Contacts of the helix formed by residues 215 - 225 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214C THR* 1.3 75.1 - - - +
216C GLY* 1.3 62.6 + - - +
218C LEU* 3.2 23.1 + - + +
236C LEU* 3.7 46.2 - - + +
238C VAL* 5.1 6.1 - - + -
251C TYR* 5.0 7.4 - - + +
252C SER* 3.5 30.1 - - - +
253C GLU* 3.6 17.4 - - + +
256C THR 3.6 6.1 - - - +
257C PRO 4.2 0.2 + - - -
259C GLN* 3.0 41.0 + - + +
260C SER 4.1 9.6 - - - +
261C ILE* 4.3 13.7 - - + -
264C VAL* 4.7 7.0 - - + -
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Residues in contact with GLY 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C THR* 3.0 4.2 + - - -
215C LEU* 1.3 78.0 - - - +
217C ASP* 1.3 60.0 + - - +
219C GLY* 3.0 5.8 + - - -
220C ARG* 3.0 30.3 + - - +
253C GLU* 4.2 7.0 - - - -
257C PRO* 3.2 32.6 + - - +
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Residues in contact with ASP 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C MET* 4.0 10.7 - - + +
151C ILE* 4.8 0.6 - - - +
152C LEU* 3.7 22.6 - - + +
155C LYS* 2.3 39.5 + - - +
213C LEU* 3.5 1.2 - - - -
214C THR* 3.0 28.2 + - - +
215C LEU 3.2 0.8 - - - -
216C GLY* 1.3 73.8 - - - +
218C LEU* 1.3 61.2 + - - +
219C GLY 3.2 0.2 - - - -
220C ARG* 2.9 37.7 + - - +
221C LEU* 3.0 27.9 + - - +
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Residues in contact with LEU 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C SER 5.5 1.1 - - - +
83C ALA* 4.1 28.0 - - + +
84C VAL* 4.7 9.6 - - + +
130C MET* 3.8 26.2 - - + -
214C THR 3.7 0.6 + - - -
215C LEU* 3.2 15.6 + - + +
216C GLY 3.1 0.4 - - - -
217C ASP* 1.3 79.3 - - - +
219C GLY* 1.3 60.5 + - - +
221C LEU* 3.5 3.4 + - + +
222C ARG* 3.2 15.6 + - - +
233C ILE* 3.2 38.1 - - + +
234C LYS 4.5 2.2 - - - +
236C LEU* 4.4 18.2 - - + +
253C GLU* 4.6 7.0 - - + +
261C ILE* 3.6 32.1 - - + -
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Residues in contact with GLY 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C LEU 3.8 2.4 + - - -
216C GLY 3.0 9.7 + - - -
218C LEU* 1.3 79.5 - - - +
220C ARG* 1.3 62.0 + - - +
222C ARG* 3.4 9.0 + - - +
223C GLU* 3.1 36.9 + - - +
253C GLU* 3.4 23.8 + - - -
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Residues in contact with ARG 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C MET* 5.0 8.3 - - - +
148C ASN* 3.9 48.2 + - + +
151C ILE* 3.7 32.2 - - - +
152C LEU* 4.0 13.4 - - + +
209C GLU* 2.7 33.3 + - - +
214C THR* 5.1 0.6 + - - -
216C GLY* 3.0 18.4 + - - +
217C ASP* 2.9 30.3 + - - +
218C LEU 3.3 0.4 - - - -
219C GLY* 1.3 74.9 - - - +
221C LEU* 1.3 61.3 + - - +
223C GLU* 3.7 2.8 + - - +
224C LEU* 3.4 22.0 + - - +
257C PRO 5.5 1.0 + - - -
258C GLN* 4.7 3.6 - - - +
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Residues in contact with LEU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C MET* 3.6 58.6 - - + +
133C HIS* 3.7 26.2 - - + -
134C LEU* 4.9 4.3 - - + +
137C VAL* 6.1 0.4 - - + -
152C LEU* 3.8 16.4 - - + -
217C ASP 3.0 14.9 + - - +
218C LEU* 3.8 8.1 - - + +
219C GLY 3.2 0.2 - - - -
220C ARG* 1.3 76.9 - - - +
222C ARG* 1.3 62.1 + - - +
224C LEU* 3.2 10.9 + - + +
225C LEU* 3.2 33.1 + - + +
233C ILE* 3.8 22.9 - - + -
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Residues in contact with ARG 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C LEU 3.2 8.0 + - - +
219C GLY* 3.8 8.5 + - - +
220C ARG 3.3 0.4 - - - -
221C LEU* 1.3 75.6 - - - +
223C GLU* 1.3 54.9 + - - +
224C LEU 3.0 2.8 + - - -
225C LEU* 3.3 8.5 + - - -
230C LYS* 2.5 68.4 + - + +
233C ILE* 3.1 46.0 + - + +
234C LYS 4.1 5.1 - - - -
235C ASN* 4.3 5.8 + - - +
253C GLU* 2.3 42.2 + - - -
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Residues in contact with GLU 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C GLN* 3.0 38.1 + - - +
148C ASN* 3.0 12.9 + - - -
219C GLY* 3.1 23.1 + - - +
220C ARG* 3.9 5.1 - - - +
221C LEU 3.4 0.2 - - - -
222C ARG* 1.3 76.7 - - + +
224C LEU* 1.3 58.2 + - - +
225C LEU 4.2 0.7 - - - +
230C LYS* 3.2 16.5 + - - +
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Residues in contact with LEU 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C LEU* 3.6 30.1 - - + -
137C VAL* 3.4 33.5 - - + +
141C ILE* 4.2 15.3 - - + -
142C PRO* 6.1 0.4 - - + -
145C GLN* 3.6 35.9 - - + +
148C ASN* 4.7 1.1 - - + -
149C TYR* 3.6 24.9 - - + +
152C LEU* 4.1 12.6 - - + -
220C ARG 3.4 13.0 + - - +
221C LEU* 3.2 8.0 + - + +
222C ARG 3.0 0.8 - - - -
223C GLU* 1.3 77.8 - - - +
225C LEU* 1.3 62.9 + - - +
226C PRO* 4.5 0.3 - - - +
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Residues in contact with LEU 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C HIS* 3.7 28.3 - - + +
136C SER* 4.2 6.1 - - - +
137C VAL* 3.8 11.2 - - + -
221C LEU* 3.2 36.8 + - + +
222C ARG* 3.3 10.6 + - - +
223C GLU 4.2 1.0 - - - +
224C LEU* 1.3 80.5 - - - +
226C PRO* 1.3 82.2 - - + +
227C GLU* 3.7 0.3 + - - +
229C ASN* 3.4 25.6 - - + +
230C LYS* 3.1 18.6 + - + -
232C LEU* 4.4 11.0 - - + -
233C ILE* 3.9 20.0 - - + -
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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