Contacts of the helix formed by residues 150 - 173 (chain V) in PDB entry 5Z58
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 ASN 150 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149V LYS* 1.3 74.5 - - - +
151V SER* 1.3 57.9 + - - +
152V LEU 3.2 0.2 - - - -
153V ALA* 3.5 6.7 - - - +
154V TYR* 2.6 40.9 + - + +
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Residues in contact with SER 151 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149V LYS* 3.5 5.4 - - - +
150V ASN* 1.3 77.0 - - - +
152V LEU* 1.3 57.6 + - - +
154V TYR* 3.4 4.0 + - - +
155V GLN* 2.9 31.2 + - - +
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Residues in contact with LEU 152 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149V LYS* 4.0 17.9 + - + +
150V ASN 3.2 0.4 - - - -
151V SER* 1.3 77.8 - - - +
153V ALA* 1.3 57.9 + - - +
155V GLN* 3.3 5.3 + - - +
156V ARG* 2.9 32.4 + - - +
387V MET* 6.0 8.1 - - + -
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Residues in contact with ALA 153 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149V LYS 3.4 17.1 + - - +
150V ASN* 3.1 8.0 + - - +
152V LEU* 1.3 79.2 - - - +
154V TYR* 1.3 58.1 + - - +
156V ARG* 3.8 5.0 - - - +
157V MET* 3.0 28.6 + - - +
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Residues in contact with TYR 154 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150V ASN* 2.6 22.6 + - + +
151V SER* 4.0 4.0 - - - +
153V ALA* 1.3 72.5 - - - +
155V GLN* 1.3 59.4 + - - +
157V MET* 3.3 5.5 + - - +
158V SER* 2.9 32.1 + - - -
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Residues in contact with GLN 155 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151V SER 2.9 18.7 + - - +
152V LEU* 3.8 5.4 - - - +
154V TYR* 1.3 75.9 - - - +
156V ARG* 1.3 57.1 + - - +
158V SER* 3.7 5.3 - - - -
159V TRP* 2.8 30.7 + - - +
386V LYS 5.6 2.7 - - - +
387V MET* 5.5 11.4 - - - -
388V ASP* 5.5 4.0 - - + +
391V PHE* 5.6 10.1 - - + -
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Residues in contact with ARG 156 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152V LEU 2.9 18.7 + - - +
153V ALA* 3.8 6.3 - - - +
155V GLN* 1.3 77.8 - - - +
157V MET* 1.3 55.8 + - - +
159V TRP* 3.2 8.3 + - - +
160V GLU* 2.9 29.5 + - - +
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Residues in contact with MET 157 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153V ALA 3.0 17.5 + - - +
154V TYR* 3.8 6.1 - - - +
156V ARG* 1.3 76.1 - - - +
158V SER* 1.3 57.4 + - - +
160V GLU* 3.2 7.7 + - - +
161V ALA* 2.9 29.2 + - - +
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Residues in contact with SER 158 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154V TYR 2.9 17.7 + - - -
155V GLN* 3.9 5.4 - - - -
157V MET* 1.3 76.4 - - - +
159V TRP* 1.3 57.0 + - - +
161V ALA* 3.4 7.0 + - - +
162V LEU* 2.9 30.2 + - - +
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Residues in contact with TRP 159 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155V GLN 2.8 19.6 + - - +
156V ARG* 3.2 8.7 + - - +
158V SER* 1.3 75.7 - - - +
160V GLU* 1.3 61.4 + - - +
162V LEU* 3.2 8.0 + - - +
163V LYS* 3.0 24.3 + - - +
385V PHE* 4.7 18.8 - - + -
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Residues in contact with GLU 160 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156V ARG 2.9 15.9 + - - +
157V MET* 3.2 7.4 + - - +
159V TRP* 1.3 73.3 - - - +
161V ALA* 1.3 66.7 + - - +
163V LYS* 3.4 7.1 + - - +
164V LYS* 3.2 21.8 + - - +
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Residues in contact with ALA 161 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157V MET 2.9 16.0 + - - +
158V SER* 3.8 7.2 - - - +
160V GLU* 1.3 77.4 - - - +
162V LEU* 1.3 57.3 + - - +
164V LYS* 3.4 6.5 + - - +
165V SER* 2.9 30.3 + - - -
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Residues in contact with LEU 162 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158V SER 2.9 18.8 + - - +
159V TRP* 3.2 8.0 + - - +
161V ALA* 1.3 75.5 - - - +
163V LYS* 1.3 64.4 + - - +
165V SER* 3.4 5.5 + - - -
166V ILE* 3.0 25.6 + - - +
188V GLU* 5.8 7.6 - - + -
189V ASN 5.7 6.3 - - - +
193V GLY* 6.1 5.2 - - - -
196V LEU* 6.0 1.1 - - - -
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Residues in contact with LYS 163 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159V TRP 3.0 15.3 + - - +
160V GLU* 3.8 7.6 - - - +
161V ALA 3.2 0.2 - - - -
162V LEU* 1.3 77.2 - - - +
164V LYS* 1.3 57.1 - - - +
166V ILE* 3.5 5.7 + - - +
167V ASN* 2.9 30.5 + - - +
196V LEU* 5.1 14.1 - - + -
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Residues in contact with LYS 164 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160V GLU 3.2 11.3 + - - +
161V ALA* 3.7 9.4 - - - +
163V LYS* 1.3 76.6 - - - +
165V SER* 1.3 59.8 + - - +
167V ASN* 3.2 7.1 + - - +
168V GLY* 2.9 27.4 + - - -
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Residues in contact with SER 165 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161V ALA 2.9 17.7 + - - -
162V LEU* 3.7 6.5 - - - -
164V LYS* 1.3 75.9 - - - +
166V ILE* 1.3 58.2 + - - +
168V GLY* 3.3 3.0 + - - -
169V LEU* 2.9 30.5 + - - +
188V GLU* 5.6 9.6 - - - -
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Residues in contact with ILE 166 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162V LEU 3.0 17.4 + - - +
163V LYS* 3.7 6.3 - - - +
165V SER* 1.3 76.2 - - - +
167V ASN* 1.3 57.9 + - - +
169V LEU* 3.2 7.3 + - - +
170V ILE* 2.9 31.6 + - - +
196V LEU* 5.3 4.9 - - + +
197V LEU* 5.0 19.7 - - + +
200V SER* 4.9 8.0 - - - -
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Residues in contact with ASN 167 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163V LYS 2.9 18.2 + - - +
164V LYS* 3.2 8.3 + - - +
166V ILE* 1.3 76.4 - - - +
168V GLY* 1.3 62.3 + - - +
170V ILE* 3.3 7.4 + - - +
171V ASN* 3.0 23.4 + - - +
200V SER* 4.8 9.4 - - - -
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Residues in contact with GLY 168 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164V LYS 2.9 14.0 + - - -
165V SER 3.7 3.4 - - - -
167V ASN* 1.3 76.6 - - - +
169V LEU* 1.3 56.9 + - - +
171V ASN* 3.1 8.3 + - - +
172V LYS* 2.9 29.4 + - - +
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Residues in contact with LEU 169 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165V SER 2.9 16.9 + - - +
166V ILE* 3.2 7.6 + - - +
168V GLY* 1.3 74.6 - - - +
170V ILE* 1.3 63.9 + - - +
172V LYS* 3.2 8.0 + - - +
173V VAL* 3.1 24.8 + - - +
181V ILE* 4.9 20.5 - - + +
184V GLU* 5.8 5.2 - - + -
185V LEU* 5.3 11.0 - - + +
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Residues in contact with ILE 170 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166V ILE 2.9 17.2 + - - +
167V ASN* 3.8 4.5 - - - +
169V LEU* 1.3 76.9 - - - +
171V ASN* 1.3 63.1 + - - +
173V VAL* 3.6 15.0 + - - +
200V SER* 4.4 27.4 - - - +
201V VAL* 5.1 3.4 - - - +
204V ALA* 4.8 15.1 - - + +
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Residues in contact with ASN 171 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167V ASN 3.0 13.6 + - - +
168V GLY* 3.1 10.7 + - - +
170V ILE* 1.3 77.5 - - - +
172V LYS* 1.3 60.6 + - - +
173V VAL 3.7 3.1 + - - +
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Residues in contact with LYS 172 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168V GLY 2.9 15.3 + - - +
169V LEU* 3.2 8.0 + - - +
171V ASN* 1.3 78.9 - - - +
173V VAL* 1.3 64.9 + - - +
174V ASN* 3.4 6.9 + - - +
177V ASN* 5.4 5.0 - - - +
181V ILE* 6.0 3.1 - - + -
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Residues in contact with VAL 173 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169V LEU 3.1 15.7 + - - +
170V ILE* 3.6 10.3 + - - +
171V ASN 3.4 5.6 - - - +
172V LYS* 1.3 78.0 - - - +
174V ASN* 1.3 62.1 - - - +
177V ASN* 5.8 2.2 - - - -
178V ILE* 5.5 3.8 - - + -
181V ILE* 4.4 20.4 - - + -
211V PHE* 5.4 5.9 - - - +
214V VAL* 5.1 9.4 - - + +
218V LEU* 5.6 10.1 - - + -
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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
------------------------------------------------------------
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