Contacts of the helix formed by residues 139 - 147 (chain C) 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 TYR 139 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C GLU* 3.4 32.5 + - - -
136C SER 2.9 8.2 + - - +
138C TYR* 1.3 88.7 - - + +
140C LEU* 1.3 65.0 + - - +
141C LYS 3.3 2.7 - - - -
142C ASP* 3.2 22.5 + - - +
143C ALA* 3.0 22.2 + - - +
150C PRO* 3.5 20.9 - - + +
153C LYS* 3.9 27.8 + - + +
154C ALA* 3.3 32.0 + - + -
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Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C SER 3.4 3.9 + - - +
137C TRP* 3.5 25.2 + - + +
139C TYR* 1.3 78.5 - - - +
141C LYS* 1.3 62.8 + - - +
143C ALA* 3.2 1.7 + - - +
144C VAL* 3.0 37.3 + - + +
150C PRO* 3.9 23.3 - - + -
315C MET* 3.8 24.2 - - + -
318C LEU* 4.1 24.0 - - + -
319C ALA* 5.5 2.0 - - + -
32D THR* 4.9 4.3 - - - -
35D ASN* 3.3 33.0 - - + +
73D MET* 4.6 2.9 - - + -
77D ILE* 4.3 11.0 - - + -
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Residues in contact with LYS 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C TYR* 4.2 18.1 + - - +
140C LEU* 1.3 72.2 - - - +
142C ASP* 1.3 88.9 + - - +
144C VAL* 3.3 3.6 + - - +
145C LEU* 3.1 32.1 + - + +
35D ASN* 2.8 18.6 + - - +
38D GLU* 3.2 44.0 - - + +
39D LEU* 4.0 28.2 - - + +
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Residues in contact with ASP 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C TYR 5.2 0.4 - - - -
139C TYR* 3.2 27.5 + - + +
141C LYS* 1.3 110.1 + - - +
143C ALA* 1.3 52.8 + - - +
145C LEU* 4.8 3.1 - - - +
146C ASP* 2.8 50.9 + - - +
153C LYS* 3.9 15.0 - - + +
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Residues in contact with ALA 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C TYR 3.0 7.6 + - - +
140C LEU 3.2 7.8 + - - +
142C ASP* 1.3 73.4 - - - +
144C VAL* 1.3 62.3 + - - +
147C GLY* 2.7 29.2 + - - -
148C GLY 3.6 20.6 - - - +
150C PRO* 3.6 25.6 - - + -
153C LYS* 3.4 16.7 - - - +
67D ASN* 3.2 4.9 + - - -
73D MET* 3.7 11.5 - - + +
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Residues in contact with VAL 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C LEU* 3.0 23.2 + - + +
141C LYS 3.6 7.2 - - - +
142C ASP 3.3 0.2 - - - -
143C ALA* 1.3 77.0 - - - +
145C LEU* 1.3 60.2 + - - +
39D LEU* 3.9 35.2 - - + -
62D LEU* 4.4 10.1 - - + -
65D ALA* 5.0 0.5 - - - +
67D ASN* 3.1 22.2 + - - +
70D ALA* 3.8 14.7 - - + +
73D MET* 3.8 18.6 - - + -
74D VAL* 4.4 19.7 - - + -
77D ILE* 4.1 17.9 - - + -
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Residues in contact with LEU 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C LYS* 3.1 20.2 + - + +
142C ASP* 4.1 3.8 - - - +
144C VAL* 1.3 78.5 - - - +
146C ASP* 1.3 69.6 + - - +
39D LEU* 3.8 22.9 - - + -
62D LEU* 4.6 12.8 - - + -
64D SER* 3.9 24.1 - - - +
65D ALA* 3.8 30.5 - - + +
66D ALA* 2.9 33.8 + - - +
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Residues in contact with ASP 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ASP* 2.8 34.6 + - - +
145C LEU* 1.3 84.3 - - - +
147C GLY* 1.3 59.0 + - - +
153C LYS* 4.3 11.9 + - - +
64D SER* 4.9 6.2 + - - +
66D ALA* 4.0 12.1 - - - +
67D ASN* 4.1 4.0 - - - +
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Residues in contact with GLY 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ALA 2.7 24.2 + - - -
145C LEU 3.6 1.2 - - - -
146C ASP* 1.3 74.7 - - - +
148C GLY* 1.3 60.5 + - - -
153C LYS* 2.8 27.9 + - - -
67D ASN* 3.6 21.8 - - - +
69D GLU* 6.2 0.2 - - - -
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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