Contacts of the helix formed by residues 145 - 159 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B LEU* 1.3 78.6 - - - +
146B SER* 1.3 64.6 - - - +
147B GLU* 3.7 15.7 + - - +
148B LEU* 3.2 32.6 + - + +
149B LYS* 3.1 21.3 + - - +
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Residues in contact with SER 146 (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 LEU 3.8 1.0 + - - -
145B THR* 1.3 72.1 - - - +
147B GLU* 1.3 65.2 + - - +
149B LYS* 3.2 13.5 + - - +
150B GLU* 2.8 50.1 + - - +
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Residues in contact with GLU 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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145B THR* 3.1 15.7 - - - +
146B SER* 1.3 86.4 - - - +
148B LEU* 1.3 58.1 + - + +
150B GLU* 3.4 15.4 + - - +
151B ASN* 3.0 28.4 + - - +
154B ARG* 5.2 1.2 + - - -
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Residues in contact with LEU 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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117B GLN* 6.1 0.4 - - + -
118B HIS* 4.0 43.1 - - + +
120B MET* 6.0 0.2 - - - +
137B LEU* 4.4 9.1 - - + +
144B LEU* 4.1 33.7 - - + -
145B THR* 3.2 27.4 + - + +
147B GLU* 1.3 76.4 - - + +
149B LYS* 1.3 58.2 + - - +
151B ASN* 3.3 12.5 + - + +
152B PHE* 3.1 26.0 + - - +
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Residues in contact with LYS 149 (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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34B VAL* 4.5 10.9 - - + +
137B LEU* 4.1 11.4 - - + -
143B GLU* 5.2 6.1 + - - -
144B LEU* 3.5 29.6 + - + +
145B THR 3.1 15.2 + - - +
146B SER* 3.8 10.8 - - - +
148B LEU* 1.3 74.9 - - - +
150B GLU* 1.3 61.4 + - - +
152B PHE* 3.2 8.6 + - - +
153B ILE* 3.0 33.6 + - + +
168B PHE* 3.9 36.9 - - + +
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Residues in contact with GLU 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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146B SER* 2.8 36.9 + - - +
147B GLU* 3.7 15.2 - - - +
149B LYS* 1.3 74.5 - - + +
151B ASN* 1.3 59.2 + - - +
153B ILE* 3.3 14.7 + - + +
154B ARG* 2.9 45.5 + - - +
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Residues in contact with ASN 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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120B MET* 4.2 20.4 - - - +
147B GLU 3.0 15.1 + - - +
148B LEU* 3.5 17.4 + - + +
149B LYS 3.3 0.2 - - - -
150B GLU* 1.3 76.0 - - - +
152B PHE* 1.3 58.1 + - - +
154B ARG* 3.1 28.9 + - - +
155B PHE* 2.9 28.0 + - - +
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Residues in contact with PHE 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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35B GLY* 3.8 7.0 - - - -
36B LEU 3.7 23.3 - - - -
37B ALA* 3.8 11.2 - - + -
120B MET* 3.7 28.7 - - + -
135B ILE* 3.6 41.3 - - + -
137B LEU* 3.8 29.4 - - + -
148B LEU 3.1 13.4 + - - +
149B LYS 3.5 6.3 - - - +
150B GLU 3.2 0.2 - - - -
151B ASN* 1.3 74.9 - - - +
153B ILE* 1.3 61.2 + - - +
155B PHE* 3.4 1.0 + - - +
156B SER* 2.9 39.1 + - - -
166B ILE* 3.9 20.4 - - + -
168B PHE* 4.0 19.7 - + - -
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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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149B LYS* 3.0 23.9 + - + +
150B GLU* 3.3 15.2 + - + +
152B PHE* 1.3 74.2 - - - +
154B ARG* 1.3 66.5 + - - +
156B SER* 3.3 2.0 + - - -
157B LYS* 2.9 30.3 + - + +
163B GLU* 4.0 32.1 - - - +
166B ILE* 4.1 23.5 - - + +
168B PHE* 3.9 28.9 - - + -
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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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147B GLU 5.2 0.8 + - - -
150B GLU* 2.9 40.4 + - - +
151B ASN* 3.1 35.2 + - - +
153B ILE* 1.3 78.6 - - - +
155B PHE* 1.3 62.1 + - - +
157B LYS* 3.3 7.5 + - - +
158B SER* 3.0 21.8 + - - -
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Residues in contact with PHE 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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15B LYS 3.9 10.5 - - - -
16B VAL* 4.4 4.5 - - + -
17B PRO* 3.8 26.7 - - + -
111B VAL* 4.0 30.5 - - + -
120B MET* 3.9 27.6 - - + -
122B PHE* 5.6 0.4 - + - -
135B ILE* 3.9 22.9 - - + -
151B ASN* 2.9 18.9 + - - +
152B PHE 3.8 3.8 - - - +
154B ARG* 1.3 76.2 - - - +
156B SER* 1.3 64.2 + - - +
158B SER* 2.7 33.9 + - - -
159B LEU* 3.3 29.9 + - + +
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Residues in contact with SER 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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37B ALA* 3.3 25.0 - - - +
135B ILE* 4.0 14.0 - - - +
152B PHE* 2.9 31.9 + - - -
153B ILE 3.6 4.5 - - - -
155B PHE* 1.3 78.1 - - - +
157B LYS* 1.3 61.0 + - - +
159B LEU* 3.1 13.7 + - - +
160B GLY 3.5 0.5 + - - -
161B LEU* 3.3 23.3 + - - +
166B ILE* 3.7 20.4 - - - -
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Residues in contact with LYS 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 27.0 + - + +
154B ARG* 3.6 7.0 - - - +
156B SER* 1.3 70.5 - - - +
158B SER* 1.3 58.1 + - - +
159B LEU 3.0 5.4 - - - -
160B GLY* 2.9 20.6 + - - -
161B LEU 3.3 19.5 + - - +
162B PRO* 4.9 4.5 - - + +
163B GLU* 3.4 36.8 + - - +
166B ILE* 4.9 2.2 - - + -
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Residues in contact with SER 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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15B LYS* 4.0 26.1 + - - +
154B ARG* 3.0 13.6 + - - -
155B PHE* 2.7 33.6 + - - -
157B LYS* 1.3 75.4 - - - +
159B LEU* 1.3 61.4 + - - +
160B GLY 3.3 1.3 + - - -
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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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8B ILE* 4.9 0.2 - - - +
9B PRO 4.5 4.3 - - - +
11B PRO* 3.9 34.0 - - + +
15B LYS* 3.6 31.6 - - + +
16B VAL* 4.2 3.1 - - + -
122B PHE* 4.2 18.2 - - + -
133B PHE* 3.8 21.9 - - + -
135B ILE* 3.8 27.1 - - + -
155B PHE* 3.5 33.2 - - + +
156B SER* 3.1 7.4 + - - +
157B LYS 3.0 1.2 - - - -
158B SER* 1.3 83.8 - - - +
160B GLY* 1.3 59.2 + - - +
161B LEU 3.5 1.3 - - - -
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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
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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