Contacts of the helix formed by residues 113 - 124 (chain C) in PDB entry 4DVQ
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 LEU 113 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111C MET 3.1 8.2 + - - +
112C ILE* 1.3 69.3 - - - +
114C GLU* 1.3 62.3 + - - +
115C PRO* 3.3 6.3 - - + -
116C TRP* 3.1 50.3 + - + +
117C VAL* 3.1 25.2 + - - +
130C PHE* 4.2 10.5 - - + -
131C LEU* 4.3 12.5 - - + +
234C THR* 4.2 6.7 - - + -
238C MET* 4.1 31.4 - - + -
487C PHE* 3.6 26.5 - - + -
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Residues in contact with GLU 114 (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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111C MET* 5.9 1.0 - - - +
112C ILE* 2.9 42.9 + - + +
113C LEU* 1.3 68.4 - - - +
115C PRO* 1.3 71.0 - - + +
117C VAL* 4.5 2.9 - - + -
118C ALA* 2.7 35.2 + - + +
121C GLN* 5.4 3.1 + - - +
241C PRO* 4.7 6.6 - - - +
242C ARG* 4.3 23.4 + - + +
253C TRP* 4.6 4.0 - - + -
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Residues in contact with PRO 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C LEU* 3.4 14.6 - - + -
114C GLU* 1.3 95.7 - - + +
116C TRP* 1.3 64.2 + - + +
118C ALA* 3.5 2.6 - - - +
119C TYR* 3.2 17.3 + - - +
234C THR* 4.7 3.4 - - + +
237C LEU* 3.9 27.1 - - + +
238C MET* 4.3 19.1 - - + +
253C TRP* 3.8 20.0 - - + -
256C HIS* 3.6 34.4 + - + +
257C PHE* 4.0 2.1 - - - -
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Residues in contact with TRP 116 (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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113C LEU* 3.1 26.5 + - + +
115C PRO* 1.3 79.2 - - + +
117C VAL* 1.3 64.1 + - - +
119C TYR* 3.4 5.5 + - - +
120C ARG* 3.2 32.2 + - - +
130C PHE* 3.7 28.9 - + - -
131C LEU* 3.7 19.7 - - + -
230C MET* 3.4 28.1 - - + -
234C THR* 3.0 26.6 + - + +
256C HIS* 3.8 15.7 - + - -
260C TRP* 3.6 22.0 - + - +
310C GLU* 5.9 0.2 - - - -
487C PHE* 3.6 31.4 - + - -
602C 1CA 3.7 39.9 - - + -
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Residues in contact with VAL 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ILE* 4.0 21.8 - - + -
113C LEU 3.1 17.7 + - - +
114C GLU* 3.9 5.8 - - + +
116C TRP* 1.3 74.8 - - - +
118C ALA* 1.3 64.8 + - - +
120C ARG* 2.9 17.6 + - - +
121C GLN* 3.0 36.6 + - - +
127C CYS* 4.6 10.8 - - - -
131C LEU* 4.3 33.4 - - + +
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Residues in contact with ALA 118 (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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114C GLU* 2.7 24.1 + - + +
115C PRO 3.5 5.6 - - - +
117C VAL* 1.3 73.7 - - - +
119C TYR* 1.3 61.3 + - - +
121C GLN* 3.4 18.3 + - - +
122C HIS* 2.9 25.5 + - - +
242C ARG* 4.2 12.5 + - - +
253C TRP* 3.9 21.8 - - + -
257C PHE* 3.9 6.8 - - + -
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Residues in contact with TYR 119 (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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115C PRO 3.2 8.4 + - - +
116C TRP 3.8 7.6 - - - +
117C VAL 3.2 0.8 + - - -
118C ALA* 1.3 77.2 - - - +
120C ARG* 1.3 71.4 + - - +
122C HIS* 3.4 1.0 + - - +
123C ARG* 3.2 44.2 + - + +
125C HIS* 4.4 3.1 + + - -
257C PHE* 3.4 46.6 - + + -
260C TRP* 3.5 34.3 + + + -
261C ASP* 2.5 40.2 + - - -
264C PHE* 3.5 45.4 - + - +
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Residues in contact with ARG 120 (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 TRP* 3.2 27.2 + - - +
117C VAL 2.9 6.4 + - - +
119C TYR* 1.3 82.2 - - - +
121C GLN* 1.3 57.7 + - - +
123C ARG 3.1 2.4 + - - -
124C GLY 2.9 24.6 + - - -
125C HIS* 3.0 34.3 + - + +
126C LYS 4.5 6.9 + - - +
127C CYS* 3.7 29.0 - - - +
128C GLY 5.7 1.0 - - - +
131C LEU* 3.8 15.7 - - + +
260C TRP* 3.5 49.9 - - - +
264C PHE* 3.5 29.9 - - - -
306C ALA 5.7 0.2 + - - -
309C MET* 5.1 4.0 - - - +
310C GLU* 4.6 17.8 - - - +
602C 1CA 4.9 2.6 + - - -
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Residues in contact with GLN 121 (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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114C GLU* 5.4 3.2 + - - +
117C VAL* 3.0 42.7 + - - +
118C ALA* 3.5 21.7 - - - +
120C ARG* 1.3 76.6 - - - +
122C HIS* 1.3 60.3 + - - +
123C ARG 3.1 1.6 + - - -
124C GLY* 3.4 10.2 + - - +
125C HIS 5.2 1.3 - - - -
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Residues in contact with HIS 122 (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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118C ALA 2.9 17.8 + - - +
119C TYR 3.8 3.8 - - - +
120C ARG 3.3 0.2 - - - -
121C GLN* 1.3 76.0 - - - +
123C ARG* 1.3 97.6 + - - +
242C ARG* 6.3 0.4 - - - +
257C PHE* 3.8 31.3 - + + -
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Residues in contact with ARG 123 (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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119C TYR* 3.2 36.8 + - + +
120C ARG 3.1 2.2 + - - +
121C GLN 3.1 0.4 - - - -
122C HIS* 1.3 108.1 + - - +
124C GLY* 1.3 62.1 + - - +
125C HIS* 3.4 32.2 + - + +
257C PHE* 5.5 3.2 - - - +
261C ASP* 3.0 37.5 + - - -
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Residues in contact with GLY 124 (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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120C ARG 2.9 4.5 + - - -
121C GLN* 3.4 9.5 + - - -
122C HIS 3.7 0.2 - - - -
123C ARG* 1.3 78.7 - - - +
125C HIS* 1.3 64.8 + - - +
302C GLU* 4.6 5.9 - - - +
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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