Contacts of the helix formed by residues 213 - 220 (chain A) in PDB entry 2XJF
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 SER 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A LEU* 3.3 18.8 - - - +
207A TRP* 5.0 1.2 - - - -
208A VAL* 3.9 1.8 + - - +
212A GLY* 1.3 71.5 - - - -
214A LEU* 1.3 58.5 + - - +
215A LYS 3.5 2.0 - - - -
216A GLU* 3.4 24.4 + - - +
217A LYS* 2.8 58.4 + - - +
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Residues in contact with LEU 214 (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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65A TYR* 3.6 28.7 - - + +
68A LEU* 3.6 31.0 - - + -
69A GLY* 4.3 15.3 - - - +
72A LEU* 3.6 11.8 - - + +
208A VAL* 3.6 25.5 + - + +
209A HIS* 3.4 45.1 - - + +
212A GLY 3.5 2.8 - - - -
213A SER* 1.3 78.5 - - - +
215A LYS* 1.3 56.6 + - + +
217A LYS* 3.4 1.1 + - - -
218A THR* 2.6 36.7 + - - +
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Residues in contact with LYS 215 (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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208A VAL 5.0 1.0 + - - -
209A HIS* 3.2 40.8 + - + +
210A TYR* 4.6 11.4 - - - -
212A GLY 4.9 0.6 + - - -
213A SER 3.5 0.4 - - - -
214A LEU* 1.3 79.4 - - + +
216A GLU* 1.3 62.8 + - - +
218A THR* 3.2 6.4 + - - -
219A VAL* 3.1 30.6 + - - +
251A SER* 5.1 6.0 + - - +
252A ASP* 3.7 21.5 - - - +
255A TYR* 3.7 48.3 - - + -
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Residues in contact with GLU 216 (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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213A SER* 3.4 27.4 + - - +
215A LYS* 1.3 79.0 - - - +
217A LYS* 1.3 67.4 + - + +
219A VAL* 3.5 5.4 + - - +
220A GLU* 3.1 37.7 + - - +
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Residues in contact with LYS 217 (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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68A LEU* 3.9 34.5 - - + -
72A LEU* 3.9 12.3 - - + -
213A SER* 2.8 45.3 + - - +
214A LEU 3.9 2.5 - - - +
216A GLU* 1.3 77.2 + - + +
218A THR* 1.3 67.5 + - - +
220A GLU* 3.3 35.0 + - - +
221A ASN* 3.5 4.5 + - - +
225A TYR* 3.8 10.8 - - + -
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Residues in contact with THR 218 (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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60A TYR* 4.1 17.0 - - + -
65A TYR* 3.5 20.0 + - + -
68A LEU* 4.3 1.2 - - - +
214A LEU* 2.6 26.3 + - - +
215A LYS* 3.2 8.3 + - - -
217A LYS* 1.3 75.4 - - - +
219A VAL* 1.3 57.8 + - - +
221A ASN 3.0 30.8 + - - +
222A LEU* 3.3 16.4 + - + -
225A TYR* 3.9 22.6 - - + -
226A VAL* 4.4 0.2 - - + -
255A TYR* 3.8 19.4 + - + +
259A ILE* 4.5 1.3 - - + -
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Residues in contact with VAL 219 (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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215A LYS 3.1 16.6 + - - +
216A GLU* 4.0 4.9 - - - +
218A THR* 1.3 77.7 - - - +
220A GLU* 1.3 62.1 + - - +
221A ASN 3.4 0.3 + - - -
222A LEU* 3.7 24.6 + - + +
255A TYR* 4.0 21.5 - - + -
258A LYS* 3.9 49.8 - - + +
259A ILE* 4.5 8.5 - - + -
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Residues in contact with GLU 220 (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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216A GLU* 3.1 26.9 + - - +
217A LYS* 3.3 39.1 + - - +
219A VAL* 1.3 76.7 - - - +
221A ASN* 1.3 62.7 + - + +
222A LEU 4.0 0.2 - - - -
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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