Contacts of the helix formed by residues 138 - 149 (chain C) in PDB entry 4J1R
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 THR 138 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C PRO 3.6 9.5 + - - +
137C GLU* 1.3 78.3 + - - +
139C VAL* 1.3 63.2 + - - +
140C TYR* 3.5 7.8 + - - +
141C ARG* 3.2 26.4 + - - +
142C VAL* 3.3 24.6 + - - +
184C PRO 3.8 8.5 - - - -
185C GLN* 3.6 16.4 - - - +
187C LEU 3.2 8.3 - - - -
188C LEU* 3.5 26.0 - - + -
189C LEU* 4.0 5.2 - - - -
502C I5R 5.4 4.3 - - + -
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Residues in contact with VAL 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C THR* 1.3 70.0 - - - +
140C TYR* 1.3 64.3 + - - +
142C VAL* 3.4 3.9 + - + +
143C ALA* 3.0 22.9 + - + +
153C LEU* 6.2 0.2 - - + -
161C TYR* 4.5 12.3 - - + -
184C PRO* 3.5 19.5 + - + +
187C LEU* 2.9 38.9 + - + +
189C LEU* 3.7 29.6 - - + -
196C LEU* 4.0 8.5 - - + -
246C VAL* 5.0 2.2 - - + -
250C LEU* 3.9 33.4 - - + -
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Residues in contact with TYR 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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138C THR* 3.2 7.5 - - - +
139C VAL* 1.3 79.6 - - - +
141C ARG* 1.3 65.5 + - + +
143C ALA* 3.3 4.4 + - + +
144C ARG* 3.0 51.6 + - + +
184C PRO* 3.3 14.4 + - + +
185C GLN* 3.3 54.1 - - + +
249C GLU* 4.8 11.9 - - - -
260D ASP* 3.1 42.2 + - + -
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Residues in contact with ARG 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C PRO 4.5 12.8 + - - -
137C GLU* 3.1 27.3 + - - +
138C THR* 3.2 18.8 + - - +
140C TYR* 1.3 81.5 - - + +
142C VAL* 1.3 55.5 + - - +
144C ARG* 3.6 32.3 + - - +
145C HIS* 3.1 26.3 + - - +
260D ASP* 5.4 1.0 + - - -
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Residues in contact with VAL 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C GLU* 3.9 20.0 - - + +
138C THR 3.3 14.3 + - - +
139C VAL* 3.7 9.9 - - + +
140C TYR 3.2 0.2 - - - -
141C ARG* 1.3 75.2 - - - +
143C ALA* 1.3 66.2 + - - +
145C HIS* 3.3 7.0 + - - +
146C TYR* 3.3 28.8 + - + -
153C LEU* 3.8 31.0 - - + -
161C TYR* 4.9 10.5 - - + +
189C LEU* 3.8 17.5 - - + -
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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
----------------------------------------------------------
139C VAL 3.0 17.6 + - - +
140C TYR* 3.9 5.4 - - + +
142C VAL* 1.3 78.4 - - - +
144C ARG* 1.3 58.8 + - - +
146C TYR* 3.1 8.3 + - - +
147C SER* 2.8 30.6 + - - -
153C LEU* 5.8 4.9 - - - -
184C PRO* 6.1 1.1 - - + -
249C GLU* 5.4 13.5 - - + +
250C LEU* 4.0 25.4 - - + -
253C GLY* 5.7 3.7 - - - -
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Residues in contact with ARG 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C TYR* 3.0 40.8 + - + +
141C ARG* 3.6 41.6 + - - +
143C ALA* 1.3 75.7 - - - +
145C HIS* 1.3 63.4 + - - +
147C SER* 4.0 9.2 - - - +
148C ARG* 3.0 62.2 + - + +
260D ASP* 2.5 39.3 + - - +
268D GLU* 5.9 0.6 + - - -
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Residues in contact with HIS 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 ARG 3.1 12.7 + - - +
142C VAL* 3.3 13.5 - - + +
143C ALA 3.2 0.2 - - - -
144C ARG* 1.3 82.6 - - - +
146C TYR* 1.3 72.3 + + - +
148C ARG* 4.1 10.8 + - - +
149C ALA* 3.6 18.0 + - - +
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Residues in contact with TYR 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 VAL* 3.3 25.9 + - + +
143C ALA* 3.1 9.4 + - - +
145C HIS* 1.3 91.9 - + + +
147C SER* 1.3 59.7 + - - +
149C ALA* 3.0 19.9 + - - +
150C LYS 3.0 9.5 + - - -
151C GLN* 3.0 42.1 + - + +
152C THR 3.5 20.0 - - - -
153C LEU* 3.4 31.2 - - + +
154C PRO* 3.5 29.4 - - + +
157C TYR* 4.6 8.0 - - - -
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Residues in contact with SER 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 2.8 18.8 + - - -
144C ARG* 3.3 12.8 + - - +
146C TYR* 1.3 70.8 - - - +
148C ARG* 1.3 64.7 + - - +
150C LYS* 2.9 22.8 + - - +
151C GLN 4.1 5.4 - - - -
253C GLY* 3.1 33.6 + - - -
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Residues in contact with ARG 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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144C ARG* 3.0 46.8 + - + +
145C HIS* 4.1 10.5 + - - +
147C SER* 1.3 79.7 + - - +
149C ALA* 1.3 59.4 + - - +
150C LYS* 3.0 14.4 + - - +
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Residues in contact with ALA 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 HIS 3.6 11.6 + - - +
146C TYR* 3.0 13.0 + - - +
148C ARG* 1.3 79.2 - - - +
150C LYS* 1.3 67.4 + - - +
151C GLN* 3.1 28.9 + - + +
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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