Contacts of the helix formed by residues 215 - 225 (chain E) in PDB entry 4KYI
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 LEU 215 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214E THR* 1.3 75.7 - - - +
216E GLY* 1.3 62.3 + - - +
218E LEU* 3.2 24.8 + - + +
236E LEU* 3.8 40.8 - - + +
238E VAL* 5.8 0.7 - - + -
251E TYR 4.6 6.3 - - - +
252E SER 3.3 33.7 - - - +
253E GLU* 3.5 18.6 - - + +
256E THR* 3.8 7.2 - - - +
257E PRO 3.5 0.2 + - - -
259E GLN* 3.0 40.7 + - + +
260E SER 4.6 0.2 - - - +
261E ILE* 4.0 13.9 - - + -
264E VAL* 3.9 21.3 - - + -
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Residues in contact with GLY 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E LEU* 1.3 70.2 - - - +
217E ASP* 1.3 66.0 + - - +
218E LEU 3.2 0.2 - - - -
219E GLY* 3.2 11.2 + - - -
220E ARG* 3.3 20.2 + - - +
253E GLU* 4.1 8.1 - - - -
257E PRO* 2.7 38.4 + - - +
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Residues in contact with ASP 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E MET* 3.8 14.9 - - + +
152E LEU* 3.5 22.9 - - + +
155E LYS* 3.1 35.8 + - - +
209E GLU* 4.3 0.3 - - - +
213E LEU* 3.8 5.3 - - - +
214E THR* 3.0 31.8 + - - +
215E LEU 3.1 0.6 - - - -
216E GLY* 1.3 76.6 - - - +
218E LEU* 1.3 63.0 + - - +
219E GLY 3.2 0.2 - - - -
220E ARG* 2.7 36.9 + - - +
221E LEU* 3.1 23.0 + - - +
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Residues in contact with LEU 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E SER 5.8 0.9 - - - +
83E ALA* 4.4 9.4 - - + +
84E VAL* 4.5 14.8 - - + +
130E MET* 3.7 30.1 - - + -
214E THR 3.8 1.0 + - - -
215E LEU* 3.2 18.5 + - + +
216E GLY 3.2 0.6 - - - -
217E ASP* 1.3 79.2 - - - +
219E GLY* 1.3 60.1 + - - +
221E LEU* 3.6 5.1 + - + +
222E ARG* 3.2 19.0 + - - +
233E ILE* 3.3 35.7 - - + +
234E LYS 4.5 2.5 - - - +
236E LEU* 4.3 27.4 - - + +
253E GLU* 4.1 9.0 - - + +
261E ILE* 3.7 24.7 - - + -
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Residues in contact with GLY 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E LEU 3.9 2.2 + - - -
216E GLY 3.2 9.2 + - - -
217E ASP 3.2 0.6 - - - -
218E LEU* 1.3 77.3 - - - +
220E ARG* 1.3 62.8 + - - +
222E ARG* 3.2 9.3 + - - +
223E GLU* 3.0 36.6 + - - +
253E GLU* 3.6 21.3 + - - -
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Residues in contact with ARG 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E MET* 5.8 1.6 - - - -
148E ASN* 3.9 44.7 + - + +
151E ILE* 3.5 32.3 - - - +
152E LEU* 3.9 24.7 - - + -
209E GLU* 3.1 28.2 + - - +
216E GLY* 3.3 16.0 + - - +
217E ASP* 2.7 39.4 + - - +
219E GLY* 1.3 75.0 - - - +
221E LEU* 1.3 62.6 + - - +
223E GLU* 3.3 5.2 + - - +
224E LEU* 3.0 23.9 + - - +
258E GLN* 4.5 3.0 - - - +
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Residues in contact with LEU 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E MET* 4.0 38.4 - - + +
133E HIS* 3.9 41.3 - - + +
134E LEU* 4.4 11.9 - - + +
137E VAL* 5.4 0.7 - - + -
152E LEU* 3.7 16.2 - - + +
217E ASP 3.1 12.5 + - - +
218E LEU* 3.8 7.0 - - + +
220E ARG* 1.3 80.0 - - - +
222E ARG* 1.3 62.4 + - - +
224E LEU* 3.2 6.6 + - + +
225E LEU* 3.1 39.6 + - + +
233E ILE* 4.0 20.2 - - + -
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Residues in contact with ARG 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E THR 5.3 0.8 + - - -
218E LEU 3.2 9.8 + - - +
219E GLY* 3.6 10.0 + - - +
220E ARG 3.2 0.4 - - - -
221E LEU* 1.3 75.7 - - - +
223E GLU* 1.3 65.6 + - + +
224E LEU 3.0 1.6 - - - -
225E LEU* 3.1 18.1 + - - +
230E LYS* 3.3 61.2 - - + +
233E ILE* 2.6 46.4 + - + +
234E LYS 3.3 17.9 + - - -
235E ASN* 4.3 6.3 + - - +
253E GLU* 2.3 40.0 + - - -
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Residues in contact with GLU 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E GLN* 2.8 40.4 + - - +
148E ASN* 3.4 11.6 + - - -
219E GLY* 3.0 26.2 + - - +
220E ARG* 3.7 3.8 + - - +
222E ARG* 1.3 78.1 - - + +
224E LEU* 1.3 60.0 + - - +
225E LEU 3.3 5.0 + - - +
230E LYS* 4.1 16.6 + - - +
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Residues in contact with LEU 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E LEU* 3.5 32.1 - - + -
137E VAL* 3.6 27.5 - - + +
141E ILE* 4.5 7.2 - - + -
145E GLN* 3.3 40.2 - - + +
148E ASN* 4.5 4.7 - - + +
149E TYR* 3.7 30.1 - - + +
152E LEU* 4.3 12.1 - - + -
220E ARG 3.0 8.2 + - - +
221E LEU* 3.3 11.9 - - + +
222E ARG 3.0 0.4 - - - -
223E GLU* 1.3 78.2 - - - +
225E LEU* 1.3 58.8 + - - +
226E PRO* 4.1 1.6 - - - +
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Residues in contact with LEU 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E HIS* 3.6 21.8 - - + +
136E SER* 3.5 24.2 - - - +
137E VAL* 4.1 8.5 - - + -
221E LEU* 3.1 24.6 + - + +
222E ARG* 3.1 10.6 + - - +
223E GLU 3.9 1.4 - - - +
224E LEU* 1.3 81.4 - - - +
226E PRO* 1.3 83.5 - - + +
229E ASN* 3.9 26.5 - - + +
230E LYS* 3.2 22.0 - - + -
232E LEU* 5.0 4.3 - - + -
233E ILE* 4.0 23.8 - - + -
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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