Contacts of the helix formed by residues 152 - 168 (chain A) in PDB entry 5ZUN
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 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A LEU 3.9 0.4 + - - -
151A ALA* 1.3 70.4 - - - +
153A PRO* 1.3 67.5 - - - +
154A GLU* 3.0 14.2 + - - +
155A SER* 3.0 35.0 + - - +
156A ALA* 2.9 26.0 + - - +
239A ASP 5.0 1.2 + - - -
240A ARG* 3.3 41.7 + - - +
241A LEU* 2.9 13.8 + - + +
243A ASP* 4.1 11.9 + - - +
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Residues in contact with PRO 153 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A ALA 3.3 10.8 - - - +
152A ASN* 1.3 87.1 - - - +
154A GLU* 1.3 61.2 + - + +
156A ALA* 3.9 4.8 - - + +
157A THR* 2.9 32.6 + - - +
243A ASP* 4.0 20.2 - - + +
245A LYS* 6.4 2.0 - - + -
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Residues in contact with GLU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ASN* 3.0 9.9 + - - +
153A PRO* 1.3 78.9 - - + +
155A SER* 1.3 58.6 + - - +
157A THR* 3.4 5.2 + - - -
158A THR* 2.9 34.4 + - - +
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Residues in contact with SER 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ALA* 6.0 1.1 - - - -
152A ASN* 3.0 28.7 + - - +
154A GLU* 1.3 76.8 - - - +
156A ALA* 1.3 58.1 + - - +
158A THR* 3.4 7.6 + - - -
159A PHE* 3.0 28.4 + - - +
240A ARG* 4.6 3.3 + - - +
241A LEU* 5.9 4.5 - - - -
402A PG4 3.9 36.4 - - - +
403A EDO 4.6 6.1 + - - -
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Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ALA* 4.1 17.5 - - + +
152A ASN 2.9 17.0 + - - +
153A PRO* 3.9 6.3 - - + +
155A SER* 1.3 75.6 - - - +
157A THR* 1.3 58.7 + - - +
159A PHE* 3.3 6.6 + - - +
160A LYS* 2.9 39.1 + - - +
214A LEU* 5.0 8.9 - - + +
402A PG4 4.5 11.6 - - - -
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Residues in contact with THR 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A PRO* 2.9 19.8 + - - +
154A GLU* 3.8 5.4 - - - -
156A ALA* 1.3 74.9 - - - +
158A THR* 1.3 65.7 + - - +
160A LYS* 3.2 10.2 + - + +
161A VAL* 3.0 32.6 + - + +
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Residues in contact with THR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLU* 2.9 18.8 + - - +
155A SER* 3.5 7.8 - - - +
156A ALA 3.4 0.2 - - - -
157A THR* 1.3 76.8 - - - +
159A PHE* 1.3 66.1 + - - +
161A VAL* 3.3 6.6 + - - +
162A LEU* 3.0 26.2 + - + +
176A SER* 5.0 13.2 - - - -
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Residues in contact with PHE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A SER 3.0 17.8 + - - +
156A ALA 3.6 3.4 - - - +
157A THR 3.2 0.4 - - - -
158A THR* 1.3 79.8 - - - +
160A LYS* 1.3 59.4 + - - +
162A LEU* 3.2 7.9 + - + +
163A ALA* 2.8 45.6 + - + +
176A SER* 3.7 23.1 - - - +
205A LEU* 4.0 13.0 - - + -
207A VAL* 3.5 34.3 - - + -
210A GLY* 3.4 39.3 - - - -
211A ILE* 3.7 2.5 - - + -
214A LEU* 3.8 22.7 - - + -
402A PG4 4.0 26.5 - - - +
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Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ALA* 2.9 24.8 + - - +
157A THR* 3.2 8.9 + - + +
159A PHE* 1.3 78.7 - - - +
161A VAL* 1.3 63.4 + - + +
163A ALA* 3.8 4.9 - - - +
164A ALA* 3.1 23.7 + - - +
214A LEU* 3.8 38.8 - - + -
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A THR* 3.0 24.4 + - + +
158A THR* 3.7 9.2 - - - +
160A LYS* 1.3 76.2 - - + +
162A LEU* 1.3 63.1 + - - +
164A ALA* 3.3 7.0 + - - +
165A LYS* 3.2 38.4 + - + +
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A THR* 3.0 21.7 + - + +
159A PHE* 3.7 10.3 - - + +
161A VAL* 1.3 76.4 - - - +
163A ALA* 1.3 63.5 + - - +
165A LYS* 3.0 29.6 + - - +
166A VAL* 3.0 19.6 + - + +
174A LEU* 4.3 14.6 - - + -
175A SER* 3.7 32.3 - - - +
176A SER* 3.7 22.2 - - - +
207A VAL* 3.7 26.0 - - + -
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Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A PHE* 2.8 33.6 + - + +
160A LYS* 3.8 5.8 - - - +
162A LEU* 1.3 77.4 - - - +
164A ALA* 1.3 56.8 + - - +
166A VAL 3.3 0.5 + - - -
167A LEU* 2.6 50.8 + - + +
207A VAL* 3.9 19.3 - - + -
211A ILE* 4.7 4.9 - - + -
214A LEU* 5.8 1.3 - - + -
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Residues in contact with ALA 164 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A LYS 3.1 17.6 + - - +
161A VAL* 3.7 7.0 - - - +
162A LEU 3.2 0.2 - - - -
163A ALA* 1.3 77.6 - - - +
165A LYS* 1.3 56.3 + - - +
167A LEU* 4.9 1.1 - - - -
168A ASN* 2.9 52.5 + - - +
169A SER* 3.4 2.4 + - - -
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Residues in contact with LYS 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A VAL* 3.2 25.2 + - + +
162A LEU* 3.0 28.5 + - - +
164A ALA* 1.3 75.3 - - - +
166A VAL* 1.3 61.5 + - - +
169A SER* 3.2 24.6 + - - +
170A VAL 3.2 0.2 + - - -
171A LEU* 3.2 44.2 + - + +
174A LEU* 4.4 12.3 - - + +
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Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A LEU* 3.0 16.1 + - + +
163A ALA 3.9 3.1 - - - +
165A LYS* 1.3 78.8 - - - +
167A LEU* 1.3 73.4 + - + +
170A VAL* 3.3 21.3 - - - +
171A LEU 3.6 18.1 + - - +
173A ASN 6.1 0.9 - - - +
174A LEU* 3.6 35.2 - - + +
207A VAL* 3.9 28.3 - - + -
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ALA* 2.6 35.6 + - + +
164A ALA* 4.9 0.4 - - - -
166A VAL* 1.3 87.1 - - + +
168A ASN* 1.3 72.9 - - - +
170A VAL* 4.3 9.5 - - - +
207A VAL* 3.4 30.7 - - + -
208A CYS* 6.4 0.2 - - - -
211A ILE* 3.6 20.9 - - + -
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Residues in contact with ASN 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ALA* 2.9 32.5 + - + +
167A LEU* 1.3 92.1 - - - +
169A SER* 1.3 60.7 + - - +
170A VAL* 3.4 6.5 + - - +
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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