Contacts of the helix formed by residues 215 - 226 (chain L) in PDB entry 3CX5
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 215 (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* 5.1 0.7 - - - -
42L HIS* 5.2 1.6 - - - -
214L ILE* 1.3 74.7 - - - +
216L HIS* 1.3 69.7 + - - +
217L GLU* 3.2 39.7 + - + +
218L ASP* 3.2 39.0 + - - +
219L LEU* 3.2 22.3 + - - +
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Residues in contact with HIS 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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30L THR* 3.1 34.1 + - + +
32L LEU* 3.2 42.3 + - + +
38L VAL* 3.7 31.4 - - + +
40L THR* 2.9 39.5 + - + +
42L HIS* 5.9 0.8 - - - +
214L ILE 4.0 2.4 + - - -
215L LYS* 1.3 73.6 - - - +
217L GLU* 1.3 67.6 + - + +
219L LEU* 3.5 1.6 + - - +
220L VAL* 3.0 27.9 + - + +
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Residues in contact with GLU 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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215L LYS* 3.2 34.7 + - + +
216L HIS* 1.3 80.8 - - + +
218L ASP* 1.3 59.6 + - - +
220L VAL* 3.1 10.5 - - + +
221L ASN* 2.8 47.2 + - - +
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Residues in contact with ASP 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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113L THR* 5.6 10.5 - - + -
215L LYS* 3.2 41.8 + - + +
217L GLU* 1.3 77.1 - - - +
219L LEU* 1.3 55.8 + - - +
221L ASN* 3.9 5.3 + - - +
222L SER* 2.8 39.2 + - - +
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Residues in contact with LEU 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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38L VAL* 4.0 11.2 - - + -
40L THR* 3.4 27.8 - - + -
51L VAL* 4.0 16.4 - - + -
113L THR* 4.5 8.1 - - - +
117L LEU* 3.5 38.4 - - + -
208L VAL* 4.8 3.6 - - + -
209L VAL 4.4 4.9 - - - +
210L GLY* 3.9 21.5 - - - +
214L ILE* 5.8 5.8 - - + -
215L LYS 3.2 13.2 + - - +
216L HIS 3.9 3.4 - - - +
218L ASP* 1.3 77.0 - - - +
220L VAL* 1.3 64.1 + - - +
222L SER* 3.2 3.1 + - - -
223L ILE* 3.1 38.2 + - + +
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Residues in contact with VAL 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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32L LEU* 4.6 25.6 - - + -
34L ASN* 4.2 21.0 + - - +
38L VAL* 4.4 23.7 - - + +
216L HIS* 3.0 21.5 + - + +
217L GLU* 3.1 26.0 - - + +
219L LEU* 1.3 76.6 - - - +
221L ASN* 1.3 65.6 + - - +
223L ILE* 4.0 4.5 - - - +
224L GLU* 3.1 32.4 + - - +
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Residues in contact with ASN 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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217L GLU* 2.8 35.4 + - - +
218L ASP* 4.0 5.6 + - - +
220L VAL* 1.3 85.8 - - - +
222L SER* 1.3 59.1 + - - +
223L ILE 3.2 0.7 - - - -
224L GLU* 3.6 14.4 - - - +
225L SER* 2.8 27.7 + - - -
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Residues in contact with SER 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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113L THR* 5.9 1.6 - - - +
114L ASP* 3.8 20.1 + - - -
117L LEU* 3.5 24.2 - - - -
218L ASP* 2.8 25.3 + - - +
219L LEU* 3.2 1.0 + - - -
221L ASN* 1.3 77.3 - - - +
223L ILE* 1.3 58.9 + - - +
225L SER* 3.2 16.6 - - - -
226L LYS* 3.1 27.3 + - - +
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Residues in contact with ILE 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* 5.7 3.8 - - - +
36L ILE* 4.1 30.1 - - + -
38L VAL* 3.9 13.2 - - + -
117L LEU* 4.0 20.4 - - + -
208L VAL* 3.8 40.4 - - + -
219L LEU* 3.1 26.4 + - + +
220L VAL* 4.0 3.4 - - - +
222L SER* 1.3 74.6 - - - +
224L GLU* 1.3 62.1 + - - +
225L SER 3.0 6.0 + - - -
226L LYS* 3.3 23.1 + - - +
228L LEU* 4.9 7.6 - - + +
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Residues in contact with GLU 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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34L ASN* 3.7 35.4 + - - +
220L VAL* 3.1 19.9 + - - +
221L ASN* 3.6 17.4 - - - +
223L ILE* 1.3 77.8 - - - +
225L SER* 1.3 65.8 + - - +
226L LYS 3.1 9.2 - - - +
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Residues in contact with SER 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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221L ASN 2.8 14.2 + - - -
222L SER* 3.2 20.4 - - - -
223L ILE 3.0 0.2 - - - -
224L GLU* 1.3 78.7 - - - +
226L LYS* 1.3 67.6 + - - +
227L ASN* 4.0 6.9 + - - -
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Residues in contact with LYS 226 (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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114L ASP* 5.2 0.8 + - - +
117L LEU* 4.3 17.0 - - - +
118L ASP* 3.5 24.1 + - - -
121L ASN* 4.4 19.1 - - - +
222L SER* 3.1 28.4 + - - +
223L ILE* 3.3 13.4 + - - +
224L GLU* 3.1 15.0 - - - +
225L SER* 1.3 85.9 - - - +
227L ASN* 1.3 68.8 + - - +
228L LEU* 3.5 24.5 - - + -
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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