6.5 + - - +
234A LEU* 3.7 8.3 - - - +
236A GLU* 3.6 25.4 + - + +
237A ASP* 3.9 21.6 + - - +
240A MET* 3.6 26.7 - - - +
245A GLU* 3.0 32.2 + - - +
129B GLU* 4.7 6.3 - - - +
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Residues in contact with SER 206 (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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204A GLN* 4.3 1.2 - - - +
205A ARG* 1.3 76.1 - - - +
207A GLU* 1.3 62.6 + - - +
208A ARG 3.4 0.2 - - - -
209A LYS* 3.7 23.3 - - - +
210A LYS* 4.1 11.1 - - - -
129B GLU* 3.4 51.0 + - - +
130B VAL 4.1 4.5 - - - -
131B ASN* 3.3 33.6 + - - +
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Residues in contact with GLU 207 (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 THR 4.4 0.2 - - - +
182A THR* 2.9 24.7 + - - -
183A GLY* 3.0 20.7 + - - +
202A GLY* 3.1 36.6 - - - +
204A GLN* 3.0 8.8 + - + +
206A SER* 1.3 78.0 - - - +
208A ARG* 1.3 58.8 + - - +
209A LYS 3.3 1.6 - - - -
210A LYS* 2.8 58.9 + - - +
211A TRP* 3.5 8.8 - - - -
90B GLU* 4.8 0.5 - - - +
131B ASN* 3.5 33.0 + - - +
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Residues in contact with ARG 208 (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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41A ALA* 4.0 13.5 - - - +
203A GLY 2.9 24.0 + - - -
204A GLN 3.6 5.9 + - - +
205A ARG* 3.2 33.9 + - - +
207A GLU* 1.3 74.3 - - - +
209A LYS* 1.3 66.7 + - - +
210A LYS 3.3 0.2 + - - -
211A TRP* 3.4 45.8 + - + +
234A LEU* 5.2 0.2 - - - +
236A GLU* 4.3 5.5 + - - -
245A GLU* 2.8 41.2 + - - +
249A LEU* 3.9 31.3 - - + +
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Residues in contact with LYS 209 (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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205A ARG 4.4 4.1 + - - +
206A SER* 3.7 22.6 + - - +
207A GLU 3.3 0.4 - - - -
208A ARG* 1.3 77.0 - - - +
210A LYS* 1.3 68.8 + - + +
211A TRP 3.2 1.2 + - - -
212A ILE* 3.7 18.2 + - - +
126B ALA 3.9 16.4 + - - +
127B PRO* 4.0 14.8 - - + +
128B LYS 5.2 0.2 - - - -
129B GLU* 3.0 41.6 + - - +
256C ASN* 5.5 1.3 - - - +
257C LYS* 3.7 34.9 - - + +
258C TRP* 4.1 14.7 - - - +
260C THR* 5.1 4.0 - - + +
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Residues in contact with LYS 210 (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 THR* 4.0 2.2 + - - -
183A GLY* 4.2 7.1 - - - +
184A ILE* 3.1 27.1 - - + +
206A SER 4.1 12.8 + - - -
207A GLU* 2.8 45.1 + - - +
209A LYS* 1.3 77.8 - - + +
211A TRP* 1.3 56.6 + - - +
212A ILE 2.9 12.1 + - - -
213A HIS* 3.0 28.9 + - + +
87B PHE* 3.0 34.2 + - + +
88B SER* 3.9 3.6 - - - +
90B GLU* 2.9 38.8 + - - -
129B GLU 5.6 0.4 - - - -
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Residues in contact with TRP 211 (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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39A LEU* 3.7 26.0 - - + -
40A GLY 3.7 30.3 - - - -
183A GLY 5.7 0.2 - - - -
184A ILE* 4.4 4.5 - - + -
201A VAL* 3.1 31.6 - - + +
202A GLY 3.0 29.3 + - - -
203A GLY* 4.2 1.1 - - - -
207A GLU 3.5 14.9 + - - -
208A ARG* 3.5 30.1 - - + +
209A LYS 3.2 0.6 + - - -
210A LYS* 1.3 77.5 - - + +
212A ILE* 1.3 61.5 + - - +
213A HIS 3.2 1.5 + - - -
214A CYS* 3.4 13.9 + - - -
215A PHE* 3.2 40.2 - + + -
249A LEU* 3.8 34.5 - - + -
253A ILE* 4.4 12.3 - - + -
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Residues in contact with ILE 212 (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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208A ARG 4.8 0.2 + - - -
209A LYS 3.7 9.1 + - - +
210A LYS 2.9 1.2 + - - -
211A TRP* 1.3 77.9 - - - +
213A HIS* 1.3 75.3 + - + +
214A CYS 3.3 1.0 + - - -
215A PHE* 3.6 36.3 + - + +
258A TRP* 4.3 13.0 - - + +
212C ILE* 4.8 7.4 - - + +
215C PHE* 4.4 32.6 - - + +
256C ASN* 3.7 32.5 - - - +
258C TRP* 3.6 26.2 - - + -
259C PHE* 6.6 0.2 - - + -
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Residues in contact with HIS 213 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A LYS* 4.8 2.6 + - - -
184A ILE* 4.3 5.2 - - + -
209A LYS 5.3 0.7 - - - -
210A LYS* 3.0 31.7 + - + +
212A ILE* 1.3 89.1 - - + +
214A CYS* 1.3 57.6 + - - +
215A PHE 3.6 0.4 + - - -
216A GLU* 5.1 3.5 + - - +
359A SO4 5.1 3.1 + - - -
360A SO4 3.2 30.4 + - - -
87B PHE* 3.2 59.5 - + + -
216C GLU* 3.7 31.4 - - + +
258C TRP* 5.7 4.3 - - + -
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Residues in contact with CYS 214 (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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35A LYS* 3.3 20.2 + - - +
37A LEU* 3.7 18.6 - - + +
39A LEU* 5.9 0.4 - - - -
184A ILE* 4.4 20.4 - - + -
199A PHE* 4.0 40.4 - - + -
201A VAL* 4.4 12.1 - - - -
211A TRP* 3.7 11.9 - - - -
212A ILE 3.3 0.2 - - - -
213A HIS* 1.3 76.9 - - + +
215A PHE* 1.3 63.5 + - - +
216A GLU 3.2 3.1 - - - -
218A VAL* 3.3 13.7 - - - +
359A SO4 5.5 0.2 - - - -
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Residues in contact with PHE 215 (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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37A LEU* 3.9 16.8 - - + -
39A LEU* 4.3 10.3 - - + -
211A TRP* 3.2 42.2 - + + -
212A ILE* 3.6 29.6 + - + +
213A HIS 3.6 0.4 - - - -
214A CYS* 1.3 73.9 - - - +
216A GLU* 1.3 56.9 + - - +
217A GLY 3.7 1.4 + - - -
218A VAL* 2.9 22.8 + - - +
253A ILE* 4.3 15.3 - - + -
256A ASN* 4.9 4.9 - - - -
258A TRP* 3.3 38.8 - + + +
259A PHE* 3.4 31.2 - + + -
212C ILE* 2.9 23.6 - - + +
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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