Contacts of the helix formed by residues 146 - 161 (chain E) in PDB entry 3KTM
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 THR 146 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66E LYS* 6.0 5.6 - - - -
145E GLU* 1.3 81.6 + - - +
147E HIS* 1.3 65.0 + - - +
148E LEU* 3.8 9.7 + - - +
149E HIS* 3.2 21.8 + - - +
150E TRP* 2.9 29.2 + - - -
177E ASP 4.1 8.1 - - - +
178E LYS* 3.5 26.5 - - + +
179E PHE* 4.8 1.3 - - - -
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Residues in contact with HIS 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E VAL* 3.6 17.7 - - + -
87E GLU* 3.2 49.8 + - + +
88E ALA 4.2 4.7 - - - -
89E ASN* 3.3 18.4 + - - -
146E THR* 1.3 75.3 - - - +
148E LEU* 1.3 62.6 + - - +
150E TRP* 3.1 4.9 + - - +
151E HIS* 2.9 29.1 + - + +
168E TYR* 3.5 28.5 - + - -
170E MET* 3.6 32.8 - - + +
177E ASP* 3.8 14.0 + - - +
179E PHE* 4.7 0.2 - - - -
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Residues in contact with LEU 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E THR* 3.3 8.7 - - - +
147E HIS* 1.3 83.3 + - - +
149E HIS* 1.3 65.9 + - - +
151E HIS* 3.3 14.6 + - + +
152E THR* 3.1 37.8 + - - +
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Residues in contact with HIS 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E ARG* 3.6 16.9 + - - -
143E VAL* 5.1 1.7 - - + +
145E GLU* 3.2 46.8 + - + +
146E THR* 3.2 22.6 + - - +
147E HIS 3.2 0.2 - - - -
148E LEU* 1.3 84.6 - - + +
150E TRP* 1.3 69.2 + + - +
152E THR* 3.2 8.1 + - - -
153E VAL* 2.9 51.1 + - + +
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Residues in contact with TRP 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E GLN* 4.4 9.9 - - + -
140E ARG* 4.0 27.8 - - - -
143E VAL* 4.0 23.3 - - + -
145E GLU* 3.4 19.6 + - + +
146E THR 2.9 24.2 + - - -
147E HIS 3.1 6.7 + - - +
149E HIS* 1.3 75.0 - + - +
151E HIS* 1.3 65.6 + - - +
153E VAL* 3.7 16.7 - - + +
154E ALA* 3.0 23.4 + - - +
170E MET* 3.8 24.5 - - + -
179E PHE* 2.5 28.5 + - + -
180E ARG* 3.3 28.7 - - - -
181E GLY* 3.6 20.2 - - - -
182E VAL* 3.7 28.1 - - + +
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Residues in contact with HIS 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ACT 3.2 37.5 + - + +
89E ASN 5.8 0.9 - - - -
90E GLN* 5.5 0.9 - - - -
147E HIS* 2.9 15.6 + - + +
148E LEU* 3.6 18.9 - - + +
150E TRP* 1.3 75.0 - - - +
152E THR* 1.3 61.0 + - - +
154E ALA* 3.0 4.7 + - - +
155E LYS* 2.8 39.1 + - + +
165E LEU* 3.6 17.2 - - + +
168E TYR* 3.1 39.6 + + + +
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Residues in contact with THR 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E LEU* 3.1 23.5 + - - +
149E HIS* 3.3 10.5 - - - -
151E HIS* 1.3 79.9 - - - +
153E VAL* 1.3 59.5 + - + +
155E LYS* 3.7 7.1 - - + +
156E GLU* 2.8 42.1 + - + +
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Residues in contact with VAL 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E GLN* 3.0 37.7 - - - +
140E ARG* 4.1 8.3 - - - +
149E HIS* 2.9 49.6 + - + +
150E TRP* 3.7 20.0 - - + +
151E HIS 3.3 0.2 - - - -
152E THR* 1.3 77.4 - - + +
154E ALA* 1.3 54.2 + - - +
156E GLU* 4.0 6.8 - - - +
157E THR* 2.7 37.2 + - - +
182E VAL* 4.5 3.4 - - + -
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Residues in contact with ALA 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E TRP 3.0 12.7 + - - +
151E HIS* 3.0 10.4 + - - +
153E VAL* 1.3 75.5 - - - +
155E LYS* 1.3 66.2 + - - +
157E THR* 3.2 2.8 + - - -
158E CYS* 3.1 27.4 + - - -
165E LEU* 3.8 15.3 - - + -
168E TYR* 4.6 2.7 - - + -
182E VAL* 4.3 6.5 - - + -
184E PHE* 3.8 38.0 - - + -
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Residues in contact with LYS 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ACT 3.2 22.7 + - - -
151E HIS* 2.8 32.6 + - + +
152E THR* 3.7 7.4 - - + +
154E ALA* 1.3 72.6 - - - +
156E GLU* 1.3 63.6 + - - +
158E CYS* 3.3 3.5 + - - +
159E SER* 3.0 28.6 + - - +
164E ASN* 5.9 2.7 - - - -
165E LEU* 3.6 23.8 + - + +
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Residues in contact with GLU 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E THR* 2.8 27.8 + - + +
153E VAL* 4.0 6.3 - - - +
155E LYS* 1.3 78.9 - - - +
157E THR* 1.3 57.4 + - - +
159E SER* 3.0 9.8 + - - -
160E GLU* 2.8 58.3 + - + +
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Residues in contact with THR 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E LEU* 4.7 7.4 - - + -
138E GLN* 3.7 16.3 + - - +
153E VAL* 2.7 24.8 + - - +
154E ALA 3.2 4.4 + - - -
156E GLU* 1.3 77.8 - - - +
158E CYS* 1.3 61.5 + - - +
160E GLU* 3.6 19.6 + - + +
161E LYS* 3.7 27.4 + - - +
184E PHE* 3.8 26.2 - - + -
186E CYS* 4.9 0.2 - - - -
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Residues in contact with CYS 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E ALA 3.1 15.7 + - - -
155E LYS 3.7 7.0 - - - +
157E THR* 1.3 74.5 - - - +
159E SER* 1.3 64.3 + - - +
161E LYS* 3.1 7.4 + - - -
163E THR* 2.8 42.4 + - - +
165E LEU* 3.6 26.7 - - - +
184E PHE* 3.8 8.3 - - - -
186E CYS* 2.0 55.4 - - - -
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Residues in contact with SER 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E LYS* 3.0 20.4 + - - +
156E GLU* 3.3 12.6 - - - -
158E CYS* 1.3 72.6 - - - +
160E GLU* 1.3 56.0 + - - +
161E LYS 2.9 4.3 - - - -
162E SER* 2.6 28.4 + - - +
163E THR 3.8 9.3 + - - +
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Residues in contact with GLU 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E GLU* 2.8 46.8 + - + +
157E THR* 3.9 19.5 + - + +
158E CYS 3.4 0.4 - - - -
159E SER* 1.3 71.8 - - - +
161E LYS* 1.3 61.1 + - + +
162E SER 3.3 0.8 + - - -
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Residues in contact with LYS 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E LYS* 6.1 1.0 - - - +
136E LEU* 4.3 30.0 - - + +
157E THR* 3.7 21.6 + - - +
158E CYS* 3.1 7.4 + - - +
159E SER 2.9 1.0 - - - -
160E GLU* 1.3 82.1 - - + +
162E SER* 1.3 70.2 + - - +
163E THR* 3.2 17.7 - - + +
186E CYS* 6.1 0.7 - - - -
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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