Contacts of the helix formed by residues 112 - 123 (chain C) in PDB entry 1L3C
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 112 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C ARG* 3.3 22.5 + - - -
90C ASP* 2.9 30.4 - - - +
91C ALA* 4.8 3.1 + - - +
92C PRO* 3.7 19.5 - - + +
109C SER 3.3 3.5 + - - +
110C GLY 3.0 8.4 + - - +
111C GLY* 1.3 74.8 - - - +
113C LEU* 1.3 64.9 + - - +
114C GLN* 3.3 2.5 - - - -
115C GLU* 3.1 22.2 + - + +
116C ILE* 3.0 31.4 + - + +
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Residues in contact with LEU 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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106C VAL* 3.9 23.1 - - + -
109C SER* 3.7 28.4 + - - -
111C GLY 3.3 6.9 + - - +
112C GLU* 1.3 74.6 - - - +
114C GLN* 1.3 65.0 + - - +
116C ILE* 3.2 5.4 + - + +
117C LEU* 2.9 46.0 + - + +
132C VAL* 4.4 8.7 - - + -
139C THR* 3.9 26.5 - - + -
142C GLU* 3.8 27.8 - - + +
143C ALA* 3.9 19.1 - - + +
146C CYS* 5.5 0.2 - - - -
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Residues in contact with GLN 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 GLY 5.1 0.2 + - - -
112C GLU 3.2 0.8 + - - -
113C LEU* 1.3 78.6 - - - +
115C GLU* 1.3 62.4 + - - +
117C LEU* 3.5 2.4 + - - +
118C ARG* 3.1 56.7 + - + +
142C GLU* 3.5 21.2 + - - +
146C CYS* 3.6 26.5 - - - -
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Residues in contact with GLU 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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92C PRO* 3.4 30.3 - - + +
112C GLU* 3.1 23.2 + - + +
114C GLN* 1.3 77.8 + - - +
116C ILE* 1.3 65.8 + - - +
118C ARG* 3.2 20.2 + - + +
119C ILE* 3.0 42.7 + - + +
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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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40C VAL* 4.1 12.3 - - + -
91C ALA* 3.8 28.7 - - + -
92C PRO* 4.4 10.3 - - + -
95C LEU* 4.0 15.0 - - + +
106C VAL* 4.3 17.5 - - + -
108C GLY 5.2 0.2 - - - +
109C SER* 3.5 29.6 - - - +
112C GLU* 3.0 20.5 + - + +
113C LEU* 3.5 9.4 - - - +
115C GLU* 1.3 76.2 - - - +
117C LEU* 1.3 58.4 + - + +
119C ILE* 3.4 4.6 + - - +
120C ILE* 2.8 49.1 + - + +
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Residues in contact with LEU 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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106C VAL* 4.3 14.1 - - + -
113C LEU* 2.9 38.0 + - + +
114C GLN 3.9 3.8 - - - +
116C ILE* 1.3 77.7 - - - +
118C ARG* 1.3 55.3 + - - +
120C ILE* 3.3 5.7 + - + +
121C LYS* 2.8 29.1 + - - +
130C ILE* 4.2 20.4 - - + +
132C VAL* 4.1 20.4 - - + -
143C ALA* 4.5 8.5 - - - +
146C CYS* 3.7 25.8 - - + -
147C LEU* 3.8 21.1 - - + -
150C LEU* 3.7 14.9 - - + +
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Residues in contact with ARG 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 GLN* 3.1 52.5 + - + +
115C GLU* 3.2 23.3 + - + +
117C LEU* 1.3 71.0 - - - +
119C ILE* 1.3 69.3 + - + +
121C LYS* 3.0 14.9 + - - +
122C ASP* 3.2 19.3 + - - +
150C LEU* 4.0 28.2 - - + +
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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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92C PRO* 3.6 41.7 - - + +
95C LEU* 3.7 29.2 - - + -
96C CYS* 4.4 12.8 - - - +
115C GLU* 3.0 26.0 + - + +
116C ILE 3.6 3.8 - - - +
118C ARG* 1.3 77.6 - - + +
120C ILE* 1.3 63.2 + - - +
122C ASP* 2.9 21.6 + - + +
123C LYS* 3.2 28.2 - - + +
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Residues in contact with ILE 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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38C VAL* 4.9 0.2 - - + -
40C VAL* 4.2 9.6 - - + -
95C LEU* 4.2 18.6 - - + -
101C ILE* 4.2 12.7 - - + +
104C ALA* 3.8 23.8 - - + -
106C VAL* 3.7 22.2 - - + -
116C ILE* 2.8 40.2 + - + +
117C LEU* 3.7 8.1 - - + +
119C ILE* 1.3 75.3 - - - +
121C LYS* 1.3 62.4 + - - +
123C LYS* 3.2 7.3 + - - +
124C LEU* 3.1 22.7 + - + +
130C ILE* 3.7 26.9 - - + -
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Residues in contact with LYS 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 LEU 2.8 13.5 + - - +
118C ARG* 3.0 11.4 + - - +
120C ILE* 1.3 80.5 - - - +
122C ASP* 1.3 67.6 + - - +
123C LYS 3.4 0.7 + - - -
124C LEU* 3.5 16.6 + - - +
130C ILE* 5.1 0.2 - - - -
150C LEU* 2.8 50.9 + - + +
151C GLY* 5.1 0.4 - - - -
152C PHE* 3.7 28.0 - - + -
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Residues in contact with ASP 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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100C ASP* 4.7 3.8 - - - +
118C ARG* 3.5 16.5 - - - +
119C ILE* 2.9 12.5 + - + +
121C LYS* 1.3 85.9 - - - +
123C LYS* 1.3 61.5 + - + +
124C LEU 3.6 1.1 - - - +
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Residues in contact with LYS 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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95C LEU* 2.6 36.0 + - + +
96C CYS* 3.3 17.2 + - - +
98C ILE* 2.6 29.6 + - + -
99C PRO 3.9 5.8 - - - +
100C ASP* 3.2 28.2 - - - +
101C ILE* 2.8 38.1 + - + -
119C ILE* 3.2 27.8 - - + +
120C ILE* 3.2 6.8 + - - +
122C ASP* 1.3 81.9 - - + +
124C LEU* 1.3 62.9 + - - +
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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