Contacts of the helix formed by residues 228 - 233 (chain A) in PDB entry 5MJ3
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 PHE 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A GLU* 3.6 27.6 - - + +
205A SER* 3.7 20.4 - - - -
206A LEU 3.5 29.4 - - - -
207A PRO* 3.6 12.8 - - + -
227A PHE* 1.3 80.0 - - - +
229A ILE* 1.3 67.4 + - - +
230A ARG* 3.5 38.4 - - + -
231A ASP* 3.0 37.2 + - - +
232A ILE 3.5 6.8 + - - -
53B HIS* 5.2 0.2 + - - -
57B ARG* 3.9 28.7 - - - -
65B THR* 6.0 0.9 - - + -
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Residues in contact with ILE 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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133A ALA* 4.1 10.1 - - + -
135A ASN 4.0 21.1 - - - +
136A TYR* 4.5 14.4 - - + +
138A GLY* 3.7 35.4 - - - +
139A ARG 5.3 0.7 - - - +
140A PHE* 4.7 8.7 - - + -
160A ARG* 3.6 21.3 - - - +
195A GLU* 4.2 2.5 - - - +
204A GLU* 2.8 21.2 + - - +
208A ILE* 4.1 15.3 - - + -
227A PHE* 4.1 7.2 + - + -
228A PHE* 1.3 70.3 - - - +
230A ARG* 1.3 63.8 + - - +
232A ILE* 3.0 23.0 + - + +
233A ILE* 3.2 14.8 + - + +
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Residues in contact with ARG 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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136A TYR* 4.0 18.9 + - + +
203A GLU* 4.4 1.8 + - - +
204A GLU* 3.0 58.5 + - - +
228A PHE* 3.5 37.0 - - + +
229A ILE* 1.3 77.7 - - - +
231A ASP* 1.3 61.6 + - - +
233A ILE* 3.7 13.5 - - - +
315A TYR* 3.1 49.2 + - + +
317A SER* 3.5 20.3 + - - -
167B ARG 4.8 4.6 + - - -
168B SER* 5.3 3.8 - - - +
171B ALA* 3.3 30.1 - - - +
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Residues in contact with ASP 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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228A PHE* 3.0 36.2 + - - +
230A ARG* 1.3 79.3 - - - +
232A ILE* 1.3 59.8 - - - +
233A ILE 3.4 1.4 + - - +
315A TYR* 2.7 35.3 + - - -
316A SER 5.5 0.5 - - - +
317A SER* 4.5 10.2 - - - +
318A SER* 5.3 3.3 + - - -
45B TRP* 5.6 0.9 - - - -
53B HIS* 3.5 51.5 + - + +
57B ARG* 4.3 4.0 + - - -
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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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131A CYS* 3.5 21.8 - - + +
132A GLU* 3.4 37.1 - - - +
133A ALA* 3.0 19.6 + - + +
140A PHE* 4.0 11.0 - - + -
227A PHE* 3.4 50.5 - - + -
228A PHE 3.9 5.2 - - - +
229A ILE* 3.0 18.6 + - + +
231A ASP* 1.3 79.9 - - - +
233A ILE* 1.3 66.4 + - - +
234A LYS* 3.4 1.2 + - - +
318A SER* 5.5 1.7 + - - -
53B HIS* 4.2 11.0 - - + +
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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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133A ALA* 3.3 9.9 - - + +
135A ASN* 3.1 43.3 - - - +
136A TYR* 3.9 23.6 - - + +
229A ILE* 3.2 16.3 + - + +
230A ARG* 3.7 13.9 + - - +
231A ASP 3.4 2.2 - - - -
232A ILE* 1.3 77.7 - - - +
234A LYS* 1.3 66.0 + - - +
235A PRO* 4.1 6.3 - - + -
262A TRP* 3.8 26.2 - - + -
312A ASP* 4.9 2.0 - - + -
317A SER* 3.5 19.3 - - - +
318A SER* 3.1 27.9 + - - -
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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