Contacts of the helix formed by residues 148 - 156 (chain B) in PDB entry 1S4Z
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 PRO 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B GLU* 3.2 28.7 - - - +
132B LEU 3.9 2.9 - - - +
133B MET* 3.4 10.9 - - + -
146B LEU 4.7 0.9 - - - +
147B VAL* 1.3 93.8 - - + +
149B ALA* 1.3 61.0 + - - +
150B LYS* 4.2 10.8 - - + +
151B GLU* 3.0 28.9 + - + +
152B ALA* 2.8 26.2 + - - +
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ILE* 6.2 2.2 - - + -
165A GLU* 4.1 19.7 - - - +
131B GLU* 5.1 0.4 + - - +
132B LEU* 2.7 31.0 + - + +
134B PHE* 3.8 26.7 - - + -
148B PRO* 1.3 72.0 - - - +
150B LYS* 1.3 60.1 + - + +
152B ALA* 3.9 0.2 - - - +
153B ASN* 2.7 42.2 + - - +
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Residues in contact with LYS 150 (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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165A GLU* 5.3 4.5 + - - -
130B GLY 4.7 2.0 + - - -
131B GLU* 3.4 37.4 + - + +
132B LEU 4.7 0.6 - - - +
148B PRO* 3.1 8.0 - - + -
149B ALA* 1.3 90.2 - - + +
151B GLU* 1.3 56.8 + - - +
153B ASN* 2.7 31.7 + - - +
154B VAL* 3.9 7.1 - - - +
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Residues in contact with GLU 151 (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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111B ARG* 4.6 17.1 + - - +
112B GLY 3.8 17.5 + - - +
113B PHE* 5.3 0.2 - - - -
147B VAL* 3.6 19.8 - - + +
148B PRO* 3.0 27.1 + - + +
150B LYS* 1.3 77.9 - - - +
152B ALA* 1.3 62.3 + - - +
154B VAL* 2.9 25.3 - - + +
155B LYS* 3.0 39.0 + - + +
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Residues in contact with ALA 152 (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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113B PHE* 5.2 1.6 - - + -
134B PHE* 3.7 32.5 - - + -
136B MET* 4.8 7.6 - - + -
147B VAL* 4.0 14.3 - - + +
148B PRO 2.8 15.7 + - - +
149B ALA 3.4 1.5 + - - +
151B GLU* 1.3 75.2 - - - +
153B ASN* 1.3 66.4 + - - +
155B LYS* 3.1 8.3 + - - +
156B CYS* 3.0 26.3 + - - +
160B VAL* 4.2 8.7 - - + +
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Residues in contact with ASN 153 (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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158A GLN* 4.0 28.8 + - - +
161A ILE* 4.1 29.4 - - + -
134B PHE* 5.6 0.4 - - + -
149B ALA 2.7 21.4 + - - +
150B LYS* 2.7 26.9 + - - +
152B ALA* 1.3 75.7 - - - +
154B VAL* 1.3 90.8 + - - +
157B PRO* 2.9 36.9 - - - +
160B VAL* 4.6 4.7 - - + +
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Residues in contact with VAL 154 (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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150B LYS 3.9 5.8 - - - +
151B GLU* 2.9 30.1 - - - +
153B ASN* 1.3 97.2 + - - +
155B LYS* 1.3 81.9 + - - +
156B CYS 3.4 0.2 + - - -
157B PRO* 4.0 5.4 - - - +
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Residues in contact with LYS 155 (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 GLY 4.8 0.7 - - - -
113B PHE* 3.5 63.7 - - + -
151B GLU* 3.0 51.2 + - + +
152B ALA 3.1 7.3 + - - +
154B VAL* 1.3 90.0 - - + +
156B CYS* 1.3 63.1 + - - +
157B PRO* 4.2 0.4 - - - +
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Residues in contact with CYS 156 (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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113B PHE* 3.4 32.3 - - + -
119B PRO* 5.3 5.8 - - + -
136B MET* 3.6 17.9 - - - -
152B ALA 3.0 10.6 + - - -
153B ASN 3.7 1.1 - - - -
154B VAL 3.3 0.2 - - - -
155B LYS* 1.3 79.2 - - - +
157B PRO* 1.3 69.8 - - - +
158B GLN* 3.2 4.5 + - + +
159B VAL* 3.5 24.6 + - + +
160B VAL* 3.3 16.3 + - - +
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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