Contacts of the helix formed by residues 158 - 171 (chain B) in PDB entry 4ZCU
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 ASP 158 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B LYS 5.7 1.3 - - - -
91B MET* 4.3 4.4 - - - +
94B ALA* 5.2 2.9 - - - -
156B VAL 3.7 0.6 - - - -
157B THR* 1.3 89.8 + - - +
159B ILE* 1.3 60.8 + - + +
160B GLU* 3.1 23.2 - - - +
161B GLU* 3.0 26.5 + - - +
162B ILE* 3.0 34.9 + - - +
164B ARG* 5.0 0.2 + - - -
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Residues in contact with ILE 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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94B ALA* 4.8 13.0 - - + +
97B SER* 5.3 6.1 - - - +
98B LEU* 3.9 37.7 - - + -
114B SER* 5.9 1.6 - - - -
115B LEU* 5.5 2.9 - - + -
118B LEU* 4.2 17.5 - - + -
158B ASP* 1.3 76.6 - - + +
160B GLU* 1.3 77.3 + - - +
162B ILE* 3.3 23.8 + - + +
163B ILE* 2.9 49.8 + - + +
166B TRP* 4.6 4.7 - - + -
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Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 4.8 17.0 - - + +
158B ASP* 3.1 27.9 - - - +
159B ILE* 1.3 91.3 - - + +
161B GLU* 1.3 58.0 + - - +
163B ILE* 3.0 11.1 + - + +
164B ARG* 2.9 51.8 + - - +
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Residues in contact with GLU 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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62B LYS* 3.0 27.5 + - - -
156B VAL* 3.3 17.2 - - + +
157B THR* 2.8 35.7 + - - +
158B ASP* 3.0 22.5 + - - +
160B GLU* 1.3 74.6 - - - +
162B ILE* 1.3 58.1 + - - +
164B ARG* 3.7 24.8 - - - +
165B PHE* 2.9 29.3 + - - +
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Residues in contact with ILE 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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91B MET* 4.1 15.0 - - - -
94B ALA* 4.1 16.8 - - + -
147B TRP* 3.9 24.2 - - + -
151B PHE* 4.0 13.0 - - + -
156B VAL* 3.7 23.8 - - + -
158B ASP 3.0 21.5 + - - +
159B ILE* 3.4 14.1 - - + +
160B GLU 3.2 0.2 - - - -
161B GLU* 1.3 77.0 - - - +
163B ILE* 1.3 57.2 + - - +
165B PHE* 3.4 3.9 + - - +
166B TRP* 2.9 63.9 + - + -
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Residues in contact with ILE 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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115B LEU* 3.7 28.3 - - + -
118B LEU* 3.7 29.4 - - + -
120B LEU* 4.0 15.0 - - + -
159B ILE* 2.9 23.7 + - + +
160B GLU* 3.0 10.7 + - - +
162B ILE* 1.3 75.0 - - - +
164B ARG* 1.3 61.0 + - + +
166B TRP* 3.1 19.6 + - + +
167B LYS* 2.9 26.2 + - - +
174B ILE* 3.8 34.9 - - + +
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Residues in contact with ARG 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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158B ASP* 5.0 0.2 + - - -
160B GLU* 2.9 31.4 + - - +
161B GLU* 3.7 39.7 + - - +
163B ILE* 1.3 77.5 - - + +
165B PHE* 1.3 62.6 + - - +
167B LYS* 3.0 13.1 + - + +
168B HIS* 3.0 32.5 + - + +
174B ILE 4.9 3.1 - - - +
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Residues in contact with PHE 165 (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 TYR* 3.6 35.7 - + - -
151B PHE* 4.4 6.7 - + - -
154B ASN* 3.4 33.2 - - - -
156B VAL* 4.1 11.0 - - + -
161B GLU 2.9 17.4 + - - +
162B ILE 3.5 4.3 - - - +
164B ARG* 1.3 76.6 - - - +
166B TRP* 1.3 72.4 + + - +
168B HIS* 3.2 12.1 + - + +
169B SER* 2.8 41.2 + - - -
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Residues in contact with TRP 166 (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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98B LEU* 4.3 9.9 - - + -
111B ILE* 4.3 15.7 - - + -
115B LEU* 4.4 14.1 - - + -
130B ILE* 3.3 48.6 - - + +
133B SER* 5.0 5.2 - - - -
134B ILE* 3.7 26.0 - - + +
147B TRP* 4.1 17.0 - + - -
150B TYR* 5.1 1.1 - + - -
151B PHE* 3.9 9.4 - + - -
159B ILE* 4.6 4.0 - - + -
162B ILE* 2.9 33.1 + - + -
163B ILE* 3.1 32.7 + - + +
165B PHE* 1.3 87.5 - + - +
167B LYS* 1.3 57.7 + - - +
169B SER* 4.3 3.8 - - - -
170B THR* 2.7 42.3 + - + +
174B ILE* 3.9 13.2 - - + -
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Residues in contact with LYS 167 (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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163B ILE 2.9 8.3 + - - +
164B ARG* 3.0 13.9 + - + +
166B TRP* 1.3 77.2 - - - +
168B HIS* 1.3 72.7 + - + +
171B GLY* 3.1 27.6 + - - -
172B ILE 3.3 20.9 - - - +
173B ASP* 3.4 28.0 + - - +
174B ILE* 3.4 30.4 - - - +
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Residues in contact with HIS 168 (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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164B ARG* 3.0 26.4 + - + +
165B PHE* 3.2 12.8 + + + +
167B LYS* 1.3 93.2 + - + +
169B SER* 1.3 58.9 + - - +
171B GLY* 4.6 1.6 + - - -
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Residues in contact with SER 169 (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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133B SER* 4.7 8.0 + - - -
150B TYR* 4.1 12.5 + - - -
165B PHE* 2.8 37.9 + - - -
166B TRP* 4.0 5.6 - - - -
167B LYS 3.2 0.2 - - - -
168B HIS* 1.3 80.3 - - - +
170B THR* 1.3 67.9 + - - +
171B GLY 3.5 0.2 - - - -
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Residues in contact with THR 170 (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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129B LEU* 4.7 14.0 - - + +
130B ILE* 4.2 24.0 - - + +
133B SER* 4.2 23.3 - - - +
166B TRP* 2.7 25.7 + - + +
169B SER* 1.3 82.7 - - - +
171B GLY* 1.3 61.4 + - - +
172B ILE* 3.2 34.9 + - - +
174B ILE* 5.4 1.0 - - - +
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Residues in contact with GLY 171 (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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167B LYS* 3.1 15.5 + - - +
168B HIS 4.6 0.8 + - - -
169B SER 3.5 1.8 - - - +
170B THR* 1.3 77.8 + - - +
172B ILE* 1.3 62.9 + - - +
173B ASP* 3.5 4.0 + - - +
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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