Contacts of the helix formed by residues 150 - 165 (chain A) in PDB entry 1KAO
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 LYS 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLN* 3.3 40.9 + - + +
23A PHE* 2.8 27.8 + - - -
26A GLY* 3.9 13.2 - - - +
42A LYS* 4.5 8.3 - - - +
148A LYS 3.8 1.8 + - - -
149A SER* 1.3 73.6 - - - +
151A THR* 1.4 59.6 + - + +
153A VAL* 3.4 0.6 + - + -
154A ASP* 2.8 58.4 + - - +
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Residues in contact with THR 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A SER* 3.2 9.6 + - - -
150A LYS* 1.4 76.9 - - + +
152A MET* 1.3 68.0 + - - +
154A ASP* 3.3 7.3 + - - +
155A GLU* 3.0 30.5 + - - +
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Residues in contact with MET 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A VAL* 4.2 14.1 - - + -
143A MET* 5.0 1.4 - - - +
144A GLU 3.6 21.1 - - - +
145A THR* 4.1 16.7 - - + +
146A SER* 3.5 28.3 - - - +
149A SER* 3.1 27.8 + - - +
151A THR* 1.3 79.2 + - - +
153A VAL* 1.3 61.7 + - - +
155A GLU* 3.3 7.5 + - - +
156A LEU* 3.0 22.0 + - - +
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Residues in contact with VAL 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.3 49.1 - - + +
22A GLN* 3.8 18.4 - - + -
23A PHE* 3.5 26.9 - - + +
145A THR* 5.4 0.7 - - - -
146A SER 4.0 8.5 - - - +
147A ALA* 4.3 0.4 - - - -
149A SER 3.1 17.9 + - - +
150A LYS 4.0 2.5 - - - +
152A MET* 1.3 76.3 - - + +
154A ASP* 1.3 65.2 + - - +
156A LEU* 3.3 7.2 + - + +
157A PHE* 3.2 30.5 + - + -
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Residues in contact with ASP 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.5 18.4 - - + -
44A ILE* 4.7 3.1 - - - +
150A LYS* 2.8 59.2 + - - +
151A THR* 3.8 7.5 - - - +
153A VAL* 1.3 78.0 - - - +
155A GLU* 1.3 59.3 + - + +
157A PHE* 3.5 1.7 + - - +
158A ALA* 3.0 29.5 + - - +
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A MET* 3.8 14.5 - - + +
151A THR* 3.0 21.8 + - - +
152A MET* 3.6 6.7 - - - +
154A ASP* 1.3 74.4 - - + +
156A LEU* 1.3 65.5 + - - +
158A ALA* 3.5 10.3 + - - +
159A GLU* 3.0 26.0 + - - +
162A ARG* 4.8 12.5 + - - -
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Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.5 20.4 - - + -
79A ILE* 4.1 26.5 - - + -
112A ILE* 3.9 17.9 - - + +
114A VAL* 3.6 33.9 - - + -
143A MET* 3.7 16.7 - - - -
145A THR* 4.4 12.3 - - + -
152A MET 3.0 13.0 + - - +
153A VAL* 3.5 9.9 - - - +
155A GLU* 1.3 76.7 - - - +
157A PHE* 1.3 76.9 + - + +
159A GLU* 3.2 4.2 + - - +
160A ILE* 3.1 19.6 + - - +
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Residues in contact with PHE 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 4.5 3.1 - - + -
8A VAL* 4.7 5.2 - - + -
19A LEU* 4.1 7.6 - - + -
20A THR* 4.5 17.0 - - - -
23A PHE* 3.5 51.8 - + + -
44A ILE* 3.8 2.8 - - - +
53A LEU* 3.8 20.0 - - + +
55A ILE* 3.6 28.9 - - + -
79A ILE* 3.6 26.5 - - + -
153A VAL* 3.2 32.5 + - + +
156A LEU* 1.3 86.6 - - + +
158A ALA* 1.3 63.7 + - - +
160A ILE* 3.3 21.3 - - + +
161A VAL* 3.4 11.4 + - - +
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Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ILE* 3.7 3.7 - - + +
45A GLU 5.4 1.3 - - - +
46A VAL* 3.6 26.2 - - + +
154A ASP 3.0 19.5 + - - +
155A GLU* 3.7 12.1 - - - +
156A LEU 3.3 0.2 - - - -
157A PHE* 1.3 74.2 - - - +
159A GLU* 1.3 64.2 + - - +
161A VAL* 3.1 14.9 + - - +
162A ARG* 3.1 36.3 + - - +
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Residues in contact with GLU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ILE* 3.6 18.6 - - + -
141A PRO* 3.9 15.5 - - + +
143A MET* 3.9 16.9 - - + +
155A GLU 3.0 19.3 + - - +
156A LEU 3.2 0.9 + - - +
158A ALA* 1.3 77.0 - - - +
160A ILE* 1.3 62.4 + - - +
162A ARG* 3.0 36.6 + - - +
163A GLN* 2.9 47.0 + - - +
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Residues in contact with ILE 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 4.0 23.1 - - + -
53A LEU* 4.9 0.7 - - + -
77A GLY* 4.4 1.8 - - - -
78A PHE 3.6 33.0 - - - +
79A ILE* 4.1 25.4 - - + -
110A PRO* 4.0 13.0 - - + +
111A VAL 4.2 3.6 - - - +
112A ILE* 3.3 24.2 - - + +
156A LEU 3.1 9.5 + - - +
157A PHE* 3.3 19.5 - - + +
159A GLU* 1.3 73.8 - - - +
161A VAL* 1.3 62.5 + - + +
163A GLN* 3.2 6.2 + - + +
164A MET* 2.9 44.3 + - - +
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.8 31.9 - - + +
44A ILE* 4.7 4.5 - - + -
46A VAL* 3.5 33.9 - - + -
51A SER* 4.2 3.6 - - - +
53A LEU* 3.6 34.1 - - + -
157A PHE 3.6 10.1 - - - +
158A ALA 3.1 9.8 + - - +
160A ILE* 1.3 76.2 - - - +
162A ARG* 1.3 62.6 + - - +
164A MET* 3.1 8.5 + - - +
165A ASN* 3.0 28.7 + - - +
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Residues in contact with ARG 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A VAL* 4.9 7.6 - - + -
47A ASP* 2.8 46.8 + - - +
155A GLU* 4.8 13.7 + - - -
158A ALA* 3.1 25.9 + - - +
159A GLU* 3.0 51.5 + - - +
161A VAL* 1.3 74.9 - - - +
163A GLN* 1.3 63.3 + - - +
165A ASN* 3.2 9.0 + - - +
166A TYR* 3.1 24.8 + - - +
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Residues in contact with GLN 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PRO* 3.8 19.3 - - + +
111A VAL 4.4 3.8 + - - +
112A ILE* 4.2 8.7 - - + -
139A GLY 5.4 1.6 - - - +
140A CYS* 5.3 1.6 - - - -
141A PRO* 3.5 34.3 - - + +
159A GLU* 2.9 39.7 + - - +
160A ILE* 3.6 11.9 - - + +
162A ARG* 1.3 78.2 - - - +
164A MET* 1.3 60.8 + - - +
166A TYR* 3.3 21.1 + - - +
167A ALA* 3.2 24.6 + - - +
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Residues in contact with MET 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.6 32.5 - - + -
5A LYS 3.7 5.2 - - - +
6A VAL* 3.9 18.6 - - - -
76A GLN* 3.3 44.9 - - + +
77A GLY* 3.7 16.4 - - - +
110A PRO* 3.8 26.3 - - + +
160A ILE* 2.9 25.4 + - + +
161A VAL* 3.6 5.2 - - - +
163A GLN* 1.3 74.6 - - - +
165A ASN* 1.3 63.4 + - - +
167A ALA* 4.1 10.9 + - - +
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Residues in contact with ASN 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ARG* 5.6 3.4 - - - +
4A TYR* 2.8 38.8 + - - -
46A VAL* 5.6 0.9 - - - +
161A VAL* 3.0 23.2 + - - +
162A ARG* 3.7 9.8 - - - +
164A MET* 1.3 79.3 + - - +
166A TYR* 1.3 61.1 + - - +
167A ALA 3.4 4.2 - - - +
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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