Contacts of the helix formed by residues 107 - 124 (chain C) in PDB entry 1KAF
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 107 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C GLU* 5.0 5.8 - - + +
106C ILE* 1.3 82.0 - - - +
108C SER* 1.3 65.3 + - - +
109C ASP* 2.5 30.5 + - - +
110C MET* 3.0 29.5 + - - +
111C GLU* 3.2 9.6 + - - +
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Residues in contact with SER 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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107C THR* 1.3 73.3 - - - +
109C ASP* 1.3 59.3 + - - +
111C GLU* 3.3 8.3 + - - +
112C GLU* 3.0 39.2 + - - +
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Residues in contact with ASP 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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107C THR* 2.5 30.9 + - - +
108C SER* 1.3 82.4 + - - +
110C MET* 1.3 56.8 + - - +
112C GLU* 3.6 14.0 + - - +
113C ASP* 3.1 36.9 + - - +
196C ARG* 2.8 28.0 + - - +
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Residues in contact with MET 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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105C GLU 4.1 7.2 - - - +
106C ILE* 3.9 20.0 - - + -
107C THR* 3.0 33.9 + - - +
109C ASP* 1.3 77.1 - - - +
111C GLU* 1.3 60.2 + - - +
113C ASP* 3.4 1.4 + - - +
114C LYS* 2.8 32.4 + - - +
136C SER 3.2 23.6 - - - +
137C ASN* 4.1 2.5 - - - -
138C TYR* 4.1 9.9 - - + +
154C ILE* 3.7 28.8 - - + +
155C ASN 4.1 0.2 - - - -
156C ASN* 3.8 26.7 - - - +
196C ARG* 3.7 22.4 - - - +
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Residues in contact with GLU 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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106C ILE* 4.1 6.2 - - + +
107C THR 3.2 8.2 + - - +
108C SER* 3.3 12.1 + - - +
110C MET* 1.3 78.7 - - - +
112C GLU* 1.3 56.8 + - + +
114C LYS* 3.1 25.7 + - - +
115C ASP* 2.9 44.6 + - - +
138C TYR* 2.6 32.3 + - - -
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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 SER* 3.0 24.1 + - - +
109C ASP* 3.8 16.4 - - - +
111C GLU* 1.3 77.2 - - + +
113C ASP* 1.3 61.9 + - - +
115C ASP* 3.3 8.7 + - - +
116C LEU* 3.0 28.8 + - - +
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Residues in contact with ASP 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ASP* 3.1 17.7 + - - +
110C MET 3.8 2.9 - - - +
112C GLU* 1.3 78.3 - - - +
114C LYS* 1.3 60.3 + - - +
116C LEU* 3.3 6.2 + - - +
117C MET* 2.9 29.1 + - - +
154C ILE* 3.9 13.9 - - + -
196C ARG* 2.8 39.7 + - - +
197C SER* 4.9 2.3 + - - -
198C ALA* 5.4 4.0 + - - -
201C ILE* 3.7 27.0 - - + +
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Residues in contact with LYS 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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110C MET 2.8 21.9 + - - +
111C GLU* 3.1 29.4 + - - +
113C ASP* 1.3 72.0 - - - +
115C ASP* 1.3 82.9 + - - +
117C MET* 3.2 13.7 + - + +
118C LEU* 2.9 47.2 + - + +
131C VAL* 4.4 8.0 - - + +
138C TYR* 3.6 52.3 + - + -
154C ILE* 4.0 10.0 - - + +
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Residues in contact with ASP 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 GLU* 2.9 32.8 + - - +
112C GLU* 3.6 6.8 - - - +
114C LYS* 1.3 101.7 + - - +
116C LEU* 1.3 61.4 + - - +
118C LEU* 3.4 9.2 + - - +
119C LYS* 3.0 25.2 + - - +
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Residues in contact with LEU 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 GLU 3.0 16.5 + - - +
113C ASP* 3.7 6.5 - - - +
115C ASP* 1.3 76.9 - - - +
117C MET* 1.3 63.2 + - - +
119C LYS* 3.3 16.3 + - + +
120C LEU* 3.0 49.3 + - + +
198C ALA* 3.8 39.9 - - + +
201C ILE* 4.0 17.7 - - + -
202C GLU* 5.7 2.0 - - + +
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Residues in contact with MET 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 ASP 2.9 17.3 + - - +
114C LYS* 3.2 11.4 + - + +
116C LEU* 1.3 79.0 - - - +
118C LEU* 1.3 70.4 + - + +
120C LEU 3.3 0.2 + - - -
121C LEU* 2.8 45.2 + - + +
131C VAL* 6.1 0.9 - - + -
138C TYR* 4.8 3.1 - - + +
139C LEU 5.2 0.2 - - - -
140C ALA* 3.6 26.2 - - + +
152C PHE* 3.7 33.2 - - + +
153C GLU 4.2 0.2 - - - -
154C ILE* 4.0 28.5 - - + +
160C MET* 4.1 17.9 - - + -
201C ILE* 4.0 9.8 - - + +
205C ILE* 3.6 12.4 - - + +
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Residues in contact with LEU 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 LYS* 2.9 42.7 + - + +
115C ASP* 3.8 7.9 - - - +
117C MET* 1.3 95.8 - - + +
119C LYS* 1.3 62.2 + - - +
121C LEU* 3.5 6.0 + - + +
122C ASP* 3.0 25.6 + - - +
128C LEU* 4.0 26.7 - - + -
131C VAL* 4.2 20.9 - - + -
140C ALA* 4.3 2.2 - - + -
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Residues in contact with LYS 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 ASP 3.0 17.8 + - - +
116C LEU* 3.5 19.3 - - + +
118C LEU* 1.3 78.1 - - - +
120C LEU* 1.3 66.5 + - + +
122C ASP* 3.5 4.4 + - - +
123C LYS* 3.0 27.8 + - + +
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Residues in contact with LEU 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 LEU* 3.0 38.1 + - + +
119C LYS* 1.3 85.0 - - + +
121C LEU* 1.3 66.5 + - - +
123C LYS* 3.6 22.3 - - + +
124C ASN* 3.0 33.1 + - - +
201C ILE 4.5 0.4 - - - -
202C GLU* 3.6 52.3 - - + +
205C ILE* 3.6 25.4 - - + -
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Residues in contact with LEU 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 MET* 2.8 41.9 + - + +
118C LEU* 3.8 9.2 - - + +
120C LEU* 1.3 77.0 - - - +
122C ASP* 1.3 61.3 + - - +
124C ASN 3.3 7.3 + - - -
126C PHE* 2.9 52.5 + - + +
128C LEU* 4.3 13.9 - - + -
140C ALA* 4.1 22.0 - - + -
152C PHE* 3.7 39.7 - - + -
205C ILE* 4.0 16.4 - - + -
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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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118C LEU 3.0 17.4 + - - +
119C LYS* 3.9 4.0 - - - +
121C LEU* 1.3 75.6 - - - +
123C LYS* 1.3 67.5 + - - +
125C GLY* 3.0 13.3 + - - -
126C PHE 4.3 10.7 + - - +
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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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119C LYS* 3.0 19.2 + - + +
120C LEU* 3.6 23.3 - - + +
121C LEU 3.3 0.2 - - - -
122C ASP* 1.3 78.9 - - - +
124C ASN* 1.3 73.0 + - - +
125C GLY 3.5 0.7 + - - -
202C GLU* 4.9 10.5 + - - -
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Residues in contact with ASN 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 LEU* 3.0 26.5 + - - +
122C ASP 3.1 1.0 - - - -
123C LYS* 1.3 96.3 - - - +
125C GLY* 1.3 60.9 + - - +
126C PHE* 3.4 18.1 + - + -
205C ILE* 3.7 16.8 + - - +
206C THR* 5.0 4.8 + - - +
209C SER* 3.6 33.9 + - - -
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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