Contacts of the helix formed by residues 136 - 147 (chain C) in PDB entry 3JXI
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 136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134C VAL* 5.6 4.3 - - + +
135C PHE* 1.3 75.5 - - - +
137C ARG* 1.3 63.4 + - - +
138C PRO* 3.3 17.3 - - + +
139C ILE* 2.9 43.9 - - - +
140C LEU* 3.1 24.3 + - - +
170C GLU* 5.4 4.7 - - - +
171C PHE* 4.0 11.3 - - - -
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Residues in contact with ARG 137 (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 ASN* 1.3 73.1 - - - +
138C PRO* 1.4 67.8 - - + +
140C LEU* 3.2 4.5 + - - -
141C PHE* 2.8 64.9 + - + +
169C GLU* 3.5 13.9 + - - +
170C GLU* 3.3 31.9 + - - +
171C PHE* 4.4 4.5 - - - -
172C ARG 2.9 42.6 + - - +
173C GLU* 4.0 0.7 - - - +
174C PRO* 3.6 27.5 - - - +
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Residues in contact with PRO 138 (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 ASN* 3.3 17.7 - - + +
137C ARG* 1.4 96.7 - - + +
139C ILE* 1.3 59.7 + - + +
141C PHE* 3.9 4.0 - - + +
142C ASP* 2.9 29.1 + - - +
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Residues in contact with ILE 139 (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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132C MET* 3.3 37.5 - - + -
134C VAL 4.0 10.1 - - - +
135C PHE* 3.5 32.3 - - + -
136C ASN* 2.9 35.2 - - - +
138C PRO* 1.3 76.8 - - + +
140C LEU* 1.3 60.2 + - - +
142C ASP* 3.3 7.8 + - - +
143C ILE* 3.0 40.0 + - + +
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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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135C PHE* 5.0 4.7 - - + -
136C ASN 3.1 17.6 + - - +
137C ARG* 3.6 2.0 - - - +
139C ILE* 1.3 80.7 - - + +
141C PHE* 1.3 67.8 + - + +
143C ILE* 3.3 7.7 + - - +
144C VAL* 3.2 29.2 + - + +
152C LEU* 4.3 9.9 - - + -
155C LEU* 3.8 35.2 - - + -
166C LEU* 4.1 11.2 - - + -
171C PHE* 4.0 35.4 - - + +
180C CYS* 3.9 31.4 - - + -
199C LEU* 4.7 2.2 - - + -
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Residues in contact with PHE 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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137C ARG* 2.8 47.6 + - + +
138C PRO* 4.1 4.5 - - + +
140C LEU* 1.3 75.0 - - + +
142C ASP* 1.3 63.2 + - - +
144C VAL* 4.0 5.2 - - - -
145C SER* 2.7 34.1 + - - +
171C PHE 3.5 17.5 - - - -
173C GLU* 3.5 39.5 - - + -
178C LYS 3.7 9.0 - - - -
179C THR 4.4 2.0 - - - -
180C CYS* 3.9 26.2 - - + -
183C LYS* 4.0 26.9 - - + -
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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 PRO 2.9 21.1 + - - +
139C ILE* 3.4 9.0 - - - +
140C LEU 3.2 0.2 - - - -
141C PHE* 1.3 76.5 - - - +
143C ILE* 1.3 63.8 + - - +
145C SER* 4.0 3.1 - - - -
146C ARG* 2.9 65.7 + - - +
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Residues in contact with ILE 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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132C MET* 5.8 0.7 - - - -
135C PHE* 4.4 5.2 - - + -
139C ILE* 3.0 36.5 + - + +
140C LEU* 3.3 6.0 + - - +
142C ASP* 1.3 77.7 - - - +
144C VAL* 1.3 53.6 + - + +
146C ARG* 3.8 18.9 - - - +
147C GLY 2.7 28.6 + - - -
148C SER 2.8 40.1 + - - +
150C ASP 3.9 4.9 - - - +
151C GLY* 3.7 33.4 - - - +
152C LEU* 3.9 26.0 - - + +
195C THR* 4.1 3.4 - - + -
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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* 3.3 19.5 - - + +
141C PHE* 3.8 9.2 - - - +
143C ILE* 1.3 80.9 - - + +
145C SER* 1.3 63.5 + - - +
152C LEU* 5.0 2.0 - - + -
180C CYS* 3.7 28.9 - - + +
183C LYS* 3.8 16.1 - - + +
184C ALA* 3.6 8.0 - - + +
187C ASN* 4.2 0.2 - - - +
193C ASN* 2.9 28.4 + - - -
195C THR* 3.9 29.2 - - + +
199C LEU* 4.0 24.5 - - + -
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Residues in contact with SER 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 PHE* 2.7 24.3 + - - +
142C ASP* 4.0 4.3 - - - -
144C VAL* 1.3 76.1 - - - +
146C ARG* 1.3 63.1 + - - +
183C LYS* 3.7 22.6 - - - +
187C ASN* 3.4 39.3 + - - +
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Residues in contact with ARG 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* 2.9 45.3 + - - +
143C ILE* 4.0 21.3 - - - +
145C SER* 1.3 78.4 - - - +
147C GLY* 1.3 62.1 + - - +
148C SER* 4.1 21.0 - - - +
150C ASP 5.1 3.0 + - - -
187C ASN 5.4 1.1 - - - +
193C ASN* 5.0 0.7 - - - -
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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 ILE 2.7 16.7 + - - -
144C VAL 3.7 1.1 + - - -
145C SER 3.5 1.2 - - - -
146C ARG* 1.3 76.3 - - - +
148C SER* 1.3 57.7 + - - +
149C PRO* 3.9 6.2 - - - +
193C ASN* 3.5 32.5 - - - +
194C ASP* 4.5 8.3 + - - +
195C THR* 4.0 5.2 - - - -
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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