Contacts of the helix formed by residues 147 - 166 (chain N) in PDB entry 1K2V
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 147 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N PRO* 6.0 1.1 - - + -
52N LEU* 3.8 22.9 - - + +
54N ILE* 3.8 37.0 - - + -
142N ALA* 2.7 22.2 + - + +
145N LEU* 3.3 25.8 - - + +
146N ASN* 1.3 80.7 - - - +
148N GLN* 1.3 64.0 + - - +
149N SER* 3.2 3.4 - - - -
150N ALA* 3.1 16.6 + - + +
151N ALA 3.0 18.0 + - - -
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Residues in contact with GLN 148 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139N THR 5.9 0.2 - - - +
142N ALA* 3.9 9.8 + - + -
143N ASP* 3.1 32.7 - - + +
146N ASN* 3.1 43.3 + - - +
147N LEU* 1.3 77.3 - - - +
149N SER* 1.3 63.2 + - - +
151N ALA* 3.2 4.4 + - - +
152N GLU* 3.0 34.1 + - - +
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Residues in contact with SER 149 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147N LEU 3.2 0.6 - - - -
148N GLN* 1.3 75.4 - - - +
150N ALA* 1.3 66.8 + - - +
152N GLU* 3.1 15.1 + - - +
153N THR* 3.0 28.3 + - - -
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Residues in contact with ALA 150 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51N ALA 4.8 1.8 - - - +
52N LEU* 4.1 23.0 - - + +
147N LEU* 3.1 24.2 + - + +
149N SER* 1.3 78.1 - - - +
151N ALA* 1.3 61.3 + - - +
153N THR* 3.4 7.6 + - - -
154N HIS* 3.0 23.9 + - - +
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Residues in contact with ALA 151 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52N LEU* 3.5 13.8 - - + +
138N LEU* 4.2 13.5 - - + +
139N THR* 4.7 6.7 - - - +
142N ALA* 3.4 31.4 - - + -
147N LEU 3.0 5.1 + - - -
148N GLN* 3.4 7.2 - - - +
149N SER 3.2 0.2 - - - -
150N ALA* 1.3 77.8 - - - +
152N GLU* 1.3 59.1 + - + +
154N HIS* 3.1 3.6 + - - +
155N LEU* 2.9 38.5 + - + +
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Residues in contact with GLU 152 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148N GLN* 3.0 23.0 + - + +
149N SER* 3.1 14.2 + - - +
151N ALA* 1.3 76.3 - - + +
153N THR* 1.3 63.3 + - - +
155N LEU* 3.8 10.1 - - + +
156N ALA* 2.9 26.3 + - - +
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Residues in contact with THR 153 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149N SER* 3.0 17.9 + - - -
150N ALA* 3.7 7.4 - - - -
152N GLU* 1.3 75.9 - - - +
154N HIS* 1.3 64.5 + - - +
156N ALA* 3.5 6.2 + - - +
157N GLN* 3.1 26.8 + - + +
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Residues in contact with HIS 154 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51N ALA* 3.7 33.8 - - + +
138N LEU* 3.3 19.3 - - + +
150N ALA 3.0 14.1 + - - +
151N ALA* 3.5 7.4 - - - +
153N THR* 1.3 77.7 - - - +
155N LEU* 1.3 61.2 + - - +
157N GLN* 3.0 16.7 + - - +
158N TYR* 2.8 27.9 + - + +
278N THR* 2.6 38.8 - - + -
279N LEU* 3.3 25.2 - - + +
282N MET* 3.6 11.7 - - + +
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Residues in contact with LEU 155 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135N ARG* 3.8 39.3 - - + +
138N LEU* 3.7 19.5 - - + -
139N THR* 4.0 20.9 - - - +
151N ALA* 2.9 27.9 + - + +
152N GLU* 3.8 10.1 - - + +
154N HIS* 1.3 75.5 - - - +
156N ALA* 1.3 61.7 + - - +
158N TYR* 3.2 9.0 + - + +
159N GLU* 3.0 27.6 + - - +
278N THR* 4.7 9.6 - - + -
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Residues in contact with ALA 156 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152N GLU 2.9 18.0 + - - +
153N THR* 3.6 7.6 - - - +
155N LEU* 1.3 77.3 - - - +
157N GLN* 1.3 61.8 + - - +
159N GLU* 3.1 21.1 - - - +
160N ASP* 3.0 30.4 + - - +
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Residues in contact with GLN 157 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153N THR* 3.1 17.1 + - + +
154N HIS* 3.0 18.8 + - - +
156N ALA* 1.3 76.5 - - - +
158N TYR* 1.3 64.6 + - - +
160N ASP* 3.9 5.7 - - - +
161N PHE* 3.0 26.6 + - + +
282N MET* 4.5 19.6 - - + +
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Residues in contact with TYR 158 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131N LEU* 3.1 32.8 - - + +
135N ARG* 4.0 29.6 - - + -
154N HIS* 2.8 14.3 + - + +
155N LEU* 3.3 15.5 - - + +
156N ALA 3.2 0.2 - - - -
157N GLN* 1.3 79.4 - - - +
159N GLU* 1.3 69.0 + - + +
161N PHE* 3.6 1.7 - - - +
162N ILE* 3.0 50.3 + - + +
199N GLU* 4.4 1.1 + - - -
200N ILE* 3.4 13.5 - - - +
278N THR* 3.7 42.2 - - + -
281N ALA* 3.6 11.1 - - + +
282N MET* 3.4 27.3 - - + -
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Residues in contact with GLU 159 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135N ARG* 6.2 1.3 - - - +
155N LEU 3.0 16.3 + - - +
156N ALA* 3.1 17.8 - - - +
158N TYR* 1.3 87.7 - - + +
160N ASP* 1.3 85.7 + - - +
162N ILE* 3.6 5.7 + - - +
163N ARG* 2.7 64.5 + - - +
203N GLU* 5.3 0.5 - - - +
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Residues in contact with ASP 160 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156N ALA* 3.0 28.0 + - - +
157N GLN* 3.9 5.3 - - - +
159N GLU* 1.3 94.4 - - - +
161N PHE* 1.3 60.8 + - - +
163N ARG* 3.4 16.3 + - - +
164N SER* 2.9 32.5 + - - -
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Residues in contact with PHE 161 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157N GLN* 3.0 21.5 + - + +
158N TYR 3.6 3.4 - - - +
160N ASP* 1.3 77.1 - - - +
162N ILE* 1.3 70.3 + - + +
164N SER* 2.7 26.0 + - - -
165N MET* 3.2 37.1 + - + +
282N MET* 3.6 49.4 - - + -
285N VAL* 3.8 15.9 - - + -
286N ARG* 3.9 27.4 - - + -
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Residues in contact with ILE 162 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158N TYR* 3.0 49.2 + - + +
159N GLU* 3.8 5.6 - - - +
161N PHE* 1.3 84.9 - - + +
163N ARG* 1.3 63.4 + - - +
165N MET 3.2 4.3 + - - -
200N ILE* 3.6 30.3 - - + -
203N GLU* 3.7 28.9 - - + +
204N TYR* 2.6 39.3 + - + +
282N MET* 4.7 2.2 - - + -
285N VAL* 3.6 19.3 - - + -
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Residues in contact with ARG 163 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159N GLU* 2.7 45.0 + - - +
160N ASP* 3.4 18.4 + - - +
162N ILE* 1.3 79.3 - - - +
164N SER* 1.3 63.8 + - - +
166N LYS* 3.2 37.9 + - - +
167N PRO* 3.9 2.4 - - - +
203N GLU* 3.9 16.7 + - - +
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Residues in contact with SER 164 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160N ASP 2.9 16.2 + - - -
161N PHE* 2.7 27.1 + - - -
163N ARG* 1.3 78.2 - - - +
165N MET* 1.3 65.6 + - - +
167N PRO* 3.1 21.6 - - - +
168N ARG* 5.5 0.2 - - - +
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Residues in contact with MET 165 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161N PHE* 3.2 34.9 + - + +
162N ILE 3.7 0.4 - - - +
163N ARG 3.1 1.0 - - - -
164N SER* 1.3 79.7 - - - +
166N LYS* 1.3 66.9 + - - +
167N PRO* 3.2 4.3 - - - -
168N ARG* 2.9 35.1 + - + +
169N PHE* 3.4 6.9 - - + -
204N TYR* 3.3 21.5 - - + +
285N VAL* 3.6 21.8 - - + +
286N ARG* 5.4 1.8 - - + -
289N ASP* 3.1 44.0 - - + +
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Residues in contact with LYS 166 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162N ILE 3.6 3.2 + - - -
163N ARG* 3.2 30.8 + - - +
165N MET* 1.3 76.6 - - - +
167N PRO* 1.3 66.7 - - + +
168N ARG 3.0 1.7 + - - -
169N PHE* 3.0 16.5 + - - +
170N VAL* 3.8 6.1 + - - +
203N GLU* 3.5 54.1 + - - +
204N TYR* 3.7 18.3 - - + +
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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