Contacts of the helix formed by residues 126 - 135 (chain C) in PDB entry 3EU9
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 126 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95C HIS* 3.6 2.0 - - - -
117C ASP* 3.5 28.2 + - + +
118C GLN 3.7 2.5 - - - -
119C LEU* 3.6 15.0 - - + -
125C SER* 1.3 74.6 - - - +
127C PRO* 1.3 75.7 - - - +
128C LEU* 3.3 8.5 + - - +
129C HIS* 3.0 46.2 + - + +
130C TRP* 3.2 12.3 + - - -
149C ASP 5.4 2.1 + - - +
152C LEU* 3.8 22.7 - - + -
160C CYS* 5.4 0.2 - - - -
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Residues in contact with PRO 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C THR* 4.7 0.2 - - - +
94C LEU* 3.9 33.2 - - + +
95C HIS* 3.6 33.0 - - + +
98C ALA* 3.5 14.6 - - + +
115C ILE 4.8 1.8 - - - +
116C VAL 3.1 27.1 - - - +
118C GLN 3.5 13.5 - - - +
126C THR* 1.3 86.9 - - - +
128C LEU* 1.3 57.0 + - - +
130C TRP* 3.2 5.6 + - + +
131C ALA* 3.0 23.6 + - - +
143C LEU* 3.9 9.0 - - + -
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Residues in contact with LEU 128 (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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116C VAL 5.2 0.6 + - - -
117C ASP* 4.8 1.8 - - - +
126C THR* 3.2 8.1 + - - +
127C PRO* 1.3 76.5 - - - +
129C HIS* 1.3 65.8 + - - +
131C ALA* 3.3 1.2 + - + +
132C THR* 2.8 33.8 + - - +
140C VAL* 3.7 44.2 - - + +
143C LEU* 3.6 20.2 - - + +
144C MET* 4.0 8.7 - - + -
148C ALA* 3.7 27.1 - - + +
149C ASP 4.1 2.5 - - - +
150C PRO* 3.8 37.9 - - + -
160C CYS* 3.7 9.2 - - - -
176C LEU* 5.8 0.2 - - + -
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Residues in contact with HIS 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LEU* 5.1 0.4 - - + -
125C SER* 3.6 16.6 - - - -
126C THR* 3.0 47.9 + - + +
128C LEU* 1.3 76.2 - - - +
130C TRP* 1.3 64.8 + - + +
132C THR* 3.6 1.7 - - - -
133C ARG* 3.0 29.8 + - - +
149C ASP 5.6 0.6 + - - -
150C PRO 4.9 0.2 + - - -
152C LEU* 2.9 31.4 + - + +
153C ILE 3.6 5.6 - - - -
154C ASP* 3.5 24.3 - - + +
158C CYS 3.6 6.7 + - - -
159C SER* 4.2 0.2 - - - -
160C CYS* 3.7 24.1 + - - -
163C LEU* 3.8 22.7 - - + +
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Residues in contact with TRP 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C VAL* 3.6 44.2 - - + -
95C HIS* 3.6 32.3 - + + +
96C TRP* 3.9 27.6 - + - -
99C ILE* 3.8 27.2 - - + +
120C GLY 4.8 1.8 + - - -
121C GLY* 4.5 11.2 - - - -
123C LEU* 6.3 0.2 - - - +
125C SER* 3.6 29.6 + - - -
126C THR 3.2 6.7 + - - +
127C PRO* 3.2 12.2 + - + +
129C HIS* 1.3 81.4 - - - +
131C ALA* 1.3 61.4 + - - +
133C ARG* 3.3 6.2 + - - +
134C GLN* 3.1 23.7 + - - +
449C GOL 3.7 48.3 + - - -
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Residues in contact with ALA 131 (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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98C ALA* 3.9 12.3 - - + +
99C ILE* 4.6 1.0 - - - +
127C PRO 3.0 14.7 + - - +
128C LEU* 3.8 4.7 - - - +
130C TRP* 1.3 77.2 - - - +
132C THR* 1.3 57.9 + - - +
134C GLN* 3.4 5.1 + - - +
135C GLY 2.9 22.7 + - - -
136C HIS* 3.1 14.1 + - + +
139C MET* 3.5 37.2 - - + -
140C VAL* 4.6 9.2 - - + -
143C LEU* 4.3 4.9 - - + -
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Residues in contact with THR 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C LEU* 2.8 22.7 + - - +
129C HIS* 3.6 4.7 - - - -
130C TRP 3.3 0.2 - - - -
131C ALA* 1.3 74.3 - - - +
133C ARG* 1.3 65.3 + - - +
135C GLY* 3.0 3.8 + - - -
140C VAL* 3.8 18.1 - - - +
160C CYS* 3.4 44.0 - - + +
163C LEU* 4.0 5.2 - - + -
164C ALA* 3.7 21.3 - - + +
169C HIS* 3.0 23.6 - - - -
172C ILE* 4.1 12.2 - - + +
176C LEU* 5.5 0.2 - - - +
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Residues in contact with ARG 133 (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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123C LEU* 4.6 4.3 - - - +
125C SER* 5.0 6.1 + - - -
129C HIS* 3.0 19.9 + - - +
130C TRP* 3.6 8.1 - - - +
132C THR* 1.3 77.4 - - - +
134C GLN* 1.3 60.3 + - - +
154C ASP* 3.1 23.6 + - - -
156C GLU* 2.7 34.3 + - - +
163C LEU* 3.6 24.6 - - + +
166C GLN* 4.6 0.8 - - - +
167C PHE* 3.5 49.4 - - + -
169C HIS* 2.8 19.8 + - - -
449C GOL 3.4 40.2 + - - +
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Residues in contact with GLN 134 (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 ILE* 3.5 31.8 - - + +
130C TRP 3.1 13.4 + - - +
131C ALA 3.8 3.8 - - - +
133C ARG* 1.3 81.2 - - - +
135C GLY* 1.3 61.6 + - - +
136C HIS* 3.4 33.4 + - + +
169C HIS* 3.7 6.1 + - - -
449C GOL 5.7 0.4 + - - -
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Residues in contact with GLY 135 (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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131C ALA 2.9 4.2 + - - -
132C THR 3.0 7.3 + - - -
133C ARG 3.2 0.2 - - - -
134C GLN* 1.3 80.9 - - - +
136C HIS* 1.3 63.3 + - - +
137C LEU* 3.3 7.4 + - - +
169C HIS* 3.4 28.5 + - - -
172C ILE* 3.6 10.0 - - - +
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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