Contacts of the helix formed by residues 148 - 159 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C LEU* 3.5 10.5 - - - -
146C PHE* 3.4 3.4 - - - +
147C GLU* 1.3 88.1 + - - +
149C LEU* 1.3 58.4 + - - +
150C MET* 3.1 18.2 + - + +
151C GLN* 2.5 43.8 + - - +
152C LEU* 3.0 25.1 + - - +
225C LYS* 3.7 33.0 - - + +
259C LYS 4.1 9.0 + - - +
260C GLY 6.3 0.2 - - - -
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Residues in contact with LEU 149 (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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80C MET* 5.3 8.5 - - - -
82C TRP* 3.7 17.5 - - + -
83C PHE* 4.5 9.9 - - + -
106C VAL* 4.1 19.5 - - + -
116C TYR* 3.9 43.3 - - + -
131C ILE* 4.0 28.0 - - + -
138C LEU* 3.5 21.4 - - + +
148C ASN* 1.3 69.7 - - - +
150C MET* 1.3 56.6 + - - +
152C LEU* 3.0 6.3 + - + +
153C VAL* 2.6 41.0 + - + +
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Residues in contact with MET 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LEU* 3.8 34.3 - - - +
80C MET* 3.7 25.1 - - + -
82C TRP* 3.7 14.1 - - + -
148C ASN* 3.1 14.5 + - + +
149C LEU* 1.3 75.2 - - - +
151C GLN* 1.3 55.4 + - - +
153C VAL* 3.3 0.9 + - - +
154C GLU* 2.7 37.9 + - - +
180C GLN* 5.5 3.1 - - - +
225C LYS* 3.5 26.0 - - + -
226C ASN* 3.4 36.3 - - + +
260C GLY* 4.7 2.0 - - - -
261C GLY 4.5 17.7 - - - +
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Residues in contact with GLN 151 (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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145C TYR 5.3 0.4 - - - -
146C PHE* 3.3 18.0 - - + -
147C GLU* 2.5 52.7 + - - +
148C ASN* 2.5 27.5 + - - +
150C MET* 1.3 72.4 - - - +
152C LEU* 1.3 62.7 + - - +
154C GLU* 3.5 6.2 + - - +
155C HIS* 3.1 23.4 + - - +
258C GLU 5.3 1.1 - - - +
259C LYS* 3.0 42.0 - - - +
260C GLY* 4.3 7.3 - - - +
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Residues in contact with LEU 152 (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* 5.0 5.8 - - + -
131C ILE* 3.5 44.9 - - + -
138C LEU* 4.3 7.4 - - + -
140C ILE* 4.4 9.9 - - + -
146C PHE* 3.5 34.9 - - + -
148C ASN 3.0 13.5 + - - +
149C LEU* 3.3 15.5 - - + +
151C GLN* 1.3 76.3 - - - +
153C VAL* 1.3 73.7 + - + +
155C HIS* 3.0 14.6 + - - +
156C TYR* 3.1 38.1 + - + -
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Residues in contact with VAL 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C TRP* 3.7 41.5 - - + +
104C PHE* 3.6 32.8 - - + -
106C VAL* 4.3 11.9 - - + -
118C LEU* 5.4 2.0 - - + -
131C ILE* 6.4 0.4 - - + -
149C LEU* 2.6 25.5 + - + +
150C MET 3.7 2.2 - - - +
152C LEU* 1.3 81.4 - - + +
154C GLU* 1.3 56.1 + - - +
156C TYR 3.3 1.6 + - - -
157C THR* 2.7 41.9 + - - +
167C LEU* 3.5 11.1 - - + +
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Residues in contact with GLU 154 (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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150C MET 2.7 23.1 + - - +
151C GLN* 3.5 8.5 - - - +
153C VAL* 1.3 73.8 - - - +
155C HIS* 1.3 63.6 + - - +
157C THR* 3.1 24.3 + - - +
158C THR* 3.1 21.2 + - - +
180C GLN* 5.3 7.6 + - - +
256C VAL* 4.0 23.2 - - + +
257C GLU 5.3 0.9 - - - +
258C GLU 4.6 13.5 - - - +
260C GLY* 4.9 9.2 - - - +
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Residues in contact with HIS 155 (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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144C VAL* 4.2 11.1 - - + +
146C PHE* 3.3 36.9 - + + -
151C GLN 3.1 4.3 + - - +
152C LEU 3.0 4.2 + - - +
154C GLU* 1.3 79.3 - - - +
156C TYR* 1.3 75.0 + + - +
158C THR* 3.4 8.9 - - - -
159C ASP* 3.4 21.9 + - + +
161C ASP* 2.8 36.5 + - - -
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Residues in contact with TYR 156 (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* 4.7 3.1 - - + -
140C ILE* 3.7 26.1 + - + +
141C ASP* 4.0 22.7 + - - +
144C VAL* 4.7 1.0 - - - +
146C PHE* 4.3 15.4 - + - -
152C LEU* 3.1 36.7 + - + +
155C HIS* 1.3 86.7 - + - +
157C THR* 1.3 63.6 + - - +
159C ASP 2.5 21.7 - - - +
161C ASP* 3.0 30.2 + - + +
163C LEU* 3.4 41.7 - - + -
166C ARG* 3.8 1.0 - - - -
167C LEU* 3.2 35.7 + - + -
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Residues in contact with THR 157 (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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104C PHE* 4.6 3.6 - - + -
153C VAL* 2.7 33.6 + - - +
154C GLU* 3.1 19.9 + - - +
156C TYR* 1.3 77.7 - - - +
158C THR* 1.3 68.8 + - - +
166C ARG* 4.2 4.0 - - - +
167C LEU* 3.0 37.2 - - - +
168C ILE* 4.8 10.5 - - - +
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Residues in contact with THR 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C GLU* 3.1 16.6 + - - +
155C HIS* 3.4 10.6 - - - -
157C THR* 1.3 85.7 - - - +
159C ASP* 1.3 85.7 + - - +
166C ARG* 4.0 13.7 + - - -
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Residues in contact with ASP 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C HIS* 3.4 9.8 + - + +
156C TYR* 2.5 38.3 - - - +
158C THR* 1.3 102.2 - - - +
160C ALA* 1.3 63.0 + - - +
161C ASP* 4.2 3.8 - - - +
166C ARG* 3.9 10.1 + - - +
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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