Contacts of the helix formed by residues 105 - 113 (chain C) in PDB entry 2JC6
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 GLU 105 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C GLY* 1.3 75.1 - - - -
106C LEU* 1.3 64.9 + - - +
107C PHE* 4.4 8.9 - - + +
108C ASP* 3.3 33.3 + - - +
109C ARG* 3.2 21.5 + - - +
148C GLU* 5.1 5.3 - - - +
150C LEU 4.8 0.7 - - - +
151C LEU* 3.8 22.2 - - + -
152C TYR* 4.6 0.4 - - - -
304C SER* 2.6 35.3 + - - -
306C TRP* 3.6 26.2 - - + +
307C ARG* 4.5 3.1 + - - +
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Residues in contact with LEU 106 (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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104C GLY 3.8 1.0 + - - -
105C GLU* 1.3 71.5 - - - +
107C PHE* 1.3 66.3 + - + +
109C ARG* 3.1 13.5 + - - +
110C ILE* 3.1 32.6 + - + +
124C LEU* 3.8 17.9 - - + -
147C PRO* 4.1 17.2 + - + +
150C LEU* 3.2 52.2 + - + +
152C TYR* 3.7 32.9 - - + +
161C ILE* 4.4 4.3 - - + -
214C LEU* 3.9 20.9 - - + -
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Residues in contact with PHE 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C GLU* 3.3 8.7 - - + +
106C LEU* 1.3 82.1 - - + +
108C ASP* 1.3 65.1 + - - +
110C ILE* 3.7 8.1 + - + +
111C VAL* 3.0 32.4 + - - +
147C PRO* 3.5 48.4 + - + -
148C GLU* 4.4 12.1 - - + -
213C ILE* 3.8 18.8 - - + -
214C LEU* 5.3 7.0 - - + -
297C ILE* 3.9 31.7 - - + +
301C PHE* 3.5 50.0 - + + +
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Residues in contact with ASP 108 (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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104C GLY* 6.2 0.2 - - - -
105C GLU* 3.3 38.8 + - - +
106C LEU 3.2 0.8 - - - -
107C PHE* 1.3 79.2 - - - +
109C ARG* 1.3 67.5 + - + +
111C VAL* 3.5 5.6 + - - +
112C GLU* 3.1 26.0 + - - +
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Residues in contact with ARG 109 (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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103C GLY* 3.2 22.5 + - - +
105C GLU 3.2 6.2 + - - +
106C LEU 3.1 9.1 + - - +
108C ASP* 1.3 76.1 - - + +
110C ILE* 1.3 67.4 + - - +
112C GLU* 3.2 25.0 + - - +
113C LYS* 3.0 34.8 + - - +
152C TYR* 3.4 46.8 - - + +
154C SER 2.5 30.7 + - - -
155C GLN* 3.3 23.7 + - - +
156C ASP 3.1 20.4 + - - -
157C GLU* 4.2 11.1 + - - +
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Residues in contact with ILE 110 (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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106C LEU* 3.1 38.5 + - + +
107C PHE* 4.0 6.7 - - + +
109C ARG* 1.3 79.5 - - + +
111C VAL* 1.3 65.3 + - - +
113C LYS* 3.0 21.9 + - - +
116C TYR* 4.0 33.9 - - + +
124C LEU* 5.0 0.2 - - + -
214C LEU* 3.7 23.8 - - + -
290C HIS* 3.0 23.0 + - + -
293C VAL* 4.3 14.1 - - + -
294C SER* 4.6 4.7 - - - +
297C ILE* 3.6 26.5 - - + -
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Residues in contact with VAL 111 (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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107C PHE 3.0 20.4 + - - +
108C ASP* 3.8 6.5 - - - +
109C ARG 3.2 0.4 - - - -
110C ILE* 1.3 77.4 - - - +
112C GLU* 1.3 58.3 + - + +
113C LYS 3.3 0.2 - - - -
290C HIS* 3.0 20.1 + - - -
294C SER* 3.5 13.9 - - - +
297C ILE* 3.5 31.9 - - + -
298C ARG* 3.7 40.3 + - + +
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Residues in contact with GLU 112 (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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108C ASP 3.1 16.9 + - - +
109C ARG* 3.2 32.0 + - - +
111C VAL* 1.3 76.8 - - + +
113C LYS* 1.3 64.3 + - - +
114C GLY* 3.5 2.2 + - - -
155C GLN* 5.5 2.3 - - - +
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Residues in contact with LYS 113 (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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109C ARG* 3.0 26.5 + - - +
110C ILE* 3.0 30.7 + - - +
111C VAL 3.3 1.0 - - - -
112C GLU* 1.3 80.6 - - - +
114C GLY* 1.3 57.4 + - - +
115C PHE 3.3 27.5 + - - +
116C TYR* 4.1 23.7 - - + -
120C ASP* 4.7 10.7 - - - +
124C LEU* 4.8 4.4 - - - +
152C TYR* 3.5 22.2 + - - -
157C GLU 6.0 2.2 - - - -
290C HIS* 4.1 3.1 - - + -
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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