Contacts of the helix formed by residues 149 - 161 (chain G) in PDB entry 1Z4A
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 149 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149E GLN* 5.3 4.3 - - - +
145G LYS 5.8 0.8 + - - -
146G ALA* 3.0 18.9 + - - +
147G ASN* 3.3 3.4 + - + +
148G GLY* 1.3 72.7 - - - +
150G MET* 1.3 64.1 + - - +
151G SER* 3.2 14.6 + - - +
152G VAL* 3.4 21.9 + - + +
153G ILE* 3.2 23.1 + - - +
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Residues in contact with MET 150 (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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145E LYS* 3.5 38.4 - - + +
146E ALA* 4.7 3.4 - - - +
149E GLN* 5.9 4.9 - - + -
152E VAL* 4.2 6.7 - - + -
38G PHE* 4.0 22.4 - - + -
148G GLY 3.1 10.7 + - - +
149G GLN* 1.3 72.8 - - - +
151G SER* 1.3 56.5 + - - +
153G ILE* 3.7 12.7 - - + +
154G PHE* 2.9 67.2 + - + -
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Residues in contact with SER 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E GLN* 5.3 6.6 - - - +
151E SER* 3.9 22.1 + - - -
152E VAL* 3.7 19.6 - - - +
155E GLN* 3.7 14.4 + - - +
149G GLN* 3.1 14.7 - - - -
150G MET* 1.3 81.9 - - - +
152G VAL* 1.3 64.2 + - - +
155G GLN* 3.5 23.4 + - - +
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Residues in contact with VAL 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G LEU* 5.0 4.9 - - + +
146G ALA* 3.8 29.2 - - + -
149G GLN* 3.4 27.0 + - + +
151G SER* 1.3 78.1 - - - +
153G ILE* 1.3 66.8 + - - +
154G PHE 3.2 0.2 - - - -
155G GLN* 2.9 20.4 + - + +
156G LEU* 2.9 29.0 + - + +
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Residues in contact with ILE 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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38G PHE* 3.5 33.9 - - + -
41G PHE* 3.8 15.4 - - + -
85G ILE* 4.8 10.5 - - + -
143G LEU* 4.4 17.3 - - + -
146G ALA* 4.5 7.4 - - + -
148G GLY* 3.5 27.8 - - - +
149G GLN 3.2 19.1 - - - +
150G MET* 3.7 16.4 - - + +
152G VAL* 1.3 77.7 - - - +
154G PHE* 1.3 49.9 + - - +
156G LEU* 3.1 10.3 + - - +
157G ASP* 2.7 33.6 + - - +
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Residues in contact with PHE 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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142E LEU* 3.7 44.0 - - + -
145E LYS* 3.4 28.7 - - + -
146E ALA 4.8 1.8 - - - -
152E VAL* 4.6 20.9 - - + -
155E GLN* 4.0 18.6 + - + +
156E LEU* 5.1 8.7 - - + -
38G PHE* 4.4 7.9 - + - -
150G MET* 2.9 53.0 + - + +
151G SER* 3.8 6.3 - - - +
153G ILE* 1.3 75.3 - - - +
155G GLN* 1.3 58.5 + - - +
157G ASP* 3.4 9.1 + - - +
158G ARG* 3.0 27.7 + - - +
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Residues in contact with GLN 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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155E GLN* 3.4 24.9 - - - +
151G SER* 3.5 17.3 + - - +
152G VAL* 2.9 22.4 + - + +
154G PHE* 1.3 75.5 - - - +
156G LEU* 1.3 61.5 + - - +
158G ARG* 3.0 10.4 + - - +
159G TYR* 2.8 31.3 + - - +
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Residues in contact with LEU 156 (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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41G PHE* 3.7 5.8 - - + -
139G ILE* 4.4 9.6 - - + +
142G LEU* 4.1 33.7 - - + +
143G LEU* 3.4 39.9 - - + +
152G VAL* 2.9 17.6 + - + +
153G ILE* 3.3 11.0 - - - +
155G GLN* 1.3 77.5 - - - +
157G ASP* 1.3 58.0 + - - +
159G TYR* 3.6 8.6 - - + +
160G LEU* 2.9 71.2 + - + +
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Residues in contact with ASP 157 (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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142E LEU* 6.2 0.5 - - - +
38G PHE* 3.3 26.6 - - + +
39G LYS* 4.3 3.3 + - - +
40G GLY* 2.6 42.5 + - - -
41G PHE* 2.8 32.2 + - + -
153G ILE 2.7 19.5 + - - +
154G PHE* 3.7 7.6 - - - +
156G LEU* 1.3 73.6 - - - +
158G ARG* 1.3 63.7 + - - +
161G GLY 3.0 17.5 + - - -
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Residues in contact with ARG 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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155E GLN* 5.3 11.4 - - - +
159E TYR* 6.2 3.8 - - - -
40G GLY* 5.4 0.2 - - - -
154G PHE 3.0 13.3 + - - +
155G GLN* 3.0 13.3 + - - +
157G ASP* 1.3 80.6 + - - +
159G TYR* 1.3 64.3 + - - +
161G GLY* 3.1 14.3 + - - -
162G GLN* 3.5 27.6 + - + +
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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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155G GLN 2.8 18.6 + - - +
156G LEU* 3.6 10.1 - - + +
158G ARG* 1.3 75.0 - - - +
160G LEU* 1.3 73.4 + - + +
162G GLN* 2.7 59.4 + - + +
163G ARG 4.0 1.2 + - - -
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Residues in contact with LEU 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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40G GLY 3.8 8.1 - - - +
41G PHE* 3.6 21.5 - - + -
43G HIS* 3.6 5.2 - - - -
44G TRP* 3.5 37.8 - - + +
89G PHE* 3.9 18.8 - - + -
139G ILE* 3.8 22.2 - - + -
156G LEU* 2.9 43.1 + - + +
157G ASP 4.3 1.3 - - - +
159G TYR* 1.3 90.7 - - + +
161G GLY* 1.3 61.2 + - - +
162G GLN 3.0 1.7 + - - -
163G ARG* 3.3 19.5 + - - +
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Residues in contact with GLY 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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40G GLY* 3.6 21.8 - - - -
43G HIS* 3.1 28.2 + - - -
157G ASP 3.0 8.5 + - - -
158G ARG* 3.5 8.5 - - - -
159G TYR 3.0 2.2 - - - -
160G LEU* 1.3 77.2 - - - +
162G GLN* 1.3 57.6 + - - +
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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