Contacts of the helix formed by residues 145 - 159 (chain F) in PDB entry 4ZHF
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 THR 145 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117F GLN* 5.0 7.9 - - - +
144F LEU* 1.3 78.4 - - - +
146F SER* 1.3 65.7 + - - +
147F GLU* 3.6 10.7 + - - +
148F LEU* 3.2 32.8 + - + +
149F LYS* 3.1 21.5 + - - +
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Residues in contact with SER 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F LEU 3.8 1.0 + - - -
145F THR* 1.3 72.3 - - - +
147F GLU* 1.3 58.0 + - - +
149F LYS* 3.2 13.2 + - - +
150F GLU* 2.8 44.1 + - - +
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Residues in contact with GLU 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F THR* 3.0 11.3 - - - +
146F SER* 1.3 79.2 - - - +
148F LEU* 1.3 59.8 + - + +
150F GLU* 3.4 5.4 + - - +
151F ASN* 3.0 28.2 + - + +
154F ARG* 5.2 1.0 + - - -
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Residues in contact with LEU 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F GLN* 3.4 28.7 - - - +
118F HIS* 3.7 39.0 - - + +
120F MET* 5.9 0.2 - - - +
137F LEU* 4.5 8.6 - - + +
144F LEU* 4.1 28.9 - - + -
145F THR* 3.2 20.4 + - - +
147F GLU* 1.3 84.9 - - + +
149F LYS* 1.3 61.7 + - - +
151F ASN* 3.3 11.5 + - + +
152F PHE* 3.0 22.3 + - - +
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Residues in contact with LYS 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F VAL* 4.5 11.1 - - + +
137F LEU* 4.1 12.6 - - + -
143F GLU* 5.1 6.5 + - - -
144F LEU* 3.5 30.2 + - + +
145F THR 3.1 14.8 + - - +
146F SER* 3.8 9.2 - - - +
148F LEU* 1.3 76.1 - - - +
150F GLU* 1.3 58.7 + - + +
152F PHE* 3.3 9.3 + - - +
153F ILE* 3.0 34.9 + - + +
168F PHE* 3.9 35.4 - - + +
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Residues in contact with GLU 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F SER* 2.8 30.3 + - - +
147F GLU* 3.7 6.5 - - - +
149F LYS* 1.3 75.3 - - + +
151F ASN* 1.3 59.8 + - - +
153F ILE* 3.3 26.4 + - - +
154F ARG* 2.8 45.0 + - - +
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Residues in contact with ASN 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F MET* 4.1 19.4 - - - +
147F GLU* 3.0 14.7 + - + +
148F LEU* 3.5 17.1 + - + +
149F LYS 3.3 0.2 - - - -
150F GLU* 1.3 76.9 - - - +
152F PHE* 1.3 57.3 + - - +
154F ARG* 3.1 29.4 + - - +
155F PHE* 3.0 29.2 + - - +
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Residues in contact with PHE 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F GLY* 3.7 8.3 - - - -
36F LEU 3.7 23.1 - - - -
37F ALA* 3.8 11.2 - - + -
120F MET* 3.7 28.5 - - + -
135F ILE* 3.6 42.4 - - + -
137F LEU* 3.8 27.4 - - + -
148F LEU 3.0 13.5 + - - +
149F LYS 3.4 6.5 - - - +
150F GLU 3.2 0.2 - - - -
151F ASN* 1.3 74.3 - - - +
153F ILE* 1.3 60.7 + - - +
155F PHE* 3.4 1.0 + - - +
156F SER* 2.9 39.3 + - - -
166F ILE* 3.9 20.2 - - + -
168F PHE* 4.0 20.2 - + - -
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Residues in contact with ILE 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F LYS* 3.0 20.7 + - + +
150F GLU* 3.3 32.7 + - - +
152F PHE* 1.3 72.0 - - - +
154F ARG* 1.3 66.1 + - - +
156F SER* 3.3 1.4 + - - -
157F LYS* 3.0 50.2 + - + +
163F GLU* 4.1 19.3 - - - +
166F ILE* 4.2 20.4 - - + +
168F PHE* 3.8 31.0 - - + -
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Residues in contact with ARG 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F GLU 5.2 0.8 + - - -
150F GLU* 2.8 41.0 + - - +
151F ASN* 3.1 35.8 + - - +
153F ILE* 1.3 80.2 - - - +
155F PHE* 1.3 61.2 + - - +
157F LYS* 3.3 8.7 + - - +
158F SER* 3.1 21.2 + - - -
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Residues in contact with PHE 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LYS 3.9 10.8 - - - -
16F VAL* 4.4 5.2 - - + -
17F PRO* 3.7 25.8 - - + -
111F VAL* 4.0 29.8 - - + -
120F MET* 3.9 27.4 - - + -
122F PHE* 5.5 0.4 - + - -
135F ILE* 4.0 22.9 - - + -
151F ASN* 3.0 17.3 + - - +
152F PHE 3.8 3.4 - - - +
153F ILE 3.3 0.2 - - - -
154F ARG* 1.3 76.4 - - - +
156F SER* 1.3 64.6 + - - +
158F SER* 2.7 32.4 + - - -
159F LEU* 3.3 31.3 + - + +
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Residues in contact with SER 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F ALA* 3.3 25.9 - - - +
135F ILE* 4.0 15.4 - - - +
152F PHE* 2.9 33.7 + - - -
153F ILE 3.6 4.5 - - - -
155F PHE* 1.3 76.5 - - - +
157F LYS* 1.3 61.4 + - - +
159F LEU* 3.1 13.2 + - - +
160F GLY 3.5 0.2 + - - -
161F LEU* 3.2 23.8 + - - +
166F ILE* 3.7 20.2 - - - -
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Residues in contact with LYS 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F ILE* 3.0 33.3 + - + +
154F ARG* 3.6 7.9 - - - +
156F SER* 1.3 71.6 - - - +
158F SER* 1.3 58.7 + - - +
159F LEU 3.0 5.4 - - - -
160F GLY* 2.9 20.3 + - - -
161F LEU 3.3 20.0 - - - +
162F PRO* 5.0 2.0 - - + -
163F GLU* 2.7 39.0 + - - +
166F ILE* 4.9 2.0 - - + -
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Residues in contact with SER 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LYS* 4.0 25.4 + - - +
154F ARG* 3.1 13.2 + - - -
155F PHE* 2.7 34.1 + - - -
157F LYS* 1.3 75.6 - - - +
159F LEU* 1.3 62.8 + - - +
160F GLY 3.3 1.1 - - - -
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Residues in contact with LEU 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F PRO 4.5 4.3 - - - +
11F PRO* 3.9 34.1 - - + +
15F LYS* 3.7 31.9 - - + +
16F VAL* 4.2 3.4 - - + -
122F PHE* 4.2 17.5 - - + -
133F PHE* 3.8 23.1 - - + -
135F ILE* 3.8 23.1 - - + -
155F PHE* 3.5 38.1 - - + +
156F SER 3.1 7.8 + - - +
157F LYS 3.0 1.4 - - - -
158F SER* 1.3 83.6 - - - +
160F GLY* 1.3 58.9 + - - +
161F LEU 3.5 1.6 - - - -
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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