Contacts of the helix formed by residues 226 - 234 (chain A) in PDB entry 1IEQ
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 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A ILE* 1.3 84.5 - - - +
227A ARG* 1.3 63.0 + - - +
228A GLU* 2.8 20.4 + - + +
229A GLY* 2.6 33.4 + - - -
230A LEU* 3.1 14.6 + - - +
256A TRP* 4.3 0.2 - - - -
257A ASN* 4.9 2.0 - - - +
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Residues in contact with ARG 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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226A ASN* 1.3 74.7 - - - +
228A GLU* 1.3 68.0 + - + +
230A LEU* 3.8 1.9 - - + +
231A MET* 3.0 63.3 + - + +
256A TRP* 3.7 33.0 - - + -
267A LEU* 5.0 13.7 - - - +
271A TYR* 4.5 14.3 - - - +
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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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226A ASN* 2.8 20.3 + - + +
227A ARG* 1.3 84.7 - - + +
229A GLY* 1.3 55.1 + - - +
231A MET* 3.4 4.0 + - - +
232A ASN* 2.9 31.1 + - - +
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Residues in contact with GLY 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 ILE* 3.4 23.6 - - - -
226A ASN* 2.6 15.7 + - - -
228A GLU* 1.3 70.8 - - - +
230A LEU* 1.3 60.0 + - - +
231A MET 3.1 1.8 - - - -
232A ASN* 4.2 7.4 - - - -
233A ILE* 2.8 39.8 + - - +
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Residues in contact with LEU 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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209A VAL* 4.1 23.1 - - + +
210A GLY* 4.4 7.2 - - - -
223A THR* 5.0 2.0 - - + -
225A ILE* 3.7 10.5 - - + +
226A ASN 3.1 15.4 + - - +
227A ARG* 3.8 5.4 - - + +
229A GLY* 1.3 74.6 - - - +
231A MET* 1.3 65.1 + - + +
234A HIS* 3.1 32.2 + - + +
235A MET* 3.0 51.8 + - + -
256A TRP* 3.9 37.0 - - + +
267A LEU* 4.9 7.9 - - + -
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Residues in contact with MET 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 ARG* 3.0 49.7 + - + +
228A GLU* 3.8 4.3 - - - +
229A GLY 3.1 0.6 - - - -
230A LEU* 1.3 83.8 - - + +
232A ASN* 1.3 57.4 + - - +
233A ILE 3.5 0.2 - - - -
235A MET* 3.7 33.7 - - + +
236A PRO* 3.1 22.8 - - - +
267A LEU* 5.9 2.5 - - - -
271A TYR* 3.1 42.4 - - + +
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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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167A ARG* 3.1 40.7 + - - +
228A GLU 2.9 19.7 + - - +
229A GLY* 3.9 5.4 - - - +
231A MET* 1.3 78.2 - - - +
233A ILE* 1.3 72.5 + - - +
236A PRO* 3.5 4.8 - - - +
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Residues in contact with ILE 233 (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 VAL* 3.5 29.5 - - + +
152A ARG* 3.8 37.7 - - - +
165A GLU 5.0 0.7 - - - +
167A ARG* 3.4 27.3 - - + +
225A ILE* 4.1 17.3 - - + -
229A GLY* 2.8 19.9 + - - +
232A ASN* 1.3 95.7 - - - +
234A HIS* 1.3 78.0 + - + +
235A MET 3.6 0.9 - - - -
236A PRO* 3.7 2.7 - - - +
237A ALA 5.7 0.2 + - - -
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Residues in contact with HIS 234 (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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148A ILE 5.1 2.9 - - - +
150A VAL* 3.9 29.1 - - + +
152A ARG* 4.0 15.2 - - + +
209A VAL* 3.7 13.1 - - + +
210A GLY* 3.6 30.4 + - - +
211A ASP* 5.9 0.2 - - - -
212A GLY 4.5 0.2 - - - -
213A GLY* 3.6 29.2 - - - -
223A THR* 4.4 11.7 - - + -
225A ILE* 4.4 13.0 - - + -
230A LEU* 3.1 29.9 + - + +
233A ILE* 1.3 91.6 - - + +
235A MET* 1.3 59.9 + - - +
236A PRO 3.8 0.2 - - - -
237A ALA* 5.0 3.2 + - - +
238A TYR* 3.7 12.3 - - - -
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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