Contacts of the helix formed by residues 226 - 234 (chain A) in PDB entry 3JXI
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 THR 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A ILE 4.5 8.5 - - - -
214A ASN* 3.7 30.4 + - + +
215A SER 4.2 4.5 - - - +
216A PRO* 4.5 2.5 - - + -
217A PHE* 3.8 8.9 - - - -
224A GLY 3.6 11.2 - - - +
225A GLN* 1.3 78.8 - - - +
227A ALA* 1.3 65.7 + - - +
228A LEU* 3.1 18.0 + - - +
229A HIS* 3.2 26.2 + - - +
230A ILE* 3.3 12.8 + - - +
249A ASP 4.9 0.9 + - - -
252A ALA* 3.9 22.2 - - + +
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Residues in contact with ALA 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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181A LEU* 3.5 35.7 - - + -
182A PRO* 4.8 7.8 - - + +
185A LEU* 3.5 23.9 - - + +
213A ILE 4.0 9.1 + - - +
215A SER 4.9 1.8 + - - -
217A PHE* 4.3 2.2 - - - -
226A THR* 1.3 73.7 - - - +
228A LEU* 1.3 55.6 + - - +
230A ILE* 3.2 12.1 + - - +
231A ALA* 2.9 25.5 + - - +
243A LEU* 3.8 7.9 - - + -
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Residues in contact with LEU 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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213A ILE* 5.2 1.0 + - - +
214A ASN* 6.1 0.2 - - - +
226A THR* 3.1 11.6 + - - +
227A ALA* 1.3 74.2 - - - +
229A HIS* 1.3 66.6 + - - +
231A ALA* 3.2 1.6 + - - +
232A ILE* 3.0 41.4 + - + +
240A VAL* 3.9 43.5 - - + +
243A LEU* 3.9 11.7 - - + +
244A VAL* 4.1 10.3 - - + -
248A ALA* 3.8 22.7 - - + -
249A ASP 3.5 23.3 - - - +
250A VAL* 4.0 14.8 - - + -
274A PRO* 4.1 12.3 - - + -
290A LEU* 5.0 2.9 - - + -
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Residues in contact with HIS 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 GLN* 3.8 8.2 - - + +
226A THR* 3.2 34.0 + - - +
228A LEU* 1.3 78.2 - - - +
230A ILE* 1.3 62.0 + - + +
232A ILE* 3.3 3.0 + - - -
233A GLU* 2.9 25.8 + - - +
252A ALA* 3.3 34.5 + - + -
253A GLN 4.1 1.1 - - - -
254A ALA* 3.7 25.7 + - + -
270A PHE* 4.4 5.6 - + + -
272A GLU 3.0 23.4 + - - -
274A PRO* 3.9 16.5 - - + +
277A LEU* 3.6 26.0 - - + +
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Residues in contact with ILE 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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182A PRO* 3.5 44.4 - - + +
185A LEU* 4.0 16.6 - - + +
186A LEU* 3.8 26.5 - - + -
217A PHE* 3.6 24.5 - - + -
225A GLN* 6.0 0.2 - - - +
226A THR 3.3 5.1 + - - +
227A ALA* 3.2 9.5 + - - +
229A HIS* 1.3 76.9 - - + +
231A ALA* 1.3 55.9 + - - +
233A GLU* 3.3 8.0 + - + +
234A ARG* 2.8 56.5 + - + +
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Residues in contact with ALA 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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185A LEU* 4.4 7.4 - - + +
227A ALA 2.9 16.0 + - - +
228A LEU 3.2 5.1 + - - +
230A ILE* 1.3 78.1 - - - +
232A ILE* 1.3 54.9 + - - +
234A ARG* 3.8 2.2 + - - -
235A ARG 3.2 4.0 + - - -
236A CYS* 2.7 39.3 + - - +
239A TYR* 4.1 14.4 - - + -
240A VAL* 3.8 28.7 - - + +
243A LEU* 4.2 9.4 - - + -
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Residues in contact with ILE 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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228A LEU* 3.0 28.7 + - + +
229A HIS* 3.7 4.0 - - - +
231A ALA* 1.3 74.2 - - - +
233A GLU* 1.3 61.2 + - - +
235A ARG* 2.8 16.5 + - - -
240A VAL* 3.8 19.5 - - + -
274A PRO* 3.4 40.6 - - + +
277A LEU* 3.8 22.2 - - + -
278A ALA* 3.9 16.8 - - + -
283A GLN* 2.9 33.4 + - - +
286A ILE* 4.1 9.2 - - + -
290A LEU* 4.1 11.4 - - + -
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Residues in contact with GLU 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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186A LEU* 6.5 0.4 - - + -
229A HIS 2.9 17.3 + - - +
230A ILE* 4.0 10.1 - - + +
232A ILE* 1.3 78.6 - - - +
234A ARG* 1.3 77.0 + - + +
235A ARG* 3.2 12.5 + - - +
277A LEU* 4.2 16.1 - - + +
281A THR* 5.5 9.1 - - - +
283A GLN* 4.8 2.1 + - - +
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Residues in contact with ARG 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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185A LEU 2.9 29.3 + - - +
186A LEU* 3.5 33.5 + - - +
188A LEU* 3.8 24.9 + - - +
230A ILE* 2.8 37.6 + - + +
231A ALA* 4.7 0.4 - - - -
233A GLU* 1.3 84.7 - - + +
235A ARG* 1.3 71.2 + - - +
236A CYS* 3.4 22.3 + - - -
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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