Contacts of the helix formed by residues 145 - 165 (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 GLN 145 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G ILE* 3.3 14.0 - - - +
142G PRO* 2.9 23.6 + - + +
144G GLU* 1.3 94.9 + - + +
146G GLN* 1.3 58.6 + - - +
147G MET 3.6 1.6 - - - -
148G ASN* 2.7 33.8 + - - +
149G TYR* 3.9 3.8 + - - +
220G ARG 4.3 0.2 - - - +
223G GLU* 3.3 45.5 + - - +
224G LEU* 3.3 29.8 - - + +
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Residues in contact with GLN 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G ILE* 2.9 35.4 + - + +
142G PRO 2.9 7.2 + - - +
143G PRO* 3.2 28.7 - - + +
144G GLU 3.3 2.2 - - - -
145G GLN* 1.3 77.5 - - - +
147G MET* 1.3 64.2 + - - +
149G TYR* 3.8 4.4 + - - +
150G GLY* 3.5 14.6 + - - -
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Residues in contact with MET 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G PRO 4.4 2.3 + - - +
144G GLU 4.8 3.3 + - - +
145G GLN 3.6 0.2 - - - -
146G GLN* 1.3 77.6 - - - +
148G ASN* 1.3 69.6 + - - +
150G GLY* 3.1 11.7 + - - -
151G ILE* 3.1 30.7 + - + +
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Residues in contact with ASN 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G GLU 5.4 2.7 + - - +
145G GLN* 2.7 39.6 + - + +
146G GLN 3.5 0.4 - - - -
147G MET* 1.3 81.5 - - - +
149G TYR* 1.3 63.2 + - - +
151G ILE* 3.1 15.8 + - - +
152G LEU* 3.2 18.1 + - - +
220G ARG* 3.9 48.9 + - + +
223G GLU* 3.7 12.1 + - - -
224G LEU* 4.6 4.7 - - + -
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Residues in contact with TYR 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G LEU* 4.0 19.6 + - + +
137G VAL* 4.3 18.0 + - + -
139G GLN* 2.7 29.5 + - + +
141G ILE* 3.4 33.2 - - + -
145G GLN 3.9 5.4 + - - +
146G GLN 3.8 10.3 + - - +
148G ASN* 1.3 79.4 - - - +
150G GLY* 1.3 64.6 + - - +
152G LEU* 3.6 2.1 + - - +
153G LYS* 3.2 59.6 + - + +
224G LEU* 3.6 38.7 - - + +
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Residues in contact with GLY 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G GLN 3.5 7.6 + - - -
147G MET 3.1 8.8 + - - -
149G TYR* 1.3 82.4 - - - +
151G ILE* 1.3 59.4 + - - +
153G LYS* 4.3 3.2 - - - +
154G GLN* 3.2 28.0 + - - +
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Residues in contact with ILE 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G MET* 3.4 31.9 - - + +
148G ASN* 3.1 8.8 + - - +
150G GLY* 1.3 77.2 - - - +
152G LEU* 1.3 63.9 + - - +
154G GLN* 3.5 13.7 + - - +
155G LYS* 3.2 44.0 + - + +
209G GLU* 3.9 17.5 - - + +
217G ASP* 4.6 7.2 - - - +
220G ARG* 4.0 27.8 - - - +
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Residues in contact with LEU 152 (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* 4.4 9.4 - - + +
134G LEU* 3.7 27.4 - - + -
148G ASN 3.2 14.0 + - - +
149G TYR 4.0 3.4 - - - +
151G ILE* 1.3 77.8 - - - +
153G LYS* 1.3 58.9 + - - +
155G LYS* 3.0 7.5 + - + +
156G ILE* 2.9 33.4 + - + +
213G LEU* 4.8 5.2 - - + -
217G ASP* 3.7 41.3 - - + +
220G ARG* 4.8 6.5 - - + -
221G LEU* 3.8 42.4 - - + +
224G LEU* 4.2 7.4 - - + -
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Residues in contact with LYS 153 (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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131G LYS* 5.8 6.7 - - - +
134G LEU* 3.9 26.6 - - + +
135G GLU* 5.2 10.1 - - - +
139G GLN* 5.3 0.2 - - - +
149G TYR* 3.2 53.9 + - + +
150G GLY* 4.6 3.4 - - - +
152G LEU* 1.3 79.2 - - - +
154G GLN* 1.3 56.7 + - - +
156G ILE* 3.9 6.9 - - + +
157G ALA* 2.8 35.0 + - - +
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Residues in contact with GLN 154 (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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150G GLY 3.2 20.6 + - - +
151G ILE* 3.7 16.1 - - - +
152G LEU 3.2 0.6 - - - -
153G LYS* 1.3 77.9 - - - +
155G LYS* 1.3 59.6 + - + +
157G ALA* 4.1 4.6 - - - +
158G LEU* 3.2 25.3 + - - +
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Residues in contact with LYS 155 (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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151G ILE* 3.2 23.7 + - + +
152G LEU* 3.0 9.5 + - - +
154G GLN* 1.3 77.6 - - + +
156G ILE* 1.3 54.3 + - - +
157G ALA 3.2 0.2 - - - -
158G LEU* 3.1 6.5 + - - +
159G TYR* 2.7 43.3 + - + -
209G GLU* 2.9 21.9 + - - -
210G ASN 2.8 28.0 + - - +
211G PRO* 4.1 13.7 - - + +
212G ARG 3.0 14.4 + - - +
213G LEU* 4.0 15.7 - - + -
214G THR* 3.4 4.8 - - - +
217G ASP* 2.3 40.2 + - - +
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Residues in contact with ILE 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G MET* 4.3 15.3 - - + +
130G MET* 4.1 7.6 - - + +
131G LYS* 3.7 53.2 - - + +
134G LEU* 3.6 28.3 - - + -
152G LEU* 2.9 20.1 + - + +
153G LYS* 3.9 5.6 - - + +
155G LYS* 1.3 74.3 - - - +
157G ALA* 1.3 52.3 + - - +
159G TYR* 3.2 7.3 + - - +
160G GLU* 2.6 45.2 + - + +
213G LEU* 4.8 13.0 - - + -
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Residues in contact with ALA 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153G LYS 2.8 19.7 + - - +
154G GLN* 4.1 5.4 - - - +
156G ILE* 1.3 74.4 - - - +
158G LEU* 1.3 58.8 + - - +
160G GLU* 4.3 8.1 - - - +
161G ASP* 2.7 39.9 + - + +
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Residues in contact with LEU 158 (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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154G GLN 3.2 18.1 + - - +
155G LYS* 3.1 4.9 + - - +
157G ALA* 1.3 77.6 - - - +
159G TYR* 1.3 69.5 + - + +
161G ASP* 4.5 3.2 - - - +
162G LYS* 3.5 40.8 + - + +
196G ILE* 3.6 32.0 - - + +
211G PRO* 3.7 27.4 - - + +
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Residues in contact with TYR 159 (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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123G ASP* 2.9 53.6 + - + -
124G VAL* 5.1 0.4 - - + -
127G MET* 3.6 34.3 - - + -
155G LYS* 2.7 28.5 + - + +
156G ILE* 3.3 11.9 - - - +
158G LEU* 1.3 85.6 - - + +
160G GLU* 1.3 61.8 + - - +
162G LYS* 3.4 8.0 + - - +
163G LEU* 3.4 20.5 + - + +
193G LEU* 4.6 10.6 - - + +
196G ILE* 4.7 11.2 - - + -
211G PRO 3.8 19.1 - - - -
212G ARG* 3.3 18.0 - - + +
213G LEU* 3.2 30.8 + - + +
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Residues in contact with GLU 160 (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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127G MET* 3.6 27.9 - - + +
131G LYS* 3.2 38.7 - - - +
156G ILE* 2.6 28.2 + - + +
157G ALA* 3.9 5.9 - - - +
159G TYR* 1.3 73.7 - - - +
161G ASP* 1.3 58.3 + - - +
163G LEU* 3.0 19.4 + - - +
164G SER* 3.0 14.2 + - - -
168G ILE 5.0 0.3 - - - +
170G ILE 4.4 8.0 - - - +
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Residues in contact with ASP 161 (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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157G ALA* 2.7 24.0 + - + +
158G LEU* 4.5 3.8 - - - +
160G GLU* 1.3 72.4 - - - +
162G LYS* 1.3 65.9 + - + +
164G SER* 3.0 21.0 + - - -
165G ARG* 3.2 39.2 + - - -
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Residues in contact with LYS 162 (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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158G LEU* 3.5 36.8 + - + +
159G TYR 3.4 6.2 + - - +
160G GLU 3.2 0.4 - - - -
161G ASP* 1.3 85.6 - - + +
163G LEU* 1.3 59.3 + - - +
165G ARG* 3.9 14.7 - - - +
166G ALA 3.9 0.9 + - - -
192G ALA* 3.2 43.0 - - - +
193G LEU* 4.5 8.7 - - + -
195G SER* 2.8 35.6 + - - +
196G ILE* 4.4 10.8 - - + -
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Residues in contact with LEU 163 (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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124G VAL* 4.2 17.3 - - + -
127G MET* 3.6 37.9 - - + -
159G TYR* 3.4 10.3 - - + +
160G GLU* 3.0 8.8 + - - +
162G LYS* 1.3 79.1 - - - +
164G SER* 1.3 56.2 + - - +
165G ARG 3.3 1.8 - - - -
166G ALA* 3.2 6.5 + - - +
168G ILE* 2.7 56.0 + - + +
170G ILE* 4.5 9.9 - - + -
189G LEU* 3.8 20.6 - - + -
192G ALA* 4.5 7.0 - - + -
193G LEU* 3.7 26.2 - - + -
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Residues in contact with SER 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160G GLU 3.0 11.3 + - - -
161G ASP* 3.0 16.4 + - - -
163G LEU* 1.3 73.9 - - - +
165G ARG* 1.3 79.0 + - - +
167G GLY* 2.9 19.4 + - - +
168G ILE 3.7 7.1 + - - +
169G VAL* 5.0 10.8 - - - -
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Residues in contact with ARG 165 (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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161G ASP* 3.2 41.5 + - - +
162G LYS* 3.9 12.6 - - - +
163G LEU 3.3 0.4 - - - -
164G SER* 1.3 89.3 + - - +
166G ALA* 1.3 58.4 + - - +
167G GLY 3.2 0.9 + - - -
192G ALA* 6.0 0.4 - - + -
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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
------------------------------------------------------------
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