Contacts of the helix formed by residues 111 - 122 (chain C) in PDB entry 3SAJ
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 111 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95C PHE* 6.3 5.2 - - + -
108C ARG* 6.3 0.4 - - - -
109C PRO* 3.1 26.7 + - + +
110C GLU* 1.3 77.7 - - - +
112C GLN* 1.3 67.0 + - - +
113C GLU 3.4 2.0 - - - -
114C ALA* 3.2 6.7 + - - +
115C LEU* 3.0 23.3 + - - +
139C VAL* 6.2 1.8 - - + -
213C ALA 3.7 20.2 - - - +
214C ASN* 4.0 2.9 - - - -
215C LEU* 3.4 52.7 - - + +
235C PHE* 4.3 14.9 - - + -
348C LEU* 4.0 28.9 - - + -
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Residues in contact with GLN 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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98C ASP* 4.1 22.9 + - - +
110C GLU* 3.8 15.5 + - + +
111C LEU* 1.3 78.6 - - - +
113C GLU* 1.3 74.2 + - + +
115C LEU* 3.4 14.6 + - - +
116C ILE* 3.4 19.9 + - - +
138C SER* 3.4 23.0 + - - +
139C VAL* 4.1 28.5 - - + +
142C ARG* 3.6 45.9 - - + +
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Residues in contact with GLU 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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110C GLU* 5.6 2.1 - - - +
111C LEU 3.4 0.4 - - - -
112C GLN* 1.3 89.0 - - + +
114C ALA* 1.3 66.7 + - - +
116C ILE* 3.5 9.8 + - - +
117C SER* 3.2 23.2 + - - -
142C ARG* 4.2 24.8 + - - +
364C TRP* 3.7 24.8 - - + -
366C GLU* 4.5 16.1 - - - +
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Residues in contact with ALA 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 LEU* 3.2 9.9 + - - +
113C GLU* 1.3 80.3 - - - +
115C LEU* 1.3 64.1 + - - +
117C SER* 3.1 3.8 + - - -
118C ILE* 3.0 25.7 + - + +
235C PHE* 3.6 24.2 - - + -
348C LEU* 3.7 12.6 - - + -
364C TRP* 3.5 38.5 - - + +
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Residues in contact with LEU 115 (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 LEU 3.0 12.8 + - - +
112C GLN* 3.6 8.7 - - - +
113C GLU 3.3 0.6 - - - -
114C ALA* 1.3 75.7 - - - +
116C ILE* 1.3 63.6 + - - +
118C ILE* 3.4 3.2 + - - +
119C ILE* 3.1 39.9 + - + +
129C TYR* 4.5 0.7 - - + -
139C VAL* 3.8 22.0 - - + -
143C VAL* 4.0 16.2 - - + -
183C VAL* 4.3 14.4 - - + -
211C ILE* 3.4 31.0 - - + -
212C LEU 4.5 1.6 - - - +
213C ALA* 3.8 33.4 - - + +
235C PHE* 3.9 13.9 - - + -
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Residues in contact with ILE 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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112C GLN 3.4 19.8 + - - +
113C GLU* 3.5 10.3 + - - +
114C ALA 3.2 0.4 - - - -
115C LEU* 1.3 76.5 - - - +
117C SER* 1.3 69.8 + - - +
119C ILE* 2.9 20.9 + - + +
120C ASP* 3.0 11.1 + - - +
142C ARG* 4.1 24.7 - - + +
143C VAL* 4.1 25.4 - - + -
146C THR* 3.9 39.0 - - + +
150C LYS* 4.6 9.0 - - - +
152C TRP* 4.3 13.4 - - + -
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Residues in contact with SER 117 (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 GLU 3.2 6.3 + - - -
114C ALA 3.1 9.1 + - - -
116C ILE* 1.3 79.6 - - - +
118C ILE* 1.3 60.3 + - - +
120C ASP* 2.8 30.5 + - - +
121C HIS* 3.1 8.8 + - - +
364C TRP* 3.0 32.8 + - - -
369C LYS* 4.2 12.7 - - - +
370C PHE* 4.3 14.8 - - - -
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Residues in contact with ILE 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 ALA 3.0 17.4 + - - +
115C LEU* 3.6 6.5 - - - +
117C SER* 1.3 74.6 - - - +
119C ILE* 1.3 61.7 + - - +
120C ASP 3.1 0.9 + - - -
121C HIS* 3.3 9.0 + - + +
122C TYR* 3.2 43.6 + - + -
211C ILE* 4.5 11.7 - - + -
233C THR* 4.3 7.4 - - + -
235C PHE* 3.9 22.0 - - + -
350C VAL* 3.8 39.9 - - + -
364C TRP* 5.1 2.7 - - + -
370C PHE* 3.8 27.4 - - + -
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Residues in contact with ILE 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 LEU* 3.1 39.8 + - + +
116C ILE* 2.9 18.0 + - + +
118C ILE* 1.3 75.2 - - - +
120C ASP* 1.3 57.0 + - - +
122C TYR* 3.9 1.9 + - - -
123C LYS* 3.3 2.4 + - - -
124C TRP* 3.2 46.3 + - + +
127C PHE* 4.3 19.1 - - + -
143C VAL* 4.9 4.3 - - + -
152C TRP* 4.0 22.0 - - + -
183C VAL* 4.2 16.4 - - + -
211C ILE* 4.0 22.4 - - + -
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Residues in contact with ASP 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 ILE* 3.0 8.0 + - - +
117C SER* 2.8 15.9 + - - +
119C ILE* 1.3 75.7 - - - +
121C HIS* 1.3 54.7 + - - +
122C TYR 3.0 4.7 - - - -
123C LYS* 2.5 43.5 + - - +
124C TRP 5.5 0.3 - - - +
125C GLN* 5.7 2.1 + - - -
150C LYS* 2.8 34.5 + - - -
152C TRP* 3.7 15.9 + - - -
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Residues in contact with HIS 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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117C SER 3.1 4.4 + - - +
118C ILE* 3.3 8.7 + - + +
120C ASP* 1.3 78.7 - - - +
122C TYR* 1.3 100.3 + + - +
123C LYS* 4.3 6.9 - - - +
361C ILE* 4.0 16.9 - - + +
370C PHE* 3.0 47.1 - + + -
372C PRO* 5.4 5.2 - - + -
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Residues in contact with TYR 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 ILE* 3.2 33.9 + - + +
119C ILE* 4.2 2.5 - - - +
120C ASP 3.0 0.6 - - - -
121C HIS* 1.3 101.7 + + - +
123C LYS* 1.3 70.5 + - - +
124C TRP* 3.2 33.6 + + + +
209C HIS* 4.8 19.7 - + - -
211C ILE* 4.2 11.7 - - + -
233C THR* 3.4 24.6 + - + -
352C GLU* 2.6 37.4 + - - -
354C LYS* 5.7 1.1 - - - -
361C ILE* 3.5 4.9 - - + +
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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