Contacts of the helix formed by residues 214 - 223 (chain A) in PDB entry 1IK2
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 GLY 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A GLY* 5.7 1.0 - - - -
212A GLY* 3.0 7.6 - - - -
213A LYS* 1.3 79.2 - - - +
215A THR* 1.3 67.4 + - - +
217A GLU* 2.8 21.3 - - - +
218A ASP* 3.2 28.9 - - - +
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Residues in contact with THR 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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201A ILE* 3.5 38.7 + - + +
202A GLY* 4.7 4.7 - - - -
203A ASP* 5.0 3.1 + - + +
213A LYS* 3.5 22.5 + - + +
214A GLY* 1.3 82.7 + - - +
216A LEU* 1.3 73.9 + - + +
217A GLU* 3.3 2.5 - - - -
218A ASP 2.9 12.1 + - - -
219A GLN* 3.1 17.4 + - - +
449A THR* 6.3 2.9 - - + -
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Residues in contact with LEU 216 (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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201A ILE* 3.9 13.9 - - + -
215A THR* 1.3 75.6 - - + +
217A GLU* 1.3 64.1 + - - +
219A GLN* 3.0 24.6 + - - +
220A ILE* 3.2 17.8 + - + +
250A ILE* 6.3 0.7 - - + -
258A LEU* 3.7 33.4 - - + +
259A ALA 3.5 24.7 - - - +
260A SER* 3.9 11.0 - - - -
261A ALA* 4.3 7.0 - - + +
446A THR 5.1 1.1 - - - +
447A LEU* 3.5 42.2 - - + +
449A THR* 5.0 10.2 - - + +
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Residues in contact with GLU 217 (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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196A ALA* 4.0 28.3 - - + +
200A ALA* 3.4 11.1 - - - +
201A ILE* 2.8 41.3 + - + +
202A GLY* 3.7 2.4 + - - -
214A GLY 2.8 26.5 - - - +
215A THR* 3.6 1.0 - - - +
216A LEU* 1.3 74.0 - - - +
218A ASP* 1.3 63.4 + - - +
220A ILE* 3.2 18.2 + - - +
221A ILE* 3.2 19.1 - - - +
258A LEU* 3.8 27.8 - - + -
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Residues in contact with ASP 218 (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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214A GLY* 3.2 36.9 - - - +
215A THR 2.9 2.0 + - - -
217A GLU* 1.3 82.0 + - - +
219A GLN* 1.3 64.2 + - + +
221A ILE* 3.1 27.9 + - - +
222A GLN* 3.6 23.1 + - - +
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Residues in contact with GLN 219 (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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215A THR* 3.1 14.7 + - - +
216A LEU* 3.0 20.9 + - - +
218A ASP* 1.3 77.8 - - + +
220A ILE* 1.3 58.8 + - - +
222A GLN* 2.8 26.1 + - - +
223A ALA* 3.0 11.3 + - - +
338A VAL 4.6 7.6 - - - +
339A LEU* 3.2 31.2 - - + +
446A THR* 3.1 55.0 + - - +
447A LEU* 4.0 9.1 - - + +
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Residues in contact with ILE 220 (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 THR* 6.0 2.2 - - + -
192A ILE* 4.0 27.6 - - + -
193A GLN* 5.3 4.3 - - - +
216A LEU* 3.4 18.8 - - + +
217A GLU* 3.5 14.6 - - - +
218A ASP 3.1 1.2 - - - -
219A GLN* 1.3 77.4 - - - +
221A ILE* 1.3 62.4 + - + +
223A ALA* 3.4 17.8 + - + +
224A ASN* 3.3 15.4 + - - +
250A ILE* 5.7 5.4 - - + -
261A ALA* 3.9 15.5 - - + -
263A ILE* 6.0 6.7 - - + -
447A LEU* 3.7 37.7 - - + -
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Residues in contact with ILE 221 (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 GLN* 3.7 30.5 - - - +
196A ALA* 6.0 2.7 - - + -
217A GLU 3.2 21.5 - - - +
218A ASP* 3.1 18.9 + - - +
219A GLN 3.1 0.6 - - - -
220A ILE* 1.3 79.0 - - + +
222A GLN* 1.3 66.2 + - - +
224A ASN* 3.0 27.2 + - - +
225A PRO* 3.3 11.9 - - + +
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Residues in contact with GLN 222 (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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218A ASP* 3.6 26.6 + - - +
219A GLN* 2.8 16.0 + - + +
221A ILE* 1.3 78.6 - - - +
223A ALA* 1.3 58.1 + - - +
224A ASN 2.9 10.9 + - - -
225A PRO* 3.2 16.2 - - - +
226A ALA* 3.4 11.3 + - - +
334A ASN* 3.9 11.7 + - - +
335A ALA* 3.6 24.7 + - - +
338A VAL* 3.8 28.8 - - + +
339A LEU* 3.8 21.1 - - + -
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Residues in contact with ALA 223 (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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219A GLN 3.0 10.9 + - - +
220A ILE* 3.4 20.2 - - + +
221A ILE 3.2 0.2 - - - -
222A GLN* 1.3 74.6 - - - +
224A ASN* 1.3 62.0 + - - +
226A ALA* 4.4 9.0 - - - -
227A LEU* 3.6 24.2 - - + +
263A ILE* 5.3 10.3 - - + +
339A LEU* 4.1 3.7 - - - +
443A ILE* 3.8 26.0 - - + -
447A LEU* 5.3 3.8 - - + -
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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