Contacts of the helix formed by residues 136 - 147 (chain B) in PDB entry 1ZHH
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 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B HIS* 5.7 6.1 - - - +
134B GLY 2.9 12.6 + - - +
135B VAL* 1.3 75.2 - - - +
137B ASP* 1.3 60.8 + - - +
138B LEU* 3.0 13.2 + - - +
139B ILE* 3.0 39.9 + - - +
140B LEU* 2.9 26.3 + - - +
161B SER* 5.6 6.9 + - - +
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Residues in contact with ASP 137 (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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123B ILE* 5.0 0.2 - - - +
126B ASP* 4.5 7.6 - - - +
136B ASN* 1.3 76.9 - - - +
138B LEU* 1.3 59.8 + - + +
140B LEU* 3.4 20.3 + - - +
141B ASP* 3.0 35.5 + - - +
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Residues in contact with LEU 138 (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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136B ASN* 3.0 9.9 + - - +
137B ASP* 1.3 78.7 - - + +
139B ILE* 1.3 59.3 + - + +
141B ASP* 3.4 18.6 + - + +
142B SER* 3.1 25.1 + - - -
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Residues in contact with ILE 139 (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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134B GLY 3.7 22.4 - - - +
135B VAL* 3.9 17.0 - - + -
136B ASN* 3.0 32.2 + - - +
138B LEU* 1.3 74.4 - - + +
140B LEU* 1.3 60.7 + - - +
142B SER* 3.2 9.0 + - - -
143B LEU* 2.9 33.4 + - + +
158B VAL* 4.3 27.6 - - + -
159B MET 3.8 20.6 - - - +
160B THR* 3.9 9.9 - - + -
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Residues in contact with LEU 140 (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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114B PHE* 3.6 31.6 - - + -
116B PHE* 3.8 19.0 - - + -
123B ILE* 3.6 23.1 - - + +
126B ASP* 4.0 30.3 - - + +
130B ALA* 4.1 12.1 - - + -
135B VAL* 3.6 14.4 - - + +
136B ASN 2.9 14.4 + - - +
137B ASP* 3.5 26.0 - - - +
139B ILE* 1.3 77.0 - - - +
141B ASP* 1.3 63.8 + - - +
143B LEU* 3.2 7.8 + - + +
144B ALA* 3.0 18.7 + - - +
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Residues in contact with ASP 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B GLY* 5.9 0.5 - - - -
123B ILE* 3.5 26.3 + - - +
137B ASP* 3.0 22.3 + - - +
138B LEU* 3.5 24.5 - - + +
139B ILE 3.3 0.2 - - - -
140B LEU* 1.3 75.2 - - - +
142B SER* 1.3 62.3 + - - +
144B ALA* 3.3 6.6 + - - +
145B ASN* 3.2 21.5 + - - +
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Residues in contact with SER 142 (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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138B LEU 3.1 14.5 + - - -
139B ILE* 3.2 12.5 + - - -
141B ASP* 1.3 73.9 - - - +
143B LEU* 1.3 59.5 + - - +
145B ASN* 3.2 8.0 + - - +
146B ARG* 2.9 50.7 + - - +
158B VAL* 6.1 1.2 - - - +
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Residues in contact with LEU 143 (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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114B PHE* 4.0 30.1 - - + -
116B PHE* 4.5 9.0 - - + -
135B VAL* 4.1 10.8 - - + -
139B ILE* 2.9 23.7 + - + +
140B LEU* 3.2 10.1 + - + +
142B SER* 1.3 76.4 - - - +
144B ALA* 1.3 61.2 + - - +
146B ARG* 3.3 8.0 + - - +
147B VAL* 3.1 31.2 + - - +
156B ILE* 3.8 39.5 - - + -
158B VAL* 5.0 1.8 - - + -
167B MET* 4.1 20.2 - - + -
169B VAL* 4.8 12.3 - - + -
187B PHE* 4.7 1.8 - - - -
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Residues in contact with ALA 144 (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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116B PHE* 3.9 18.3 - - + -
118B THR* 4.4 9.6 - - + -
122B GLY* 6.5 0.2 - - - -
123B ILE* 4.5 4.3 - - + -
140B LEU 3.0 11.9 + - - +
141B ASP* 3.5 12.1 - - - +
143B LEU* 1.3 77.1 - - - +
145B ASN* 1.3 60.8 + - - +
147B VAL 3.5 17.0 - - - +
148B SER* 5.3 0.2 - - - -
171B ARG* 4.8 2.9 + - - -
187B PHE* 3.8 20.9 - - + -
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Residues in contact with ASN 145 (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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221A HIS* 4.8 11.0 + - - -
141B ASP 3.2 12.6 + - - +
142B SER* 3.6 11.8 + - - +
144B ALA* 1.3 77.5 - - - +
146B ARG* 1.3 67.6 + - - +
147B VAL 3.5 0.3 + - - -
148B SER* 4.2 13.2 - - - -
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Residues in contact with ARG 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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22A THR* 2.8 55.6 + - + +
221A HIS* 5.9 0.2 + - - -
142B SER* 2.9 38.3 + - - +
143B LEU* 3.3 12.2 + - - +
145B ASN* 1.3 82.9 - - - +
147B VAL* 1.3 58.0 + - - +
148B SER* 3.2 10.4 + - - -
154B TYR* 3.6 14.2 - - - -
156B ILE* 3.7 36.1 - - + +
157B ASN 4.7 7.9 + - - +
158B VAL* 4.1 21.2 - - - +
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Residues in contact with VAL 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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143B LEU 3.1 17.9 + - - +
144B ALA 3.5 10.0 - - - +
145B ASN 3.4 0.2 - - - -
146B ARG* 1.3 74.7 - - - +
148B SER* 1.3 58.1 + - - +
149B PHE 3.7 9.6 - - - +
154B TYR* 3.7 38.8 - - + -
156B ILE* 4.1 12.3 - - + -
169B VAL* 4.0 22.4 - - + -
170B ARG* 4.4 2.0 - - - -
171B ARG* 3.2 44.0 + - + +
187B PHE* 3.7 9.4 - - + -
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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