Contacts of the helix formed by residues 214 - 225 (chain L) in PDB entry 1KYO
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 214 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40L THR* 4.8 0.2 - - - -
42L HIS* 3.9 22.7 - - + +
212L ASN 3.5 5.2 + - - +
213L ILE* 1.3 84.9 - - - +
215L HIS* 1.3 65.9 + - - +
216L GLU* 4.5 5.4 - - + +
217L ASP* 3.6 31.6 + - + +
218L LEU* 3.7 8.0 + - - +
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Residues in contact with HIS 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L THR* 3.6 38.4 + - + +
31L GLN* 4.7 0.2 - - - -
32L LEU* 3.6 44.0 - - + +
38L VAL* 4.8 9.6 - - + +
40L THR* 2.8 33.7 + - + +
42L HIS* 4.2 15.0 + - + -
214L LYS* 1.3 71.6 - - - +
216L GLU* 1.3 77.9 + - + +
217L ASP 3.1 1.0 + - - -
218L LEU* 3.2 12.5 + - - +
219L VAL* 3.2 24.4 + - + +
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Residues in contact with GLU 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214L LYS* 3.6 4.3 - - + +
215L HIS* 1.3 89.7 - - + +
217L ASP* 1.3 62.2 + - - +
219L VAL* 3.6 13.2 - - + +
220L ASN* 2.9 37.6 + - - +
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Residues in contact with ASP 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L THR* 4.6 20.3 - - + +
213L ILE* 5.4 3.6 - - + -
214L LYS* 3.6 33.0 + - + +
215L HIS 3.1 0.8 - - - -
216L GLU* 1.3 80.0 - - - +
218L LEU* 1.3 61.4 + - - +
220L ASN* 4.3 1.6 - - - +
221L SER* 2.8 30.0 + - - -
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Residues in contact with LEU 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L VAL* 3.8 14.8 - - + -
40L THR* 3.4 29.2 - - + -
50L VAL* 4.0 24.9 - - + -
112L THR* 4.9 7.4 + - - +
116L LEU* 3.6 30.3 - - + -
207L VAL* 5.0 1.1 - - + -
208L VAL 4.4 3.6 - - - -
209L GLY* 4.2 15.7 - - - +
213L ILE* 4.4 7.9 - - + -
214L LYS 3.7 7.7 + - - +
215L HIS 3.2 6.9 + - - +
217L ASP* 1.3 76.2 - - - +
219L VAL* 1.3 66.9 + - - +
220L ASN 2.9 3.6 + - - -
221L SER* 3.0 3.3 + - - -
222L ILE* 2.9 35.7 + - + +
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Residues in contact with VAL 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L LEU* 5.0 19.5 - - + -
33L SER 5.0 4.9 - - - +
34L ASN* 3.7 21.7 + - - +
38L VAL* 5.0 13.3 - - + +
215L HIS* 3.2 30.0 + - + +
216L GLU* 3.6 21.1 - - + +
218L LEU* 1.3 78.5 - - - +
220L ASN* 1.3 67.8 + - - +
222L ILE* 3.8 8.2 + - - +
223L GLU* 3.2 28.9 + - - +
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Residues in contact with ASN 220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216L GLU* 2.9 28.7 + - - +
217L ASP* 4.3 1.6 - - - +
218L LEU 3.0 0.8 - - - -
219L VAL* 1.3 85.7 - - - +
221L SER* 1.3 59.9 + - - +
222L ILE 3.0 1.8 - - - -
223L GLU* 3.0 16.4 + - - +
224L SER* 2.9 28.9 + - - -
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Residues in contact with SER 221 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L THR* 5.9 0.5 - - - +
113L ASP* 2.9 30.5 + - - -
116L LEU* 3.7 18.1 - - - +
217L ASP 2.8 20.7 + - - -
218L LEU* 3.0 5.1 + - - -
220L ASN* 1.3 78.1 - - - +
222L ILE* 1.3 59.9 + - - +
224L SER* 3.4 17.7 - - - -
225L LYS* 3.5 17.9 + - - +
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Residues in contact with ILE 222 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L ASN* 5.5 4.3 - - + +
36L ILE* 4.6 21.3 - - + -
38L VAL* 3.7 18.4 - - + -
116L LEU* 4.0 21.5 - - + -
207L VAL* 3.6 34.5 - - + -
218L LEU* 2.9 35.5 + - + +
219L VAL 3.9 5.2 - - - +
221L SER* 1.3 76.3 - - - +
223L GLU* 1.3 59.7 + - - +
224L SER 3.0 9.7 + - - -
225L LYS* 3.3 19.8 + - - +
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Residues in contact with GLU 223 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L ASN* 2.9 34.3 + - - +
219L VAL* 3.2 16.2 + - - +
220L ASN* 3.0 19.4 + - - +
222L ILE* 1.3 77.4 - - - +
224L SER* 1.3 64.5 + - - +
225L LYS 4.5 2.0 - - - -
226L ASN* 4.3 20.3 + - - +
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Residues in contact with SER 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220L ASN 2.9 9.0 + - - -
221L SER* 3.4 19.5 - - - -
222L ILE 3.0 0.6 - - - -
223L GLU* 1.3 80.4 - - - +
225L LYS* 1.3 74.9 + - - +
226L ASN* 3.4 4.0 + - - +
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Residues in contact with LYS 225 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113L ASP* 4.4 12.1 + - - -
116L LEU* 4.8 11.5 - - - +
117L ASP* 3.3 27.3 + - - +
120L ASN* 5.9 11.4 - - + +
221L SER 3.5 20.8 + - - +
222L ILE* 3.3 16.4 + - - +
223L GLU* 4.5 0.6 - - - -
224L SER* 1.3 81.7 - - - +
226L ASN* 1.3 69.1 + - - +
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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