Contacts of the helix formed by residues 146 - 164 (chain B) in PDB entry 5K7W
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 TYR 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465A ARG* 5.9 2.9 - - - -
142B ARG 4.0 22.0 - - - -
143B PHE* 3.0 17.0 + + - +
144B GLU 3.4 0.4 - - - -
145B GLU* 1.3 102.6 + - + +
147B PRO* 1.3 67.2 - - - +
148B LYS 3.3 3.4 - - - -
149B LEU* 3.2 33.3 + - + +
150B ARG* 2.9 18.7 + - - +
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Residues in contact with PRO 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B GLU 5.0 2.9 - - - +
145B GLU 3.4 9.9 - - - +
146B TYR* 1.3 87.8 - - - +
148B LYS* 1.3 60.2 + - + +
150B ARG* 3.5 25.9 + - + +
151B GLU* 2.8 29.7 + - - +
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Residues in contact with LYS 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B TYR 3.3 0.8 - - - -
147B PRO* 1.3 77.5 - - + +
149B LEU* 1.3 73.9 + - + +
151B GLU* 3.3 6.5 + - - +
152B LEU* 3.1 23.4 + - - +
395B LEU* 4.2 31.9 - - + +
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A THR* 3.5 33.2 - - + -
143B PHE* 3.7 33.3 - - + -
146B TYR* 3.2 35.5 + - + +
148B LYS* 1.3 83.8 - - + +
150B ARG* 1.3 61.1 + - - +
152B LEU* 3.4 9.3 + - - +
153B ILE* 3.3 25.3 + - - +
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Residues in contact with ARG 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ALA 5.5 3.4 - - - +
143B PHE* 3.7 29.2 + - + +
144B GLU* 4.1 26.8 + - - +
146B TYR 2.9 15.7 + - - +
147B PRO* 3.7 21.6 + - - +
149B LEU* 1.3 76.2 - - - +
151B GLU* 1.3 57.2 + - - +
153B ILE* 3.3 6.5 + - + +
154B ARG* 2.8 30.9 + - + +
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Residues in contact with GLU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B PRO 2.8 18.9 + - - +
148B LYS* 3.7 8.3 - - - +
149B LEU 3.2 0.2 - - - -
150B ARG* 1.3 74.1 - - - +
152B LEU* 1.3 60.8 + - - +
154B ARG* 2.9 45.7 + - - -
155B LEU* 2.8 50.0 + - + +
395B LEU* 4.1 9.4 - - + -
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B LYS 3.1 13.4 + - - +
149B LEU* 3.7 11.0 - - - +
150B ARG 3.3 0.2 - - - -
151B GLU* 1.3 76.5 - - - +
153B ILE* 1.3 67.5 + - + +
155B LEU* 4.0 1.6 - - - +
156B LYS* 3.0 45.3 + - + +
309B VAL* 4.4 16.2 - - + +
392B ILE* 4.2 9.0 - - + -
395B LEU* 4.0 34.9 - - + +
396B ARG* 4.0 15.0 - - + +
397B PRO* 4.0 25.6 - - + -
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Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B PHE* 3.9 23.3 - - + -
149B LEU 3.3 13.9 + - - +
150B ARG* 3.3 8.6 + - + +
151B GLU 3.3 0.2 - - - -
152B LEU* 1.3 80.2 - - + +
154B ARG* 1.3 57.8 + - - +
156B LYS* 3.3 4.1 + - + +
157B ASP* 2.9 45.1 + - - +
309B VAL* 3.7 35.4 - - + +
310B ASP* 5.2 3.1 - - - +
336B HIS* 4.0 23.1 - - + +
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Residues in contact with ARG 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ARG* 2.8 20.7 + - + +
151B GLU* 2.9 42.2 + - - +
153B ILE* 1.3 79.0 - - - +
155B LEU* 1.3 81.1 + - - +
157B ASP* 3.3 6.6 + - - +
158B GLU* 3.0 39.5 + - + +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B GLU* 2.8 39.6 + - + +
152B LEU 4.1 1.6 - - - +
154B ARG* 1.3 104.1 - - - +
156B LYS* 1.3 57.5 + - - +
158B GLU* 3.2 22.0 + - - +
159B LEU* 2.9 28.4 + - - +
389B THR* 5.5 0.4 - - - +
391B GLU* 4.0 30.1 - - + +
392B ILE* 3.6 21.6 - - + +
395B LEU* 4.0 17.3 - - + -
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Residues in contact with LYS 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU* 3.0 40.0 + - + +
153B ILE* 3.9 4.0 - - - +
155B LEU* 1.3 75.6 - - - +
157B ASP* 1.3 57.9 + - - +
159B LEU* 3.3 8.4 + - + +
160B ILE* 3.0 37.1 + - - +
306B HIS* 2.9 29.5 + - + +
309B VAL* 4.1 18.8 - - + -
335B GLU 4.6 1.2 + - - -
336B HIS* 2.8 55.3 + - + +
339B LEU* 4.3 6.9 - - - +
392B ILE* 3.9 24.9 - - + -
396B ARG* 5.5 0.4 - - + -
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Residues in contact with ASP 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ILE* 2.9 33.1 + - - +
154B ARG* 3.7 6.2 - - - +
156B LYS* 1.3 75.7 - - - +
158B GLU* 1.3 57.9 + - - +
160B ILE* 3.4 10.4 + - - +
161B ALA* 2.9 29.9 + - - +
332B HIS* 4.5 16.8 + - - -
335B GLU* 5.4 2.1 - - - +
336B HIS* 2.6 30.1 + - - -
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ARG* 3.0 31.0 + - + +
155B LEU* 3.5 24.3 - - - +
157B ASP* 1.3 74.3 - - - +
159B LEU* 1.3 58.5 + - - +
161B ALA* 3.3 5.6 + - - +
162B LYS* 2.8 65.7 + - + +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B LEU 2.9 14.0 + - - +
156B LYS* 3.5 13.7 - - + +
158B GLU* 1.3 78.6 - - - +
160B ILE* 1.3 61.4 + - + +
162B LYS* 3.4 9.5 + - + +
163B SER* 2.8 29.6 + - - +
306B HIS* 5.2 6.3 - - + -
339B LEU* 5.4 2.9 - - + -
386B THR* 3.9 31.4 - - - +
387B GLY 3.4 22.4 - - - +
388B CYS* 4.1 12.8 - - + -
389B THR* 4.9 10.8 - - + -
392B ILE* 3.8 21.3 - - + -
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Residues in contact with ILE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LYS* 3.0 26.8 + - + +
157B ASP* 3.6 10.3 - - - +
159B LEU* 1.3 79.1 - - + +
161B ALA* 1.3 63.6 + - - +
163B SER* 3.2 8.0 + - - -
164B ASN* 3.0 48.3 + - - +
335B GLU* 3.5 58.3 - - + +
336B HIS* 3.8 20.6 - - + -
343B ARG* 4.3 12.6 - - - +
386B THR* 5.3 4.7 - - + -
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Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ASP 2.9 17.4 + - - +
158B GLU* 3.3 6.5 + - - +
160B ILE* 1.3 77.1 - - - +
162B LYS* 1.3 64.6 + - + +
163B SER 3.3 0.9 + - - -
164B ASN* 3.4 23.8 + - - +
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Residues in contact with LYS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLU* 2.8 57.3 + - + +
159B LEU* 3.9 9.0 - - + +
160B ILE 3.3 0.2 - - - -
161B ALA* 1.3 75.3 - - + +
163B SER* 1.3 59.5 + - - +
164B ASN 3.8 1.7 + - - +
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Residues in contact with SER 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B LEU* 2.8 22.1 + - - -
160B ILE* 3.3 5.5 + - - -
161B ALA 3.2 0.4 - - - -
162B LYS* 1.3 76.3 - - - +
164B ASN* 1.3 59.3 + - - +
341B ARG* 2.9 44.6 + - - +
343B ARG* 5.2 1.1 + - - -
386B THR* 3.4 34.3 - - - +
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Residues in contact with ASN 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ILE* 3.0 37.7 + - - +
161B ALA* 3.4 19.2 + - - +
162B LYS 3.5 1.9 - - - +
163B SER* 1.3 79.6 - - - +
165B THR* 1.3 70.8 + - - +
166B PRO* 3.9 1.4 - - - +
335B GLU* 5.4 1.6 + - - +
341B ARG* 4.5 0.9 - - - -
343B ARG* 3.1 28.6 + - - +
355B PRO* 3.6 23.8 + - + +
356B GLY* 3.2 8.4 - - - +
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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
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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