Contacts of the helix formed by residues 226 - 230 (chain A) in PDB entry 3Q7I
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 ALA 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A PHE* 3.6 25.7 - - + -
217A LEU* 4.1 6.3 - - + -
218A LEU* 4.5 0.9 - - + -
221A TYR* 3.5 38.1 - - + -
223A ASP 3.1 16.2 + - - +
225A LYS* 1.3 75.4 - - - +
227A VAL* 1.3 64.5 + - - +
228A ALA 3.1 0.9 + - - -
229A ASN 3.1 10.3 + - - -
230A HIS* 3.3 17.0 + - - +
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Residues in contact with VAL 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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214A ARG* 4.2 25.8 - - + -
217A LEU* 4.1 11.2 - - + +
218A LEU* 4.2 19.5 - - + -
224A GLU* 3.1 18.4 + - + +
226A ALA* 1.3 77.2 - - - +
228A ALA* 1.3 63.2 + - - +
231A PHE* 3.1 43.0 + - + +
244A PHE* 5.7 2.2 - - + +
245A GLY* 4.0 21.1 - - - +
246A ILE* 4.4 9.4 - - + -
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Residues in contact with ALA 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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129A TRP* 3.9 2.1 - - - -
224A GLU 4.7 0.2 + - - -
225A LYS* 3.3 14.6 + - - +
226A ALA 3.1 1.0 - - - -
227A VAL* 1.3 80.2 - - - +
229A ASN* 1.3 65.6 + - - +
230A HIS 3.6 0.2 + - - -
231A PHE 4.2 0.3 - - - +
247A ASP* 6.1 0.4 - - - +
250A HIS* 2.8 44.7 + - + +
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Residues in contact with ASN 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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129A TRP* 2.9 30.9 + - - +
130A ARG* 2.9 21.7 + - - +
131A GLY* 3.6 8.3 + - - -
132A PHE* 3.4 45.4 - - - +
137A ILE* 4.8 1.6 - - - +
193A LEU* 4.0 2.3 - - - +
225A LYS 4.0 3.8 - - - +
226A ALA 3.1 2.2 + - - +
228A ALA* 1.3 81.4 - - - +
230A HIS* 1.3 69.5 + - + +
231A PHE 3.8 0.4 - - - -
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Residues in contact with HIS 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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131A GLY* 3.6 11.4 - - - -
132A PHE* 3.1 11.2 + - + -
137A ILE* 4.4 2.5 - - + -
189A PRO 3.0 19.5 + - - -
190A GLU 3.5 19.3 - - - -
192A THR 2.7 23.5 + - - +
193A LEU* 3.5 9.2 - - - -
194A LEU* 2.8 33.1 + - + +
217A LEU* 3.7 24.7 - - + -
221A TYR* 2.9 32.7 + + - -
226A ALA 3.3 21.3 - - - +
227A VAL 3.1 2.4 + - - +
229A ASN* 1.3 85.9 + - + +
231A PHE* 1.4 59.2 + - - +
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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