Contacts of the helix formed by residues 226 - 235 (chain A) in PDB entry 5I75
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 SER 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A CYS* 4.5 0.4 - - - -
210A THR 4.6 0.4 - - - -
220A TRP* 3.6 18.0 - - - -
225A THR* 1.4 73.8 - - - +
227A PRO* 1.3 60.2 - - - +
228A ALA* 4.0 0.7 + - - +
229A GLU* 3.1 27.6 + - - +
230A GLU* 2.7 37.2 + - - +
408A ILE* 4.5 2.9 - - - +
412A GLU* 3.4 29.7 + - - -
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Residues in contact with PRO 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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197A TRP* 3.7 15.7 - - - +
198A THR 3.6 6.7 - - - +
199A SER 3.4 24.9 - - - +
200A CYS* 4.0 7.4 - - - -
204A TRP* 5.1 0.5 + - - -
205A ASN* 4.0 3.9 + - - +
209A CYS* 3.8 10.7 - - - -
210A THR 3.2 23.6 - - - +
211A ASN* 3.5 20.6 - - + -
226A SER* 1.3 87.5 - - - +
228A ALA* 1.3 57.1 + - - +
230A GLU* 3.8 0.9 - - - +
231A PHE* 2.9 29.3 + - - +
412A GLU* 4.2 9.0 - - + +
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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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186A TYR* 4.6 1.4 + - - -
197A TRP* 3.8 20.1 + - + +
226A SER* 3.1 1.0 - - - -
227A PRO* 1.3 78.9 - - - +
229A GLU* 1.3 59.3 + - - +
231A PHE* 3.1 2.9 + - - +
232A TYR* 2.9 30.8 + - - +
407A PHE 4.8 2.7 - - - +
408A ILE* 3.8 20.3 - - + +
412A GLU* 3.6 39.9 - - + +
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Residues in contact with GLU 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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220A TRP* 5.0 2.6 - - - -
224A SER 4.7 1.0 - - - +
225A THR* 3.6 28.1 - - + +
226A SER* 3.1 30.7 + - - +
228A ALA* 1.3 78.2 - - - +
230A GLU* 1.3 57.6 + - - +
232A TYR* 4.1 0.2 - - - +
233A THR* 2.8 46.6 + - - +
408A ILE* 3.6 27.7 - - + +
566A PHE* 6.0 2.5 - - + -
567A GLN* 5.9 1.4 + - - +
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Residues in contact with GLU 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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204A TRP* 3.9 4.6 - - - -
205A ASN* 3.2 31.6 - - - +
206A THR* 2.8 43.0 + - - -
208A ASN* 4.8 0.2 - - - +
209A CYS* 4.0 7.0 - - - -
225A THR* 2.4 34.4 + - - +
226A SER 2.7 23.2 + - - +
227A PRO 3.8 0.9 - - - +
229A GLU* 1.3 72.9 - - - +
231A PHE* 1.3 56.7 + - - +
233A THR* 4.7 2.7 - - - -
234A ARG* 2.9 49.8 + - - +
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Residues in contact with PHE 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 TYR* 5.1 4.0 - + - -
186A TYR* 3.4 48.7 - + - -
189A SER* 4.5 13.5 - - - -
196A PRO* 3.5 31.2 - - + -
197A TRP* 3.6 28.7 - + + -
204A TRP* 3.5 31.2 - + - +
227A PRO 2.9 19.3 + - - +
228A ALA 3.1 4.6 + - - +
230A GLU* 1.3 77.7 - - - +
232A TYR* 1.3 59.1 + - - +
235A HIS* 3.2 52.7 + + - +
236A VAL* 3.4 6.6 + - + +
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Residues in contact with TYR 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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182A TRP* 3.3 39.8 - + - -
186A TYR* 3.2 20.8 + + - +
228A ALA 2.9 14.3 + - - +
231A PHE* 1.3 78.0 - - - +
233A THR* 1.3 62.4 + - - +
236A VAL* 3.5 16.4 - - + -
237A LEU* 3.1 51.7 + - + +
403A PRO* 4.0 8.4 - - + +
404A SER* 3.9 11.0 - - - -
407A PHE* 4.2 22.0 - + + -
408A ILE* 3.6 33.2 - - + -
486A ALA* 5.3 1.7 - - - +
566A PHE* 3.6 25.9 - + - -
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Residues in contact with THR 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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229A GLU* 2.8 33.0 + - - +
230A GLU* 4.3 1.1 - - - -
232A TYR* 1.3 79.5 - - - +
234A ARG* 1.3 70.4 + - + +
237A LEU* 4.7 3.1 - - - -
238A GLN 3.0 5.0 + - - -
239A ILE* 2.9 51.6 + - + +
240A HIS* 4.1 6.8 + - + +
408A ILE* 4.8 0.5 - - - +
566A PHE* 4.6 18.8 - - + -
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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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204A TRP* 2.8 40.1 + - + +
206A THR* 3.6 23.0 - - - +
230A GLU* 2.9 38.5 + - - +
233A THR* 1.3 90.1 - - + +
235A HIS* 1.3 60.6 + - - +
238A GLN* 3.9 8.0 + - - +
240A HIS* 3.3 66.9 + - + +
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Residues in contact with HIS 235 (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 TYR* 3.0 42.9 + + - -
189A SER* 5.4 1.2 + - - -
203A SER* 5.6 0.2 - - - -
204A TRP* 3.3 46.7 - + + +
230A GLU 3.9 0.2 + - - -
231A PHE* 3.2 43.4 + + + +
233A THR 3.6 0.4 - - - -
234A ARG* 1.3 80.6 - - - +
236A VAL* 1.3 67.6 + - - +
238A GLN* 4.0 14.6 - - - +
254A GLN* 6.1 0.3 - - - -
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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