Contacts of the helix formed by residues 216 - 225 (chain G) 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 GLY 216 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214G THR* 2.7 9.6 + - - -
215G LEU* 1.3 75.5 - - - +
217G ASP* 1.3 52.2 + - - -
218G LEU 3.0 1.8 - - - -
219G GLY* 2.7 5.5 + - - -
220G ARG* 2.7 42.5 + - - +
253G GLU* 4.4 4.0 - - - -
257G PRO* 3.1 26.1 + - - +
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Residues in contact with ASP 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G MET* 3.8 13.2 - - + +
151G ILE* 4.6 0.9 - - - +
152G LEU* 3.7 19.1 - - + +
155G LYS* 2.3 39.1 + - - +
213G LEU* 3.3 6.0 - - + -
214G THR* 2.8 31.9 + - - +
216G GLY* 1.3 76.4 - - - +
218G LEU* 1.3 57.4 + - - +
220G ARG* 2.7 42.7 + - - +
221G LEU* 3.0 29.1 + - - +
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Residues in contact with LEU 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G ALA* 3.9 19.1 - - + +
84G VAL* 4.2 15.7 - - + +
130G MET* 4.3 24.6 - - + +
214G THR 3.4 8.8 + - - +
215G LEU* 3.4 16.8 - - + +
217G ASP* 1.3 80.5 - - - +
219G GLY* 1.3 59.2 + - - +
221G LEU* 3.8 2.8 - - + +
222G ARG 3.6 7.8 + - - -
233G ILE* 3.1 36.4 - - + +
234G LYS 3.7 20.6 - - - +
236G LEU* 3.7 29.8 - - + +
253G GLU* 4.7 3.1 - - - +
261G ILE* 4.4 9.9 - - + -
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Residues in contact with GLY 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215G LEU 3.7 2.6 + - - -
216G GLY* 2.7 9.9 + - - -
218G LEU* 1.3 78.2 - - - +
220G ARG* 1.3 63.2 + - - -
221G LEU 3.3 0.2 - - - -
222G ARG* 3.3 16.0 + - - +
223G GLU* 3.3 25.0 + - - +
253G GLU* 3.2 28.0 - - - -
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Residues in contact with ARG 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148G ASN* 3.9 50.1 + - + +
151G ILE* 4.0 22.6 - - - +
152G LEU* 4.8 9.6 - - + -
209G GLU* 2.7 32.1 + - - +
214G THR* 4.7 1.6 + - - -
216G GLY* 2.7 20.7 + - - +
217G ASP* 2.7 47.1 + - - +
219G GLY* 1.3 73.6 - - - +
221G LEU* 1.3 64.1 + - - +
223G GLU* 3.1 18.0 + - - +
224G LEU* 3.1 13.9 + - - +
257G PRO 5.2 0.6 + - - -
258G GLN* 4.6 3.2 - - - +
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Residues in contact with LEU 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G MET* 3.8 50.5 - - + +
133G HIS* 3.8 20.0 - - + +
134G LEU* 4.5 6.1 - - + +
152G LEU* 3.8 21.3 - - + +
217G ASP 3.0 13.6 + - - +
218G LEU* 3.8 7.6 - - + +
220G ARG* 1.3 80.0 - - - +
222G ARG* 1.3 56.5 + - - +
224G LEU* 2.9 21.3 + - + +
225G LEU* 3.0 38.9 + - + +
233G ILE* 4.4 14.8 - - + -
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Residues in contact with ARG 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G THR* 4.2 6.9 + - - +
218G LEU 3.6 3.8 + - - +
219G GLY* 3.3 8.0 + - - +
220G ARG 3.2 0.8 - - - -
221G LEU* 1.3 79.3 - - - +
223G GLU* 1.3 62.9 + - + +
224G LEU 3.1 1.1 + - - -
225G LEU* 3.5 7.6 + - - -
230G LYS* 3.2 54.3 + - + +
233G ILE* 2.8 57.1 + - + +
234G LYS* 4.0 0.4 - - - +
235G ASN* 3.7 23.0 - - - +
253G GLU* 2.5 43.7 + - - -
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Residues in contact with GLU 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145G GLN* 3.3 40.1 + - - +
148G ASN* 3.7 9.8 + - - -
219G GLY* 3.3 17.4 + - - +
220G ARG* 3.1 5.7 + - - +
222G ARG* 1.3 77.7 - - + +
224G LEU* 1.3 57.6 + - - +
225G LEU 3.5 4.6 - - - +
230G LYS* 4.4 13.4 + - - +
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Residues in contact with LEU 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134G LEU* 3.6 20.4 - - + -
137G VAL* 3.3 30.8 - - + +
141G ILE* 3.9 11.2 - - + -
145G GLN* 3.3 35.9 - - + +
148G ASN* 4.6 1.6 - - + -
149G TYR* 3.6 47.1 - - + +
152G LEU* 4.2 12.6 - - + -
220G ARG 3.1 9.3 + - - +
221G LEU* 2.9 12.2 + - + +
223G GLU* 1.3 78.4 - - - +
225G LEU* 1.3 63.9 + - - +
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Residues in contact with LEU 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G HIS* 3.5 40.8 - - + +
136G SER* 3.9 7.2 - - - +
137G VAL* 3.8 9.9 - - + -
221G LEU* 3.0 35.2 + - + +
222G ARG* 3.5 8.5 + - - +
223G GLU 4.3 1.2 - - - +
224G LEU* 1.3 81.3 - - - +
226G PRO* 1.3 80.5 - - + +
229G ASN* 3.4 26.5 - - + +
230G LYS* 3.2 16.8 + - + -
232G LEU* 5.0 0.4 - - + -
233G ILE* 4.1 19.5 - - + -
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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