Contacts of the helix formed by residues 149 - 156 (chain A) in PDB entry 3P9K
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 ILE 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A GLY* 1.3 77.3 - - - +
150A PRO* 1.3 76.6 - - + +
151A PHE 4.0 3.4 - - - +
152A ASN* 3.2 41.0 + - + +
153A LYS* 3.0 26.5 + - - +
318A LEU 4.5 1.6 - - - +
320A HIS 3.5 23.8 - - - +
321A ASN 3.7 14.6 - - - +
322A PRO* 3.7 31.9 - - + -
323A GLY 5.1 1.8 - - - +
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Residues in contact with PRO 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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136A SER* 3.4 24.5 - - - +
139A TYR* 3.6 22.0 - - + +
140A LEU* 3.9 19.7 - - + +
143A ALA* 3.8 20.4 - - + -
148A GLY 4.1 1.3 - - - +
149A ILE* 1.3 82.6 - - + +
151A PHE* 1.3 62.0 + - - +
153A LYS* 3.2 7.3 + - + +
154A ALA* 3.2 18.4 + - - +
318A LEU* 3.4 26.5 - - + +
319A ALA* 3.3 18.6 - - - +
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Residues in contact with PHE 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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132A VAL* 4.2 15.3 - - + -
133A LEU* 4.4 7.4 - - + -
136A SER* 3.3 27.1 - - - +
149A ILE 3.3 0.4 - - - -
150A PRO* 1.3 75.3 - - - +
152A ASN* 1.3 64.0 + - - +
154A ALA* 3.0 12.4 + - - +
155A TYR* 3.0 46.1 + + + -
157A MET 3.4 19.5 - - - -
158A SER 3.7 3.1 - - - -
159A ALA* 3.3 35.7 - - + -
162A TYR* 3.7 30.1 - + + -
163A HIS* 5.9 0.2 - + - -
169A PHE* 5.8 1.3 - + - -
319A ALA 3.0 15.2 + - - +
320A HIS* 3.6 25.4 - + + +
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Residues in contact with ASN 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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149A ILE* 3.2 44.6 + - + +
151A PHE* 1.3 77.9 - - - +
153A LYS* 1.3 57.2 + - + +
156A GLY* 2.6 33.0 + - - -
157A MET* 3.4 18.4 - - - +
158A SER* 3.4 33.2 - - - +
320A HIS 4.2 1.9 - - - +
322A PRO* 5.6 0.2 - - - +
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Residues in contact with LYS 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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139A TYR* 3.7 28.4 - - + +
142A ASP* 3.9 24.2 + - + +
143A ALA* 3.6 20.2 - - - +
146A ASP* 4.5 8.9 + - - +
147A GLY 3.0 28.9 + - - -
148A GLY* 4.4 5.5 - - - -
149A ILE 3.0 17.5 + - - +
150A PRO* 3.5 6.7 - - + +
151A PHE 3.2 0.2 - - - -
152A ASN* 1.3 77.8 - - + +
154A ALA* 1.3 61.2 + - - +
156A GLY* 4.3 2.4 + - - -
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Residues in contact with ALA 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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135A GLU* 3.9 18.1 - - + +
139A TYR* 3.3 39.5 + - + -
150A PRO 3.2 4.1 + - - +
151A PHE* 3.0 10.2 + - - +
153A LYS* 1.3 80.9 - - - +
155A TYR* 1.3 74.9 + - + +
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Residues in contact with TYR 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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131A LYS 4.0 0.3 + - - -
132A VAL* 2.5 38.7 + - + -
135A GLU* 3.1 22.0 - - + +
136A SER* 4.8 1.1 - - - -
151A PHE* 3.0 56.9 + + + +
154A ALA* 1.3 90.7 - - + +
156A GLY* 1.3 63.7 + - - +
157A MET* 3.6 18.0 + - + +
162A TYR* 3.6 40.6 - + + -
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Residues in contact with GLY 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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152A ASN* 2.6 22.0 + - - -
153A LYS 4.3 2.3 + - - -
154A ALA 3.8 0.6 - - - -
155A TYR* 1.3 72.0 - - - +
157A MET* 1.3 63.5 + - - +
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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