Contacts of the helix formed by residues 148 - 159 (chain B) in PDB entry 1K9A
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 ASN 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B MET* 4.7 5.6 - - + -
138B LEU* 4.0 6.1 - - - -
146B PHE* 3.9 3.8 - - - +
147B GLU* 1.3 81.2 - - + +
149B LEU* 1.3 61.8 + - - +
150B MET* 2.7 21.5 + - - +
151B GLN* 2.5 68.8 + - - +
152B LEU* 3.4 3.5 + - - +
227B ASP 4.2 8.1 - - - +
228B ALA 3.6 13.2 - - - +
257B GLU 4.3 2.8 + - - -
258B GLU 3.8 3.6 + - - -
260B GLY 3.7 10.9 + - - -
261B GLY* 5.5 0.2 - - - -
262B LEU* 4.9 17.8 - - + +
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B MET* 3.7 7.8 - - - +
82B TRP* 3.6 17.5 - - + -
83B PHE* 3.7 36.6 - - + -
106B VAL* 3.8 10.1 - - + -
116B TYR* 4.3 17.0 - - + -
131B ILE* 4.2 25.1 - - + -
138B LEU* 3.5 22.9 - - + -
148B ASN* 1.3 71.3 - - - +
150B MET* 1.3 57.0 + - - +
152B LEU* 3.0 8.9 + - + +
153B VAL* 2.7 37.2 + - + +
228B ALA 3.2 15.2 + - - +
229B THR* 4.3 5.2 - - + -
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Residues in contact with MET 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 4.0 34.3 - - - +
80B MET* 3.9 27.3 - - + -
82B TRP* 3.8 12.2 - - + -
148B ASN* 2.7 21.2 + - - +
149B LEU* 1.3 74.0 - - - +
151B GLN* 1.3 54.0 + - - +
153B VAL* 4.1 0.3 - - - +
154B GLU* 2.8 33.6 + - - +
180B GLN* 4.4 11.9 - - - +
256B VAL* 4.9 8.3 - - + -
257B GLU 5.1 1.1 - - - +
258B GLU* 3.4 57.5 - - + +
262B LEU* 5.2 4.3 - - - -
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Residues in contact with GLN 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B PHE* 3.4 20.4 - - + -
147B GLU* 2.5 49.3 + - - +
148B ASN* 2.5 35.1 + - - +
150B MET* 1.3 74.1 - - - +
152B LEU* 1.3 61.0 + - - +
154B GLU* 3.7 6.3 - - - +
155B HIS* 3.0 22.0 + - - +
258B GLU 3.2 14.8 - - - +
259B LYS* 2.6 30.2 + - + +
260B GLY* 3.2 17.8 + - - -
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B VAL* 5.6 0.7 - - + -
118B LEU* 4.3 17.5 - - + -
131B ILE* 3.6 46.2 - - + -
138B LEU* 4.8 2.9 - - + -
139B SER 5.2 0.9 - - - +
140B ILE* 4.1 11.9 - - + +
146B PHE* 3.8 30.3 - - + -
148B ASN 3.4 2.3 + - - +
149B LEU* 3.0 16.9 + - + +
151B GLN* 1.3 76.8 - - - +
153B VAL* 1.3 73.2 + - + +
155B HIS* 2.7 24.8 + - - +
156B TYR* 3.0 35.3 + - + -
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B TRP* 3.2 62.6 - - + +
104B PHE* 3.7 19.7 - - + -
106B VAL* 4.1 14.4 - - + -
149B LEU* 2.7 12.9 + - + +
150B MET 4.1 0.4 - - - +
152B LEU* 1.3 82.5 - - + +
154B GLU* 1.3 60.5 + - - +
156B TYR 3.4 0.3 + - - -
157B THR* 2.6 44.1 + - - +
167B LEU* 3.6 8.9 - - + +
258B GLU* 5.9 1.1 - - - +
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Residues in contact with GLU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B MET 2.8 20.1 + - - +
151B GLN* 3.7 6.1 - - - +
153B VAL* 1.3 77.0 - - - +
155B HIS* 1.3 68.5 + - - +
157B THR* 3.2 13.9 + - - -
158B THR* 2.8 36.0 + - - -
258B GLU* 3.0 37.7 + - + +
259B LYS* 5.5 11.0 - - + +
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Residues in contact with HIS 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B VAL* 3.7 25.7 - - + +
146B PHE* 3.1 28.5 - + + -
151B GLN 3.0 13.9 + - - +
152B LEU 2.7 15.1 + - - +
154B GLU* 1.3 78.1 + - - +
156B TYR* 1.3 67.5 + + + +
158B THR* 3.1 27.3 + - - -
159B ASP* 3.4 8.8 + - + +
161B ASP* 3.3 32.5 + - + +
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Residues in contact with TYR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LEU* 4.7 0.2 - - + -
140B ILE* 4.0 25.8 + - + +
141B ASP* 3.4 23.6 + - - +
144B VAL* 4.0 7.8 - - - +
146B PHE* 4.4 5.6 - + - -
152B LEU* 3.0 39.1 + - + -
153B VAL 3.7 0.2 - - - -
155B HIS* 1.3 90.3 - + - +
157B THR* 1.3 62.4 + - - +
158B THR 3.2 1.6 - - - -
159B ASP 3.4 10.3 - - - +
160B ALA 3.2 26.9 - - - -
161B ASP* 3.9 19.1 - - + -
163B LEU* 3.5 25.5 - - + +
166B ARG* 3.5 8.3 - - - -
167B LEU* 2.8 43.3 + - + -
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Residues in contact with THR 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B PHE* 4.6 3.2 - - + -
153B VAL* 2.6 36.5 + - - +
154B GLU* 3.2 9.3 + - + -
156B TYR* 1.3 78.9 - - - +
158B THR* 1.3 61.0 + - - +
159B ASP 3.5 0.2 - - - -
166B ARG* 4.0 11.4 - - - -
167B LEU* 3.6 31.4 - - - +
168B ILE 5.4 4.7 - - - +
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Residues in contact with THR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B GLU* 2.8 30.7 + - - -
155B HIS* 3.2 14.6 - - + -
157B THR* 1.3 81.4 - - - +
159B ASP* 1.3 60.4 + - + +
166B ARG* 4.9 5.2 - - - -
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Residues in contact with ASP 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B HIS* 3.4 5.7 + - + +
156B TYR* 3.4 21.1 - - - -
157B THR 3.5 1.8 - - - -
158B THR* 1.3 85.7 - - + +
160B ALA* 1.3 66.3 + - - +
161B ASP* 2.5 44.1 + - + +
166B ARG* 4.0 6.1 - - - +
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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