Contacts of the helix formed by residues 228 - 236 (chain A) in PDB entry 3QK2
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 LYS 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A SCN 3.3 26.9 - - - -
144A SER 3.9 11.4 - - - +
145A PHE* 3.0 38.2 + - + +
226A VAL* 3.8 1.6 - - - -
227A ASN* 1.3 92.1 - - - +
229A GLU* 1.3 64.0 + - - +
231A LEU* 4.2 7.6 - - + -
232A MET* 3.0 23.7 + - - +
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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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1A SCN 3.4 5.5 - - - -
158A CYS* 3.5 35.9 - - + +
196A PHE* 3.6 11.7 - - + -
198A LEU* 4.6 5.1 - - + +
226A VAL* 3.8 14.3 - - - +
227A ASN 3.3 15.3 - - - +
228A LYS* 1.3 72.1 - - - +
230A TYR* 1.3 63.3 + - - +
233A TYR* 3.1 18.9 + - - +
257A PHE* 3.5 23.9 - - + -
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Residues in contact with TYR 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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1A SCN 3.6 13.8 - - - -
228A LYS 3.5 0.4 - - - -
229A GLU* 1.3 75.7 - - - +
231A LEU* 1.3 83.6 + - + +
232A MET 3.2 0.2 + - - -
233A TYR* 3.3 4.4 + + - +
234A SER* 2.8 54.9 + - - -
252A LEU 5.5 0.9 - - - -
253A LYS* 4.1 4.7 - - - -
254A GLU* 3.5 48.9 + - + +
257A PHE* 3.7 46.5 - + + -
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Residues in contact with LEU 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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1A SCN 3.8 28.3 - - - +
145A PHE* 3.7 36.7 - - + -
228A LYS* 3.5 11.3 + - + +
229A GLU 3.4 0.4 - - - -
230A TYR* 1.3 97.2 - - + +
232A MET* 1.3 56.7 + - - +
234A SER* 3.9 4.2 - - - -
235A ALA* 2.9 31.2 + - - +
238A ARG* 5.2 1.4 + - - +
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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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138A PHE* 4.0 13.7 - - + -
142A LEU* 4.0 22.7 - - + -
145A PHE* 3.7 23.4 - - + -
146A LEU* 3.7 29.4 - - + -
160A ALA* 3.7 20.6 - - + -
194A ILE* 4.7 0.7 - - + -
196A PHE* 3.8 17.0 - - + -
226A VAL* 3.7 14.8 - - + -
228A LYS 3.0 19.0 + - - +
229A GLU 3.6 4.0 - - - +
230A TYR 3.1 0.2 - - - -
231A LEU* 1.3 73.8 - - - +
233A TYR* 1.3 66.6 + - - +
235A ALA* 3.2 3.1 + - - +
236A LEU* 3.0 41.2 + - + +
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Residues in contact with TYR 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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183A PHE* 3.7 8.7 - + - -
185A SER* 3.6 24.2 - - - -
187A HIS* 4.2 9.4 - + - -
196A PHE* 3.7 27.1 - + + -
229A GLU 3.1 15.0 + - - +
230A TYR* 4.0 4.9 - + - +
232A MET* 1.3 79.1 - - - +
234A SER* 1.3 69.9 + - - +
236A LEU* 3.1 15.8 + - - +
237A THR* 3.3 31.5 + - + +
243A VAL* 4.6 0.9 - - - +
246A GLU* 2.6 31.4 + - - -
251A GLY* 3.4 2.8 - - - -
252A LEU* 3.3 49.1 + - + -
257A PHE* 4.6 8.3 - + + -
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Residues in contact with SER 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 TYR* 2.8 53.9 + - - -
231A LEU* 3.9 5.6 - - - -
233A TYR* 1.3 79.5 - - - +
235A ALA* 1.3 61.7 + - - +
237A THR* 2.7 27.7 + - - -
238A ARG* 3.0 25.0 + - - +
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Residues in contact with ALA 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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141A GLU 5.7 0.2 - - - +
142A LEU* 3.8 21.8 - - + -
145A PHE* 3.8 10.1 - - + -
231A LEU 2.9 19.6 + - - +
232A MET 3.2 4.2 + - - +
234A SER* 1.3 76.7 - - - +
236A LEU* 1.3 57.2 + - - +
237A THR 3.1 4.2 + - - -
238A ARG* 3.2 46.8 + - - +
239A ASP 5.0 0.2 - - - +
241A PHE* 3.4 10.7 - - + -
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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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142A LEU* 3.7 28.7 - - + -
187A HIS* 2.8 53.1 + - + +
194A ILE* 3.8 29.6 - - + -
196A PHE* 4.0 16.2 - - + -
232A MET* 3.0 37.3 + - + +
233A TYR* 3.1 7.1 + - - +
235A ALA* 1.3 75.3 - - - +
237A THR* 1.3 56.4 + - - +
238A ARG 3.5 0.4 - - - -
241A PHE* 3.4 27.1 - - + +
242A SER 3.4 7.1 + - - -
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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