Contacts of the helix formed by residues 224 - 240 (chain A) in PDB entry 3SKU
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 ILE 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A LEU* 5.5 0.4 - - + -
29A THR* 3.8 9.0 - - - +
30A ASP* 3.2 41.5 - - - +
31A PRO* 5.9 0.4 - - + -
36A ARG* 3.2 41.7 - - + +
132A GLN* 5.6 1.8 - - + -
133A PRO* 4.0 4.9 - - + -
222A ARG 3.8 1.1 + - - +
223A PHE* 1.3 78.0 - - - +
225A PRO* 1.3 79.5 - - + +
226A GLU* 3.1 7.0 + - + +
227A ASN* 3.0 38.6 + - - +
228A GLN* 3.4 4.0 + - - +
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Residues in contact with PRO 225 (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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36A ARG* 3.7 15.0 - - - +
113A MET* 4.5 15.3 - - - -
115A TYR* 5.6 2.5 - - - +
133A PRO* 4.1 9.4 - - + -
144A VAL* 3.9 13.0 - - + +
148A ASN* 3.7 27.8 - - - +
223A PHE 3.8 0.8 - - - +
224A ILE* 1.3 91.5 - - + +
226A GLU* 1.3 62.8 + - - +
228A GLN* 3.2 19.6 - - + +
229A ARG* 3.3 23.2 + - - +
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Residues in contact with GLU 226 (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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28A LEU* 3.6 32.4 - - + +
146A GLU* 3.0 23.4 - - - +
224A ILE* 3.1 7.9 + - + +
225A PRO* 1.3 76.6 - - - +
227A ASN* 1.3 66.0 + - - +
229A ARG* 2.7 58.9 + - - +
230A THR* 3.5 8.9 + - - +
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Residues in contact with ASN 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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28A LEU* 2.8 46.8 + - + +
223A PHE* 3.7 29.1 - - + -
224A ILE* 3.0 35.2 + - - +
226A GLU* 1.3 72.6 - - - +
228A GLN* 1.3 68.4 + - - +
230A THR* 2.9 19.8 + - - -
231A VAL* 3.0 18.3 + - + +
129D PHE* 5.6 7.8 - - + +
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Residues in contact with GLN 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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135A TRP* 3.3 40.2 - - + +
139A ASP* 3.5 25.6 - - - +
142A SER 3.6 8.7 + - - +
143A ALA* 3.2 22.4 - - + -
222A ARG* 4.3 3.5 - - - +
223A PHE* 3.8 33.4 + - + +
224A ILE 3.4 9.7 + - - +
225A PRO* 3.2 14.5 + - + +
227A ASN* 1.3 76.5 - - - +
229A ARG* 1.3 56.5 + - - +
230A THR 2.8 0.9 + - - -
231A VAL* 3.0 5.5 + - - +
232A ALA* 2.7 36.8 + - - +
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Residues in contact with ARG 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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143A ALA* 4.1 14.1 - - + -
144A VAL* 3.5 33.3 + - - +
145A SER* 2.8 33.9 + - - +
146A GLU* 3.9 19.7 + - - +
148A ASN* 4.3 1.4 + - - +
152A LEU* 5.6 8.1 - - + -
154A HIS* 4.5 2.4 + - - -
225A PRO* 3.3 12.6 + - - +
226A GLU* 2.7 65.2 + - - +
227A ASN 3.2 0.6 - - - -
228A GLN* 1.3 78.6 - - - +
230A THR* 1.3 57.1 + - - +
232A ALA* 4.0 3.5 + - - +
233A VAL* 3.0 27.5 + - - +
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Residues in contact with THR 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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26A ASP 6.1 0.7 - - - +
28A LEU* 5.0 7.1 - - - +
226A GLU* 3.5 10.6 + - - -
227A ASN* 2.9 13.9 + - - -
228A GLN 2.8 0.8 + - - -
229A ARG* 1.3 74.0 - - - +
231A VAL* 1.3 58.8 + - + -
232A ALA 3.0 1.3 - - - -
233A VAL* 2.6 38.9 + - + +
234A TYR* 2.8 17.6 + - + +
130D PRO 5.9 0.4 - - - +
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Residues in contact with VAL 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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140A SER 4.9 3.5 - - - +
223A PHE* 4.8 15.0 - - + -
227A ASN* 3.0 12.8 + - + +
228A GLN* 3.0 7.4 + - - +
230A THR* 1.3 77.5 - - - +
232A ALA* 1.3 57.9 + - - +
233A VAL 3.2 4.0 + - - -
234A TYR* 3.3 9.9 + - - -
235A SER* 3.9 9.3 + - - +
236A LEU 5.2 0.3 + - - -
128D THR 5.0 2.2 - - - +
129D PHE 3.3 14.8 - - - +
130D PRO* 2.6 35.4 - - + +
131D THR* 3.9 1.3 - - - +
132D GLY* 3.2 31.9 - - - +
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Residues in contact with ALA 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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139A ASP 4.9 4.7 - - - +
140A SER 4.5 9.4 - - - +
141A PHE* 3.8 14.1 - - - +
142A SER 3.0 41.1 - - - +
154A HIS* 3.3 18.9 - - + +
228A GLN* 2.7 19.8 + - + +
229A ARG* 4.1 5.8 - - - +
231A VAL* 1.3 76.6 - - - +
233A VAL* 1.3 57.1 + - + +
236A LEU* 4.5 6.9 - - - +
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Residues in contact with VAL 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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154A HIS* 3.1 31.4 - - + +
229A ARG 3.0 18.6 - - - +
230A THR* 2.6 32.9 + - + +
231A VAL 3.9 0.2 - - - -
232A ALA* 1.3 71.2 - - - +
234A TYR* 1.3 62.3 + - + +
235A SER 3.7 1.1 - - - -
236A LEU* 3.3 12.0 - - - +
237A LYS* 2.8 49.4 + - + +
241A TRP* 4.8 8.0 - - + -
244A PRO* 4.9 14.6 - - + -
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Residues in contact with TYR 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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25A LEU* 5.9 2.9 - - - +
230A THR* 2.8 22.8 + - + +
231A VAL* 3.3 3.1 + - - -
233A VAL* 1.3 73.9 - - + +
235A SER* 1.3 66.0 + - - +
236A LEU 3.0 1.3 - - - -
237A LYS* 3.0 21.3 + - + +
238A ILE* 3.1 38.1 + - + +
59D SER* 5.4 3.3 + - - -
130D PRO* 3.2 39.3 - - + +
131D THR* 2.2 33.0 + - - -
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Residues in contact with SER 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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231A VAL 3.9 6.8 + - - -
234A TYR* 1.3 80.3 - - - +
236A LEU* 1.3 58.1 + - - +
238A ILE* 3.0 38.2 - - - +
239A ALA* 3.7 8.5 + - - +
131D THR* 3.8 19.0 - - - +
132D GLY* 4.5 13.5 - - - -
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Residues in contact with LEU 236 (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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140A SER 5.7 1.1 - - - +
141A PHE* 4.6 6.3 - - + -
154A HIS* 4.3 23.6 - - + -
155A ALA* 4.5 11.4 - - + +
191A TYR* 3.3 34.2 - - + +
192A ALA* 5.4 0.4 - - - -
193A LEU* 3.4 33.8 - - + +
231A VAL 5.2 0.6 + - - -
232A ALA 4.5 9.2 - - - +
233A VAL* 3.3 12.3 - - - +
234A TYR 3.0 0.4 - - - -
235A SER* 1.3 76.4 - - - +
237A LYS* 1.3 66.0 + - - +
239A ALA* 3.0 18.6 + - + +
240A GLY 3.2 7.1 + - - -
241A TRP* 3.5 30.9 + - + +
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Residues in contact with LYS 237 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A VAL* 2.8 34.7 + - + +
234A TYR* 3.0 15.0 + - + +
236A LEU* 1.3 74.8 - - - +
238A ILE* 1.3 56.4 + - + +
240A GLY* 2.7 28.9 + - - -
241A TRP* 3.4 20.6 + - + +
243A GLY 2.6 33.8 + - - +
244A PRO* 3.4 14.1 - - - +
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Residues in contact with ILE 238 (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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234A TYR* 3.1 33.1 + - + +
235A SER* 3.0 44.6 - - - +
237A LYS* 1.3 78.7 - - + +
239A ALA* 1.3 61.8 + - + +
240A GLY* 3.3 1.0 + - - -
131D THR* 4.8 11.2 - - + +
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Residues in contact with ALA 239 (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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191A TYR* 3.5 25.3 + - + -
193A LEU* 6.4 1.8 - - + -
235A SER 3.8 10.1 - - - +
236A LEU* 3.0 15.8 + - + +
237A LYS 2.9 1.0 + - - -
238A ILE* 1.3 81.7 - - + +
240A GLY* 1.3 56.8 + - - +
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Residues in contact with GLY 240 (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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191A TYR* 3.2 29.2 + - - -
236A LEU 3.2 1.0 + - - -
237A LYS 2.7 16.2 + - - -
238A ILE 4.2 1.6 - - - -
239A ALA* 1.3 74.4 - - - +
241A TRP* 1.3 64.5 + - - +
242A HIS* 3.8 6.2 + - - -
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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