Contacts of the helix formed by residues 108 - 124 (chain F) 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 SER 108 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109F ASP* 1.3 72.5 + - - +
110F MET* 3.5 6.4 - - - +
111F GLU* 3.6 18.9 + - - +
112F GLU* 3.4 29.7 + - - +
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Residues in contact with ASP 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F SER* 1.3 79.8 - - - +
110F MET* 1.3 61.6 + - - +
111F GLU 3.1 1.7 + - - -
112F GLU* 3.3 10.2 + - - +
113F ASP* 2.8 38.6 + - - +
196F ARG* 3.5 13.9 - - - +
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Residues in contact with MET 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F SER 3.5 3.7 - - - +
109F ASP* 1.3 77.9 - - - +
111F GLU* 1.3 56.2 + - - +
113F ASP* 4.2 0.7 - - - -
114F LYS* 2.8 30.9 + - - +
136F SER 4.5 1.1 - - - +
137F ASN* 4.7 1.3 - - - +
138F TYR* 3.9 31.2 - - + -
154F ILE* 3.1 55.0 - - + +
155F ASN 3.9 7.6 - - - -
156F ASN* 3.5 25.8 - - - +
196F ARG* 3.2 20.2 - - - +
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Residues in contact with GLU 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F SER* 3.6 21.0 + - - +
109F ASP 3.1 0.4 - - - -
110F MET* 1.3 81.6 - - - +
112F GLU* 1.3 69.0 + - + +
114F LYS* 3.8 10.9 - - - +
115F ASP* 3.0 40.6 + - - +
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Residues in contact with GLU 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F SER 3.4 14.0 + - - +
109F ASP* 3.3 12.5 + - - +
111F GLU* 1.3 85.0 - - + +
113F ASP* 1.3 60.1 + - - +
115F ASP* 3.8 5.7 - - - +
116F LEU* 3.0 31.1 + - - +
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Residues in contact with ASP 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F ASP* 2.8 25.1 + - - +
110F MET 3.8 2.7 - - - +
112F GLU* 1.3 76.5 - - - +
114F LYS* 1.3 60.6 + - - +
116F LEU* 3.1 6.4 + - - +
117F MET* 2.9 28.9 + - - +
154F ILE* 4.3 7.4 - - + -
196F ARG* 2.9 45.1 + - - +
197F SER* 4.7 2.3 - - - -
198F ALA* 4.7 9.9 + - - +
201F ILE* 3.8 27.5 - - + +
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Residues in contact with LYS 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F MET* 2.8 26.7 + - - +
111F GLU* 3.8 13.9 - - - +
113F ASP* 1.3 74.0 - - - +
115F ASP* 1.3 97.0 + - - +
117F MET* 3.4 2.4 + - - +
118F LEU* 3.0 49.1 + - + +
138F TYR* 3.5 56.5 + - + -
154F ILE* 4.3 11.1 - - + +
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Residues in contact with ASP 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F GLU* 3.0 29.8 + - - +
112F GLU* 3.8 5.9 - - - +
114F LYS* 1.3 110.9 + - - +
116F LEU* 1.3 58.8 + - - +
118F LEU* 3.4 5.9 + - - +
119F LYS* 2.8 31.7 + - - +
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Residues in contact with LEU 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F GLU 3.0 19.0 + - - +
113F ASP* 3.5 5.6 - - - +
115F ASP* 1.3 76.9 - - - +
117F MET* 1.3 63.9 + - - +
119F LYS* 3.2 35.5 + - - +
120F LEU* 2.9 47.9 + - + +
198F ALA* 3.8 41.1 - - + +
201F ILE* 4.1 15.0 - - + -
202F GLU* 4.5 6.1 - - - +
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Residues in contact with MET 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F ASP 2.9 16.0 + - - +
114F LYS* 3.6 5.6 - - - +
116F LEU* 1.3 77.5 - - - +
118F LEU* 1.3 63.9 + - + +
120F LEU 3.3 0.2 + - - -
121F LEU* 2.9 48.9 + - + +
138F TYR* 5.1 3.6 - - - +
140F ALA* 4.6 4.9 - - - -
152F PHE* 3.7 31.0 - - + +
153F GLU* 3.8 6.7 - - - +
154F ILE* 3.6 32.5 - - + -
160F MET* 3.3 39.0 - - + -
201F ILE* 4.1 7.1 - - + +
205F ILE* 3.6 12.6 - - + +
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Residues in contact with LEU 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F LYS* 3.0 42.8 + - + +
115F ASP* 3.9 4.7 - - - +
117F MET* 1.3 79.6 - - + +
119F LYS* 1.3 62.7 + - - +
121F LEU* 3.4 4.3 + - + +
122F ASP* 3.1 25.1 + - - +
128F LEU* 4.1 15.3 - - + -
131F VAL* 4.0 35.4 - - + -
138F TYR* 5.3 0.9 - - + -
140F ALA* 4.3 12.1 - - + -
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Residues in contact with LYS 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F ASP 2.8 19.7 + - - +
116F LEU* 3.4 31.9 - - - +
118F LEU* 1.3 77.6 - - - +
120F LEU* 1.3 70.2 + - + +
122F ASP* 3.3 5.9 + - - +
123F LYS* 3.0 28.6 + - + +
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Residues in contact with LEU 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F LEU* 2.9 32.5 + - + +
119F LYS* 1.3 89.0 - - + +
121F LEU* 1.3 65.5 + - - +
123F LYS* 3.8 18.8 - - + +
124F ASN* 2.9 35.1 + - - +
201F ILE* 4.3 0.4 - - + -
202F GLU* 3.2 56.1 - - - +
205F ILE* 3.4 32.3 - - + +
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Residues in contact with LEU 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F MET* 2.9 33.6 + - + +
118F LEU* 3.8 6.5 - - - +
119F LYS 3.3 0.2 - - - -
120F LEU* 1.3 76.6 - - - +
122F ASP* 1.3 60.0 + - - +
124F ASN 3.5 0.5 + - - -
125F GLY 3.1 4.2 + - - -
126F PHE* 2.8 58.1 + - + +
128F LEU* 4.4 14.1 - - + -
140F ALA* 3.7 29.4 - - + -
152F PHE* 3.8 40.4 - - + -
205F ILE* 4.1 15.5 - - + -
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Residues in contact with ASP 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F LEU 3.1 17.9 + - - +
119F LYS* 3.5 6.5 - - - +
121F LEU* 1.3 75.2 - - - +
123F LYS* 1.3 67.8 + - - +
125F GLY* 3.0 13.8 + - - +
126F PHE 4.9 2.7 - - - +
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Residues in contact with LYS 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F LYS* 3.0 18.7 + - + +
120F LEU* 3.8 21.6 - - + +
122F ASP* 1.3 81.1 + - - +
124F ASN* 1.3 69.4 + - - +
125F GLY 3.4 0.5 + - - -
202F GLU* 5.8 2.4 + - - -
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Residues in contact with ASN 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F LEU* 2.9 34.5 + - - +
121F LEU 3.5 0.2 + - - -
123F LYS* 1.3 87.2 - - - +
125F GLY* 1.3 62.0 + - - +
126F PHE* 3.4 28.3 + - + -
205F ILE* 3.6 15.3 - - - +
206F THR* 5.4 2.2 + - - +
209F SER* 3.4 25.7 + - - -
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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