Contacts of the helix formed by residues 224 - 232 (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 ASN 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A THR* 5.3 5.0 - - - +
188A THR* 4.9 18.0 - - - +
193A GLN* 5.2 4.8 + - - -
220A ILE* 3.3 22.4 + - - +
221A ILE* 3.0 14.7 + - - +
222A GLN 2.9 2.4 + - - -
223A ALA* 1.3 76.6 - - - +
225A PRO* 1.4 60.2 - - + +
226A ALA 3.1 4.2 + - - -
227A LEU* 3.3 4.0 + - - +
228A GLU* 2.7 65.3 + - - +
246A LYS* 5.5 2.9 + - - -
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Residues in contact with PRO 225 (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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221A ILE* 3.3 9.6 - - + +
222A GLN* 3.2 17.7 - - - +
224A ASN* 1.4 85.6 - - + +
226A ALA* 1.3 65.8 + - - +
228A GLU* 3.8 10.8 - - + +
229A ALA* 3.5 12.1 + - + +
328A GLU 5.3 0.7 - - - +
331A ALA* 3.5 45.1 - - + +
332A THR* 3.5 16.4 - - - +
334A ASN* 5.9 0.7 - - + -
335A ALA* 4.1 4.7 - - + +
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Residues in contact with ALA 226 (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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222A GLN 3.4 14.1 + - - +
223A ALA* 4.4 0.7 - - - -
224A ASN 3.1 0.8 + - - -
225A PRO* 1.3 82.3 - - - +
227A LEU* 1.3 64.4 + - + +
228A GLU 3.4 0.2 + - - -
230A PHE* 3.6 27.2 + - - +
335A ALA* 3.7 10.4 - - + +
336A PHE* 3.7 28.1 - - + -
339A LEU* 4.5 1.3 - - + -
439A MET* 4.6 1.9 - - - +
443A ILE* 3.5 30.7 - - + -
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Residues in contact with LEU 227 (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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223A ALA* 3.6 20.4 - - + +
224A ASN 3.3 5.3 + - - +
226A ALA* 1.3 78.4 - - - +
228A GLU* 1.3 57.6 + - + +
230A PHE* 3.4 2.1 - - - -
231A GLY* 2.7 36.9 + - - -
232A ASN* 3.6 1.5 - - - +
244A PHE* 4.2 30.7 - - + -
263A ILE* 5.0 15.7 - - + -
436A PHE* 3.8 15.2 - - + -
439A MET* 5.1 2.9 - - + -
440A VAL* 3.8 39.5 - - + +
443A ILE* 3.7 27.4 - - + -
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Residues in contact with GLU 228 (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 THR* 4.5 9.0 - - - +
224A ASN* 2.7 59.7 + - - +
225A PRO* 4.2 5.6 - - + +
226A ALA 3.3 0.4 - - - -
227A LEU* 1.3 74.9 - - + +
229A ALA* 1.3 63.4 + - - +
230A PHE 3.2 0.7 + - - -
232A ASN* 3.2 47.7 + - + +
233A ALA 3.9 4.9 + - - -
240A ASN* 4.0 24.5 + - - +
244A PHE* 5.4 1.6 - - + -
284A HIS* 4.3 7.5 - - + -
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Residues in contact with ALA 229 (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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225A PRO* 3.5 19.2 + - + +
226A ALA 4.4 0.7 - - - +
227A LEU 3.4 0.2 - - - -
228A GLU* 1.3 78.8 - - - +
230A PHE* 1.3 59.1 + - - +
231A GLY 3.8 0.2 - - - -
233A ALA* 6.5 0.2 - - - -
283A TYR* 3.7 1.8 - - - +
284A HIS* 3.7 17.7 + - - -
285A ILE* 3.3 37.2 + - + +
288A GLN* 4.5 10.5 - - - +
328A GLU* 5.3 4.0 - - + +
332A THR* 3.9 23.3 - - + +
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Residues in contact with PHE 230 (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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226A ALA 3.6 21.5 - - - +
227A LEU 3.3 3.2 + - - +
228A GLU 3.1 0.4 - - - -
229A ALA* 1.3 78.7 - - + +
231A GLY* 1.3 55.3 + - - +
283A TYR* 3.1 44.4 + + - -
285A ILE* 3.4 43.7 - - + -
332A THR* 4.7 0.4 - - + -
336A PHE* 4.2 12.8 - + - -
350A TYR* 5.4 3.8 - + - -
353A THR* 3.6 26.0 - - + -
435A MET* 4.8 15.3 - - + -
436A PHE* 3.7 15.7 - - + +
439A MET* 3.6 38.6 - - + -
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Residues in contact with GLY 231 (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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227A LEU 2.7 14.8 + - - -
228A GLU 3.5 0.8 + - - -
229A ALA 3.8 0.2 - - - -
230A PHE* 1.3 76.6 - - - +
232A ASN* 1.3 68.7 + - - +
233A ALA 5.0 0.2 - - - +
236A VAL* 6.0 0.3 - - - +
243A ARG* 4.6 8.1 + - - +
244A PHE* 3.7 16.5 - - - -
268A LEU* 4.9 7.9 - - - +
272A ARG* 5.3 5.6 + - - -
283A TYR* 4.3 10.1 - - - +
436A PHE* 3.7 14.8 - - - -
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Residues in contact with ASN 232 (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 THR* 4.6 5.7 + - - +
228A GLU* 3.2 40.6 + - - +
231A GLY* 1.3 79.6 - - - +
233A ALA* 1.3 76.1 + - - +
234A LYS 4.4 0.2 - - - +
236A VAL* 4.3 8.0 - - - +
240A ASN* 3.4 24.4 - - - +
241A SER 2.7 36.5 + - - +
242A SER* 3.8 8.7 + - - -
244A PHE* 3.1 26.2 - - - -
272A ARG* 4.3 9.5 + - - -
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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