Contacts of the helix formed by residues 149 - 158 (chain A) in PDB entry 3SJN
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 ASN 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A PHE* 3.6 8.4 - - + -
142A PRO* 3.3 11.2 - - - +
143A ALA 2.9 43.8 + - - +
145A LYS 3.9 0.8 + - - -
146A PRO 3.3 18.7 + - - +
147A GLU 3.2 1.4 - - - -
148A ASP* 1.3 76.9 - - - +
150A VAL* 1.3 58.5 + - - +
151A ALA 3.3 2.0 - - - -
152A ILE* 3.2 16.4 + - - +
153A VAL* 3.0 32.4 + - - +
181A ILE* 3.8 20.0 - - - +
184A ALA 5.1 1.8 - - - +
185A VAL* 3.8 20.9 - - + -
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Residues in contact with VAL 150 (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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147A GLU* 3.5 27.6 - - + +
148A ASP 3.4 0.8 - - - -
149A ASN* 1.3 77.3 - - - +
151A ALA* 1.3 58.3 + - - +
153A VAL* 3.3 1.6 + - - +
154A GLN* 2.9 36.2 + - + +
184A ALA* 3.8 19.1 - - + +
188A ALA* 3.8 23.6 - - + +
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Residues in contact with ALA 151 (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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147A GLU 5.2 0.2 + - - -
148A ASP 4.2 10.2 + - - +
149A ASN 3.3 0.2 - - - -
150A VAL* 1.3 79.6 - - - +
152A ILE* 1.3 58.1 + - + +
154A GLN* 4.2 3.9 - - - +
155A GLY* 3.1 23.9 + - - -
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Residues in contact with ILE 152 (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 PHE* 3.7 36.8 - - + -
141A ILE 4.5 8.7 - - - +
143A ALA* 4.4 13.7 - - + +
148A ASP 4.0 15.0 - - - +
149A ASN* 3.2 28.8 + - - +
151A ALA* 1.3 77.5 - - + +
153A VAL* 1.3 61.7 + - - +
155A GLY* 3.2 3.7 + - - -
156A LEU* 3.1 26.6 + - + +
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Residues in contact with VAL 153 (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 PHE* 3.9 15.5 - - + -
149A ASN 3.0 20.6 + - - +
150A VAL 3.7 3.4 - - - +
152A ILE* 1.3 74.6 - - - +
154A GLN* 1.3 56.9 + - - +
156A LEU* 3.1 12.7 + - - +
157A LYS* 3.0 30.2 + - + +
164A ILE* 4.2 11.4 - - + -
185A VAL* 3.9 31.9 - - + -
188A ALA* 3.8 31.6 - - + +
189A ALA* 3.8 17.7 - - + +
193A MET* 4.7 0.8 - - + +
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Residues in contact with GLN 154 (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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150A VAL* 2.9 26.5 + - + +
151A ALA* 4.2 4.7 - - - +
153A VAL* 1.3 74.3 - - - +
155A GLY* 1.3 61.1 + - - +
157A LYS* 3.2 32.5 + - - +
158A ASP* 3.1 39.1 + - - +
188A ALA* 4.8 8.9 - - + +
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Residues in contact with GLY 155 (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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151A ALA 3.1 16.3 + - - -
152A ILE 3.2 5.8 + - - -
154A GLN* 1.3 77.2 - - - +
156A LEU* 1.3 57.0 + - - +
158A ASP* 3.0 18.9 - - - +
159A GLN* 3.4 21.0 + - - +
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Residues in contact with LEU 156 (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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138A GLY* 4.7 10.3 - - - +
139A THR 5.0 6.5 - - - +
140A PHE* 3.6 35.4 - - + -
152A ILE* 3.1 24.4 + - + +
153A VAL* 3.1 8.7 + - - +
155A GLY* 1.3 76.0 - - - +
157A LYS* 1.3 63.1 + - - +
158A ASP 3.4 0.2 - - - -
159A GLN* 3.3 16.6 - - - +
160A GLY 3.3 5.0 + - - -
161A PHE* 3.2 52.7 + - + +
164A ILE* 3.8 23.8 - - + -
329A GLN* 4.0 10.1 - - + +
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Residues in contact with LYS 157 (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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153A VAL* 3.0 21.5 + - + +
154A GLN* 3.2 28.7 + - - +
156A LEU* 1.3 77.4 - - - +
158A ASP* 1.3 59.0 + - - +
160A GLY* 3.3 17.2 + - - -
161A PHE 4.4 8.4 - - - +
188A ALA 4.3 4.7 - - - +
189A ALA* 3.3 28.9 - - - +
193A MET* 3.8 35.0 - - + -
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Residues in contact with ASP 158 (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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154A GLN* 3.1 32.4 + - - +
155A GLY* 3.0 26.0 - - - +
157A LYS* 1.3 73.4 - - - +
159A GLN* 1.3 63.5 + - - +
160A GLY* 3.2 1.9 - - - -
347A ASN* 5.2 1.4 - - - +
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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