Contacts of the helix formed by residues 140 - 153 (chain C) in PDB entry 4J4L
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 ASP 140 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138C THR 4.1 0.8 + - - -
139C PRO* 1.3 71.6 - - - +
141C PRO* 1.4 76.3 - - - +
142C THR* 3.0 37.0 + - - -
143C THR* 3.3 26.0 + - - +
144C ASN* 3.6 15.4 + - - -
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Residues in contact with PRO 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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139C PRO 3.6 7.8 - - - +
140C ASP* 1.4 93.3 - - - +
142C THR* 1.3 52.5 + - - +
144C ASN* 3.3 10.6 + - + +
145C ALA* 2.7 35.2 + - - +
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Residues in contact with THR 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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140C ASP* 3.0 18.7 + - - -
141C PRO* 1.3 75.9 - - - +
143C THR* 1.3 66.4 + - - +
145C ALA* 3.3 15.1 + - + +
146C SER* 3.4 13.4 + - - +
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Residues in contact with THR 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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140C ASP* 3.3 27.5 + - - +
142C THR* 1.3 74.6 - - - +
144C ASN* 1.3 57.4 + - - +
146C SER* 3.0 11.3 + - - +
147C LEU* 2.7 40.0 + - + +
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Residues in contact with ASN 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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92C LEU 5.6 1.2 + - - -
93C GLU* 5.6 1.4 + - - +
96C VAL* 3.6 43.7 - - + +
139C PRO* 3.8 24.3 + - - +
140C ASP 3.6 14.9 + - - +
141C PRO* 3.3 12.8 + - + +
142C THR 3.2 0.4 - - - -
143C THR* 1.3 84.2 - - - +
145C ALA* 1.3 60.7 + - - +
147C LEU* 3.9 11.1 - - - +
148C LEU* 3.1 26.2 + - - +
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Residues in contact with ALA 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 PRO 2.7 19.1 + - - +
142C THR* 3.3 10.0 + - + +
144C ASN* 1.3 74.3 - - - +
146C SER* 1.3 57.2 + - - +
148C LEU* 3.8 8.1 - - - +
149C THR* 3.0 26.0 + - - +
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Residues in contact with SER 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 THR* 3.4 9.1 + - - +
143C THR* 3.0 15.1 + - - +
145C ALA* 1.3 75.3 - - - +
147C LEU* 1.3 66.7 + - - +
148C LEU 3.0 1.3 - - - -
149C THR* 3.1 9.9 + - - -
150C LYS* 3.0 25.3 + - - +
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Residues in contact with LEU 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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62C LEU* 5.8 2.5 - - + +
96C VAL* 3.9 26.2 - - + -
97C TYR* 3.7 27.8 - - + +
143C THR* 2.7 25.9 + - + +
144C ASN* 3.9 12.3 - - - +
146C SER* 1.3 72.6 + - - +
148C LEU* 1.3 56.1 + - - +
150C LYS* 3.5 12.1 - - + +
151C LEU* 3.1 46.9 + - + +
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Residues in contact with LEU 148 (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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96C VAL* 3.9 20.0 - - + +
99C GLU* 3.8 23.3 - - + +
100C TYR* 3.9 33.9 - - + -
144C ASN 3.1 21.1 + - - +
145C ALA* 3.8 8.7 - - - +
146C SER 3.0 0.4 - - - -
147C LEU* 1.3 77.7 - - - +
149C THR* 1.3 62.6 + - + +
151C LEU* 3.5 6.3 + - + +
152C GLN* 3.0 49.9 + - + +
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Residues in contact with THR 149 (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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145C ALA 3.0 17.5 + - - +
146C SER* 3.1 15.9 + - - -
148C LEU* 1.3 78.8 - - + +
150C LYS* 1.3 55.5 + - - +
152C GLN* 3.3 14.0 + - + +
153C ALA* 3.0 31.7 + - - +
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Residues in contact with LYS 150 (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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146C SER 3.0 17.1 + - - +
147C LEU* 3.5 14.1 - - + +
149C THR* 1.3 76.7 - - - +
151C LEU* 1.3 67.2 + - + +
153C ALA* 3.7 10.5 + - - +
154C GLN* 3.1 39.6 + - - +
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Residues in contact with LEU 151 (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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62C LEU* 3.8 25.6 - - + -
96C VAL* 5.8 0.9 - - + +
97C TYR* 4.0 28.3 - - + -
100C TYR* 3.9 31.7 + - + -
147C LEU* 3.1 33.3 + - + +
148C LEU* 3.5 7.8 + - + +
149C THR 3.3 0.2 - - - -
150C LYS* 1.3 84.3 - - + +
152C GLN* 1.3 61.7 + - - +
153C ALA 3.1 6.0 + - - -
154C GLN* 3.6 26.2 + - - +
159C GLN* 3.8 12.1 - - - +
162C THR* 4.4 17.5 + - + +
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Residues in contact with GLN 152 (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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99C GLU 5.5 1.4 + - - -
100C TYR* 4.2 17.3 + - + +
102C GLN 5.7 1.0 + - - -
104C ARG* 3.8 23.3 + - - +
148C LEU* 3.0 37.6 + - + +
149C THR* 3.6 14.5 - - + +
151C LEU* 1.3 76.4 - - - +
153C ALA* 1.3 57.3 + - - +
154C GLN 3.4 0.7 - - - -
159C GLN* 3.0 20.9 + - - +
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Residues in contact with ALA 153 (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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149C THR 3.0 17.6 + - - +
150C LYS* 3.9 10.1 - - - +
151C LEU 3.1 1.4 - - - -
152C GLN* 1.3 76.7 - - - +
154C GLN* 1.3 64.1 + - + +
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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