Contacts of the helix formed by residues 228 - 240 (chain A) in PDB entry 3K5N
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
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Residue Dist Surf HB Arom Phob DC
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157A ILE* 3.7 26.2 - - + -
159A THR* 3.4 26.0 - - + -
163A GLY* 5.4 1.6 - - - -
224A ASN* 3.4 26.8 + - + +
227A GLN* 1.3 82.6 - - - +
229A ASP* 1.3 91.6 + - - +
230A LEU 3.6 1.1 - - - -
231A ARG* 6.3 0.4 - - - -
232A MET* 2.8 54.5 + - - +
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Residues in contact with ASP 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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155A ILE* 4.1 18.7 - - + +
156A ASP* 4.2 10.7 - - - +
157A ILE* 3.3 30.5 + - + +
223A TRP 3.7 18.0 + - - +
224A ASN 3.6 2.4 + - - +
225A VAL* 3.0 28.1 + - + +
228A PHE* 1.3 105.0 - - - +
230A LEU* 1.3 62.8 + - + +
232A MET* 3.9 1.2 - - - +
233A LEU* 3.1 29.1 + - + +
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Residues in contact with LEU 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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155A ILE* 5.0 12.3 - - + -
220A ILE* 5.2 10.5 - - + -
225A VAL* 2.5 26.3 + - + +
226A VAL* 4.3 12.3 - - + -
229A ASP* 1.3 72.5 - - + +
231A ARG* 1.3 67.7 + - - +
233A LEU* 2.8 23.1 + - + +
234A GLN* 2.9 13.3 + - - +
246A LEU* 3.7 28.0 - - + -
253A LEU* 4.2 16.2 - - + +
255A TRP* 3.9 13.5 - - + -
267A ALA* 4.7 2.0 - - + -
274A ILE* 3.8 39.7 - - + -
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Residues in contact with ARG 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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226A VAL 2.9 24.2 + - - +
227A GLN* 3.1 43.7 + - - +
228A PHE* 6.3 0.6 - - - -
229A ASP 3.4 0.2 - - - -
230A LEU* 1.3 77.5 - - - +
232A MET* 1.3 79.7 + - - +
234A GLN* 3.0 18.6 + - + +
235A LYS* 3.4 22.8 + - + +
255A TRP* 3.6 21.5 - - + -
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Residues in contact with MET 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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157A ILE* 4.4 13.7 - - + -
162A HIS 5.0 1.6 - - - +
163A GLY* 3.5 36.8 - - - +
228A PHE* 2.8 42.4 + - + +
229A ASP 3.9 2.0 - - - +
231A ARG* 1.3 92.0 - - - +
233A LEU* 1.3 61.4 + - - +
235A LYS* 2.5 60.6 + - + +
236A HIS* 2.8 28.3 + - + -
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Residues in contact with LEU 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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155A ILE* 5.1 5.4 - - + -
157A ILE* 4.3 28.3 - - + -
165A LEU* 4.1 26.0 - - + -
168A ILE* 4.9 2.9 - - + -
205A LEU* 4.4 13.4 - - + +
208A LEU* 3.8 26.9 - - + -
229A ASP 3.1 15.2 + - - +
230A LEU* 2.8 27.6 + - + +
232A MET* 1.3 82.2 - - - +
234A GLN* 1.3 60.2 + - - +
235A LYS 3.2 0.5 + - - -
236A HIS* 3.2 13.4 + - - +
237A ALA* 3.2 13.2 + - - +
244A LEU* 4.2 14.5 - - + +
246A LEU* 5.4 1.6 - - + -
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Residues in contact with GLN 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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230A LEU 2.9 10.4 + - - +
231A ARG* 3.0 10.3 + - + +
233A LEU* 1.3 76.6 - - - +
235A LYS* 1.3 53.0 + - - +
237A ALA* 5.4 0.8 - - + +
238A GLU* 2.4 66.8 + - + +
244A LEU* 4.0 23.3 - - + +
252A GLU* 4.9 6.7 + - - -
253A LEU* 3.9 16.7 + - - -
254A GLU* 5.6 0.2 - - - +
255A TRP* 2.1 49.0 + - + +
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Residues in contact with LYS 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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162A HIS 5.2 4.0 + - - -
231A ARG* 3.4 22.0 + - - +
232A MET* 2.5 47.7 + - + +
234A GLN* 1.3 78.5 - - - +
236A HIS* 1.3 58.4 + - + +
238A GLU* 3.4 10.3 - - - +
239A ARG* 2.5 39.1 + - + +
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Residues in contact with HIS 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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163A GLY 3.7 17.3 + - - -
164A GLU* 3.7 7.6 - - + +
165A LEU* 3.5 51.1 + - + +
201A ARG* 4.7 5.4 - - + -
205A LEU* 3.9 11.9 - - + -
232A MET* 2.8 29.5 + - + -
233A LEU* 3.8 6.5 + - - +
234A GLN 3.2 0.4 - - - -
235A LYS* 1.3 80.2 - - + +
237A ALA* 1.3 54.2 + - - +
239A ARG* 2.8 4.6 + - - -
240A TYR* 2.7 68.1 + + + -
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Residues in contact with ALA 237 (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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205A LEU* 4.2 8.6 - - + +
233A LEU 3.2 4.9 + - - +
234A GLN* 3.2 7.0 + - + +
236A HIS* 1.3 78.1 - - - +
238A GLU* 1.3 62.5 + - - +
239A ARG 3.2 0.3 + - - -
241A ARG* 3.2 2.3 + - - -
242A LEU* 2.7 56.3 + - + +
244A LEU* 3.6 39.3 - - + -
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Residues in contact with GLU 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 GLN* 2.4 61.9 + - + +
235A LYS* 3.4 8.7 - - - +
237A ALA* 1.3 71.3 - - - +
239A ARG* 1.3 64.3 + - - +
241A ARG* 3.8 9.2 + - - +
242A LEU 4.7 0.2 - - - -
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Residues in contact with ARG 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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235A LYS* 2.5 22.8 + - + +
236A HIS* 2.8 6.9 + - - +
238A GLU* 1.3 77.1 + - + +
240A TYR* 1.3 71.3 + - + +
241A ARG* 3.3 15.7 - - - +
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Residues in contact with TYR 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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201A ARG* 3.8 25.5 - - + +
202A PRO* 3.9 33.8 - - + +
205A LEU* 3.7 16.4 - - + -
236A HIS* 2.7 51.1 + + + +
239A ARG* 1.3 87.5 - - + +
241A ARG* 1.3 78.2 + - - +
242A LEU* 3.0 21.8 + - + +
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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