Contacts of the helix formed by residues 145 - 149 (chain B) in PDB entry 1SIW
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 GLU 145 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B THR* 4.0 16.0 - - - +
48B PRO 5.4 0.9 - - - +
49B GLY* 3.8 3.8 - - - -
50B GLN* 3.0 33.4 + - - +
51B GLY* 3.0 32.2 + - - +
143B ASN 3.2 1.0 - - - -
144B TRP* 1.3 82.4 - - + +
146B ASP* 1.3 68.8 + - - +
147B ASP 3.3 0.3 + - - -
148B LEU* 3.3 6.6 + - - -
149B GLY 3.2 20.1 + - - +
154B LYS* 5.0 7.4 - - + +
155B LEU* 3.6 29.0 - - + +
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Residues in contact with ASP 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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1094A LYS* 2.9 25.7 + - - +
1095A TRP* 3.6 8.4 + - + +
1110A LEU 5.0 0.4 - - - +
1118A TRP* 3.7 8.4 - - + -
20B HIS* 3.1 9.9 + - - -
46B THR* 3.7 9.3 + - - +
143B ASN* 2.7 49.6 + - - +
144B TRP 3.3 2.4 + - - +
145B GLU* 1.3 77.5 - - - +
147B ASP* 1.3 91.1 + - - +
149B GLY* 3.1 11.3 + - - -
179B TYR* 5.3 0.2 - - - -
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Residues in contact with ASP 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLN* 4.3 3.3 - - - +
286A GLU* 2.7 28.4 - - - +
1094A LYS* 3.5 5.5 + - - +
1118A TRP* 3.4 6.4 - - + -
1153A ARG* 2.9 42.2 + - - +
46B THR* 3.1 15.6 + - - -
146B ASP* 1.3 88.2 - - - +
148B LEU* 1.3 67.5 + - - +
149B GLY 3.3 0.5 + - - -
177B MET* 3.9 7.6 - - - +
179B TYR* 2.9 31.0 + - - -
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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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284A TYR* 5.1 0.2 - - + -
1151A SER* 2.7 33.9 + - - +
1152A GLN* 4.6 6.5 + - + +
1153A ARG* 4.2 15.0 - - + +
46B THR* 3.9 3.5 - - + +
47B LYS 4.5 0.7 - - - +
48B PRO* 3.8 33.9 - - + +
145B GLU 3.3 5.7 + - - -
147B ASP* 1.3 77.9 - - - +
149B GLY* 1.3 60.0 + - - +
150B GLY 3.1 7.4 + - - +
152B PHE* 6.6 0.4 - - + -
155B LEU* 3.6 24.9 - - + -
175B THR* 3.7 29.8 - - + -
176B PHE 4.0 2.7 - - - +
177B MET* 3.9 27.6 - - + -
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Residues in contact with GLY 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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1112A ARG* 3.2 26.7 + - - -
1118A TRP* 4.0 3.1 - - - -
1131A ASP* 4.7 0.2 - - - +
1149A VAL* 4.0 16.4 - - - -
1150A VAL 4.3 0.2 - - - -
144B TRP* 4.5 1.3 - - - -
145B GLU* 3.2 21.1 + - - +
146B ASP 3.1 15.9 + - - -
148B LEU* 1.3 74.5 - - - +
150B GLY* 1.3 55.5 + - - -
154B LYS* 5.1 1.2 + - - +
155B LEU* 4.0 6.4 - - - +
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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