Contacts of the helix formed by residues 146 - 156 (chain D) in PDB entry 1SZP
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 146 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A ASN* 3.0 56.8 - - - +
247A VAL 3.3 8.7 - - - -
248A ALA* 4.6 1.1 - - - +
145D VAL* 1.3 84.7 - - - +
147D ALA* 1.3 62.8 + - - +
148D ALA 3.3 7.1 + - - -
149D ASP* 3.4 25.1 + - + +
150D PHE 3.2 14.9 + - - -
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Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A PHE* 4.7 13.0 - - + -
226A PRO* 3.4 13.5 - - + +
229A LEU* 5.1 3.8 - - + -
244A LEU* 3.7 10.2 + - + +
247A VAL* 2.5 40.8 + - + +
249A TYR* 4.4 9.0 - - + -
145D VAL 4.3 0.4 - - - -
146D THR* 1.3 70.2 + - - +
148D ALA* 1.3 66.4 + - - +
150D PHE* 3.0 22.6 + - - +
151D HIS 3.3 3.8 + - - -
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Residues in contact with ALA 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A ASP* 4.2 11.9 - - + +
244A LEU* 3.3 37.8 - - + +
245A ASN* 3.7 13.7 - - - +
146D THR* 3.3 9.3 + - - +
147D ALA* 1.3 73.4 - - - +
149D ASP* 1.3 67.5 + - - +
150D PHE 2.9 1.0 + - - -
151D HIS* 3.2 18.5 - - - +
152D MET* 3.6 4.7 + - - +
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Residues in contact with ASP 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ASN* 5.3 1.0 - - - +
145D VAL* 4.3 10.3 - - + +
146D THR* 3.4 38.1 + - + +
147D ALA 3.2 0.6 - - - -
148D ALA* 1.3 78.1 - - - +
150D PHE* 1.3 65.1 + - - +
152D MET* 3.5 13.4 + - - +
153D ARG* 3.7 25.4 + - - +
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Residues in contact with PHE 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A PHE* 3.8 22.0 - + - -
225A ARG* 5.3 3.1 - - - -
226A PRO* 4.0 20.2 - - + -
249A TYR* 4.0 35.9 - + + -
145D VAL* 4.3 13.9 - - + -
146D THR 3.2 8.4 + - - +
147D ALA* 3.0 16.4 + - - +
148D ALA 3.0 1.4 - - - -
149D ASP* 1.3 72.8 - - - +
151D HIS* 1.3 54.8 + - - +
152D MET 2.8 0.5 + - - -
153D ARG* 2.7 46.7 + - + +
154D ARG* 3.5 23.2 + - + -
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Residues in contact with HIS 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ARG* 4.7 3.8 + - - -
226A PRO* 4.0 20.3 - - + +
227A VAL* 3.4 38.7 + - + +
244A LEU* 5.0 11.7 - - + -
147D ALA 3.3 1.5 + - - +
148D ALA* 3.2 14.8 - - - +
150D PHE* 1.3 74.4 - - - +
152D MET* 1.3 63.2 + - - +
154D ARG* 4.0 8.5 - - - -
155D SER* 3.0 31.7 + - - -
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Residues in contact with MET 152 (chain D).
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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148D ALA 3.6 3.8 + - - +
149D ASP* 3.5 14.2 + - - +
150D PHE 2.8 4.9 + - - -
151D HIS* 1.3 77.5 - - - +
153D ARG* 1.3 56.5 + - + +
154D ARG 2.6 15.0 + - - -
155D SER* 3.1 14.3 + - - -
156D GLU* 3.6 10.3 + - - +
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Residues in contact with ARG 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D PRO* 3.8 32.7 - - - +
145D VAL* 4.5 22.7 - - - +
149D ASP* 3.7 22.7 + - - +
150D PHE* 2.7 24.8 + - + +
152D MET* 1.3 74.7 - - + +
154D ARG* 1.3 59.3 + - - +
156D GLU* 4.2 14.2 + - - +
157D LEU* 5.2 1.2 - - - +
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Residues in contact with ARG 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ARG* 3.2 39.2 + - - +
150D PHE* 3.5 19.9 + - + +
151D HIS* 4.3 14.1 - - - +
152D MET 2.6 6.7 + - - -
153D ARG* 1.3 74.8 - - - +
155D SER* 1.3 57.6 + - - +
157D LEU* 3.0 28.6 - - - +
176D GLU* 5.5 1.7 - - - -
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Residues in contact with SER 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ARG* 4.8 3.3 + - - +
151D HIS* 3.0 35.1 + - - -
152D MET* 3.1 4.4 + - - -
154D ARG* 1.3 71.3 - - - +
156D GLU* 1.4 52.4 + - - +
157D LEU* 2.9 21.9 + - - +
176D GLU* 5.9 2.2 - - - -
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Residues in contact with GLU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D MET 3.6 10.5 + - - +
153D ARG* 4.5 10.9 - - - +
154D ARG 3.4 1.6 - - - -
155D SER* 1.4 73.3 - - - +
157D LEU* 1.3 58.4 + - - +
158D ILE* 4.2 2.4 + - - +
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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