Contacts of the helix formed by residues 142 - 149 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLU* 5.0 12.6 - - + +
116A GLU* 3.5 23.1 - - + -
142A THR* 4.0 17.9 - - + -
112B SER* 4.0 19.3 - - - -
113B GLU* 5.5 0.7 - - + +
116B GLU* 2.4 29.9 + - + +
141B ARG* 1.3 79.0 - - - +
143B HIS* 1.3 68.6 + - - +
145B THR* 2.6 25.1 + - - +
146B LEU* 2.8 21.4 + - - +
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Residues in contact with HIS 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLU* 2.8 35.4 + - - +
119A VAL* 3.6 26.0 - - + +
120A LYS* 3.7 23.9 - - + +
123A ARG* 3.0 41.7 + - - -
144A TYR* 3.8 30.7 - + + -
142B THR* 1.3 73.0 - - - +
144B TYR* 1.3 63.8 + - - +
146B LEU* 3.2 6.0 + - - +
147B ALA 3.1 14.6 + - - -
162B MET* 3.7 21.9 - - - +
163B PRO* 3.6 24.5 - - + +
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Residues in contact with TYR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLU* 5.0 0.8 + - - -
143A HIS* 3.8 44.0 - + + -
144A TYR* 5.2 0.8 - - - +
163A PRO* 4.9 2.7 - - + -
116B GLU* 3.5 18.9 + - - +
119B VAL* 3.7 22.1 - - + +
123B ARG* 4.5 4.7 + - - -
129B SER 4.4 4.9 + - - -
131B THR* 2.8 35.5 + - - +
142B THR 3.3 0.4 - - - -
143B HIS* 1.3 80.0 - - - +
145B THR* 1.3 63.9 + - + +
147B ALA* 3.0 7.3 + - - +
148B LEU* 3.0 45.2 + - + +
163B PRO* 4.2 20.8 - - + +
164B GLY 4.7 6.7 - - - -
165B HIS 4.4 3.2 + - - -
166B VAL* 4.0 17.9 - - + +
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Residues in contact with THR 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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112B SER* 3.6 22.5 + - - +
115B VAL* 3.7 20.0 - - + -
116B GLU* 3.9 8.7 - - + +
139B HIS* 3.4 25.6 - - - +
140B GLY* 3.2 11.2 - - - -
141B ARG 3.4 0.2 + - - -
142B THR* 2.6 37.9 + - - +
144B TYR* 1.3 75.3 - - + +
146B LEU* 1.3 59.2 + - - +
148B LEU* 3.7 9.2 - - + +
149B THR* 2.8 32.2 + - - -
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Residues in contact with LEU 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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120A LYS* 3.8 27.1 - - + +
140B GLY 3.5 13.9 - - - +
141B ARG* 3.7 17.3 - - + +
142B THR 2.8 19.6 + - - +
143B HIS 3.4 4.9 - - - +
145B THR* 1.3 77.9 + - - +
147B ALA* 1.3 62.1 + - - +
149B THR* 3.2 22.3 + - - +
151B LYS 4.9 3.7 - - - +
155B TYR* 3.3 52.0 - - + +
156B SER* 4.2 7.9 + - - +
159B MET* 4.8 1.3 - - - -
162B MET* 4.0 25.3 - - + +
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Residues in contact with ALA 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 HIS 3.1 10.8 + - - +
144B TYR* 3.0 13.1 + - - +
146B LEU* 1.3 76.0 - - - +
148B LEU* 1.3 59.9 + - - +
149B THR 3.4 1.6 + - - +
162B MET* 4.0 13.7 - - + +
163B PRO* 3.5 27.4 - - + +
166B VAL* 3.5 20.0 - - + +
168B ARG* 2.7 24.4 + - - -
193D ASN 5.2 0.2 - - - +
194D ASP* 3.9 4.0 - - - +
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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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115B VAL* 3.5 32.5 - - + -
119B VAL* 4.3 4.7 - - + -
131B THR* 3.5 25.6 - - - +
133B ALA* 3.2 15.3 - - + +
137B ALA* 4.3 0.5 - - - +
139B HIS* 3.7 18.5 - - + -
144B TYR* 3.0 41.6 + - + +
145B THR* 3.3 10.3 + - + +
147B ALA* 1.3 75.9 - - - +
149B THR* 1.3 54.1 + - - +
150B GLY 3.4 0.5 + - - -
166B VAL* 4.0 13.5 - - + -
168B ARG* 2.7 28.1 + - - -
204B VAL* 4.2 18.8 - - + -
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Residues in contact with THR 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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137B ALA 3.3 19.5 - - - +
138B TYR* 3.8 19.5 - - + -
139B HIS* 2.9 20.1 + - - +
140B GLY 3.4 9.6 + - - +
145B THR 2.8 23.5 + - - -
146B LEU* 3.2 20.3 - - + +
147B ALA 3.2 0.7 - - - +
148B LEU* 1.3 77.4 - - - +
150B GLY* 1.3 57.7 + - - +
151B LYS* 3.1 16.2 + - + +
155B TYR* 3.9 22.9 - - + -
168B ARG* 3.4 7.4 + - - -
193D 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