Contacts of the helix formed by residues 159 - 173 (chain A) in PDB entry 1KO1
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 PRO 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ARG* 5.2 1.6 - - - +
158A GLN* 1.3 95.2 - - + +
160A LEU* 1.3 66.7 + - - +
161A GLU* 3.2 8.7 - - + +
162A GLY* 3.0 8.7 + - - +
163A VAL* 3.0 18.4 + - - +
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Residues in contact with LEU 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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23A ALA* 4.3 17.5 - - + +
24A VAL* 3.7 36.8 - - + +
27A GLU* 5.7 4.3 - - + -
120A ARG* 4.0 24.4 - - - +
158A GLN 3.9 0.2 + - - -
159A PRO* 1.3 72.1 - - - +
161A GLU* 1.3 54.5 + - - +
163A VAL* 3.0 8.4 + - - +
164A VAL* 2.8 50.2 + - + +
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Residues in contact with GLU 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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159A PRO* 3.2 6.6 - - + +
160A LEU* 1.3 77.1 - - - +
162A GLY* 1.3 59.1 + - - +
164A VAL* 3.3 9.2 + - - +
165A ALA* 2.9 29.3 + - + +
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Residues in contact with GLY 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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158A GLN* 3.2 22.9 - - - -
159A PRO* 3.0 12.0 + - - +
161A GLU* 1.3 78.9 - - - +
163A VAL* 1.3 54.8 + - - +
165A ALA* 3.1 7.2 + - - +
166A SER* 2.7 38.5 + - - -
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Residues in contact with VAL 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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19A SER 5.7 0.2 - - - +
24A VAL* 3.5 28.0 - - + -
110A LEU* 3.8 23.3 - - + -
120A ARG* 4.8 7.0 - - - +
154A VAL* 3.8 8.1 - - + -
156A ILE* 4.2 20.4 - - + +
158A GLN* 3.6 26.6 - - + +
159A PRO 3.0 14.6 + - - +
160A LEU* 3.0 10.4 + - + +
162A GLY* 1.3 74.1 - - - +
164A VAL* 1.3 53.9 + - - +
166A SER* 3.2 2.5 + - - -
167A THR* 2.8 39.7 + - - +
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Residues in contact with VAL 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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24A VAL* 4.4 10.8 - - - +
27A GLU* 3.9 28.0 - - + -
28A VAL* 3.9 12.0 - - + +
31A GLN* 3.7 22.7 - - - +
160A LEU* 2.8 37.1 + - + +
161A GLU* 3.4 7.9 - - - +
163A VAL* 1.3 76.8 - - - +
165A ALA* 1.3 57.6 + - - +
167A THR* 3.1 3.4 + - - -
168A ILE* 2.8 51.2 + - + +
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Residues in contact with ALA 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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161A GLU* 2.9 20.0 + - + +
162A GLY* 3.6 7.6 - - - +
164A VAL* 1.3 77.8 - - - +
166A SER* 1.3 62.3 + - - +
167A THR 3.2 0.3 + - - -
168A ILE* 3.2 11.3 + - - +
169A GLU* 2.9 24.3 + - - +
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Residues in contact with SER 166 (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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154A VAL* 4.2 15.9 - - - -
155A ASP 5.7 0.7 - - - -
158A GLN* 2.9 22.7 + - - -
162A GLY 2.7 23.7 + - - -
163A VAL 3.7 3.6 - - - -
165A ALA* 1.3 72.9 - - - +
167A THR* 1.3 57.7 + - - +
169A GLU* 3.4 11.8 + - - +
170A VAL* 3.0 33.1 + - - +
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Residues in contact with THR 167 (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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13A LEU* 4.1 17.0 - - + -
24A VAL* 3.7 10.3 - - - +
28A VAL* 3.9 21.5 - - + -
108A ILE* 3.7 24.9 - - + -
110A LEU* 4.4 3.3 - - - +
154A VAL* 3.9 16.8 - - - +
163A VAL* 2.8 25.6 + - - +
164A VAL 3.5 4.3 - - - -
166A SER* 1.3 74.9 - - - +
168A ILE* 1.3 65.4 + - - +
170A VAL* 3.1 5.6 + - - +
171A ILE* 3.0 28.2 + - + +
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Residues in contact with ILE 168 (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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28A VAL* 4.0 19.5 - - + -
31A GLN* 3.5 32.8 - - + +
32A LEU* 4.3 24.0 - - + -
164A VAL* 2.8 36.1 + - + +
165A ALA* 3.6 8.3 - - - +
167A THR* 1.3 77.9 - - - +
169A GLU* 1.3 59.1 + - - +
171A ILE* 3.2 9.1 + - - +
172A LYS* 2.9 35.3 + - + +
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Residues in contact with GLU 169 (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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165A ALA 2.9 16.2 + - - +
166A SER* 3.6 11.5 - - - +
167A THR 3.2 0.2 - - - -
168A ILE* 1.3 78.9 - - - +
170A VAL* 1.3 58.5 + - + +
172A LYS* 3.2 4.5 + - - +
173A LYS* 2.8 32.8 + - + +
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Residues in contact with VAL 170 (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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108A ILE* 3.6 29.6 - - + -
152A LEU* 3.1 45.8 - - + +
153A VAL 4.6 7.0 - - - +
154A VAL* 4.4 11.0 - - + -
166A SER 3.0 18.4 + - - +
167A THR* 3.1 3.3 + - - +
169A GLU* 1.3 77.2 - - + +
171A ILE* 1.3 62.7 + - - +
173A LYS* 3.3 38.3 - - - +
174A GLY 3.9 3.1 + - - -
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Residues in contact with ILE 171 (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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11A TYR* 3.4 39.5 + - + +
28A VAL* 3.8 27.6 - - + -
32A LEU* 3.9 19.5 - - + -
82A VAL* 4.4 13.2 - - + -
84A LEU* 3.9 19.3 - - + -
108A ILE* 3.8 20.6 - - + -
167A THR* 3.0 19.7 + - + +
168A ILE* 3.2 6.9 + - - +
170A VAL* 1.3 78.9 - - - +
172A LYS* 1.3 67.3 + - + +
174A GLY 3.5 9.4 - - - +
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Residues in contact with LYS 172 (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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32A LEU* 4.4 21.9 - - + +
168A ILE* 2.9 25.8 + - + +
169A GLU* 3.2 4.0 + - - +
171A ILE* 1.3 82.3 - - + +
173A LYS* 1.3 53.9 + - - +
174A GLY* 2.7 17.3 + - - -
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Residues in contact with LYS 173 (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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152A LEU* 3.3 35.8 - - + +
169A GLU* 2.8 19.7 + - + +
170A VAL* 3.3 29.2 - - - +
172A LYS* 1.3 72.0 - - - +
174A GLY* 1.3 60.9 + - - +
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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