Contacts of the helix formed by residues 142 - 149 (chain A) in PDB entry 1SZU
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 142 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A SER* 4.1 20.2 - - - -
113A GLU* 6.0 0.9 - - + -
116A GLU* 2.5 30.6 + - + +
141A ARG* 1.3 78.2 - - - +
143A HIS* 1.3 66.8 + - - +
145A THR* 2.5 27.9 + - - +
146A LEU* 2.7 21.1 + - - +
113B GLU* 5.1 11.9 - - + -
116B GLU* 3.5 23.6 - - + +
142B THR* 4.0 18.4 - - + -
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Residues in contact with HIS 143 (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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141A ARG 4.0 0.4 + - - -
142A THR* 1.3 72.7 - - - +
144A TYR* 1.3 63.1 + - - +
146A LEU* 3.2 5.4 + - - +
147A ALA 3.1 15.8 + - - -
162A MET* 3.8 22.5 - - - +
163A PRO* 3.6 23.2 - - + +
116B GLU* 2.7 48.1 + - - +
119B VAL* 3.6 29.1 - - + +
120B LYS* 3.8 13.0 - - + +
123B ARG* 3.1 36.8 + - - -
144B TYR* 3.8 32.3 - + + -
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Residues in contact with TYR 144 (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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116A GLU* 3.5 19.8 + - - +
119A VAL* 3.9 21.5 - - + +
123A ARG* 4.7 4.5 + - - -
129A SER 4.5 5.2 + - - -
131A THR* 2.7 34.6 + - - +
142A THR* 3.3 1.2 + - - -
143A HIS* 1.3 79.0 - - - +
145A THR* 1.3 60.0 + - + +
147A ALA* 3.0 18.9 + - - +
148A LEU* 3.0 39.4 + - + +
163A PRO* 4.3 20.1 - - + +
164A GLY 4.8 6.7 - - - -
165A HIS 4.4 3.3 + - - -
166A VAL* 3.9 16.8 - - + +
116B GLU* 5.1 0.6 + - - -
143B HIS* 3.8 43.1 - + + -
144B TYR* 5.2 1.0 - - - +
163B PRO* 4.8 3.1 - - + -
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Residues in contact with THR 145 (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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112A SER* 3.7 19.0 + - - +
115A VAL* 3.9 20.0 - - + -
116A GLU* 4.0 9.0 - - + -
139A HIS* 3.3 27.7 - - - +
140A GLY* 3.2 9.9 - - - -
141A ARG 3.3 0.2 + - - -
142A THR* 2.5 41.2 + - - +
144A TYR* 1.3 74.4 - - + +
146A LEU* 1.3 55.1 + - - +
148A LEU* 3.6 10.0 - - + +
149A THR* 2.6 38.3 + - - -
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Residues in contact with LEU 146 (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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140A GLY 3.5 14.6 - - - +
141A ARG* 3.6 19.1 - - + +
142A THR 2.7 16.6 + - - +
143A HIS 3.4 4.9 - - - +
145A THR* 1.3 76.2 - - - +
147A ALA* 1.3 64.4 + - - +
149A THR* 3.1 22.8 + - - +
151A LYS 4.9 1.2 - - - +
155A TYR* 3.5 46.4 - - + +
156A SER* 3.8 17.4 + - - +
159A MET* 4.5 2.7 - - - -
162A MET* 3.9 19.9 - - + +
120B LYS* 3.6 30.5 - - + +
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Residues in contact with ALA 147 (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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143A HIS 3.1 8.2 + - - +
144A TYR* 3.0 12.2 + - - +
146A LEU* 1.3 77.2 - - - +
148A LEU* 1.3 57.8 + - - +
149A THR 3.3 2.1 - - - +
162A MET* 3.9 17.4 - - + +
163A PRO* 3.4 28.0 - - + +
166A VAL* 3.6 19.9 - - + +
168A ARG* 2.9 24.4 + - - -
193C ASN 5.1 0.2 - - - +
194C ASP* 4.1 3.1 - - - +
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Residues in contact with LEU 148 (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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115A VAL* 3.6 31.2 - - + -
119A VAL* 4.4 5.2 - - + -
131A THR* 3.4 30.7 - - + +
132A ILE 5.0 0.2 - - - +
133A ALA* 3.2 20.4 - - + +
137A ALA* 4.1 0.5 - - - +
139A HIS* 3.5 21.2 - - + -
144A TYR* 3.0 37.8 + - + +
145A THR* 3.6 12.3 - - + +
146A LEU 3.3 0.2 - - - -
147A ALA* 1.3 73.0 - - - +
149A THR* 1.3 60.4 + - - +
150A GLY 3.3 0.5 + - - -
166A VAL* 4.0 13.0 - - + -
168A ARG* 2.9 23.9 + - - -
204A VAL* 4.2 11.7 - - + -
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Residues in contact with THR 149 (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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137A ALA 3.3 19.5 - - - +
138A TYR* 3.8 19.1 - - + -
139A HIS 2.9 19.0 + - - +
140A GLY 3.3 9.6 + - - -
145A THR 2.6 22.8 + - - -
146A LEU* 3.1 19.9 - - + +
147A ALA 3.3 5.5 - - - +
148A LEU* 1.3 76.3 - - - +
150A GLY* 1.3 58.0 + - - +
151A LYS* 3.2 25.0 + - + +
155A TYR* 3.9 12.1 - - + -
168A ARG* 3.4 2.8 + - - -
193C ASN 3.6 4.3 - - - +
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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