Contacts of the helix formed by residues 145 - 164 (chain A) in PDB entry 1KEK
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 SER 145 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A SER* 3.7 1.3 - - - -
144A SER* 1.3 78.8 - - - +
146A VAL* 1.3 64.5 + - - +
147A GLN* 3.3 9.6 + - - +
148A GLU* 3.0 26.3 + - - +
149A ALA* 3.0 22.2 + - - +
176A THR* 3.7 12.4 + - - +
179A GLU* 6.0 1.3 - - - -
181A GLN* 6.5 0.2 - - - -
281A GLU* 3.8 25.8 - - - -
478A THR* 5.8 3.8 - - - -
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Residues in contact with VAL 146 (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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8A THR 3.5 21.5 - - - +
9A ASP 3.8 14.1 - - - +
10A GLY* 4.0 1.6 - - - +
13A ALA* 3.8 6.0 - - + +
145A SER* 1.3 74.7 - - - +
147A GLN* 1.4 62.5 + - - +
149A ALA* 3.2 16.6 + - - +
150A HIS 3.4 5.0 + - - -
176A THR* 3.9 19.7 - - + +
179A GLU* 3.5 33.4 + - + +
181A GLN* 3.9 26.7 - - + +
183A ILE* 3.7 22.4 - - + +
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Residues in contact with GLN 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A SER* 3.2 7.9 + - - +
146A VAL* 1.4 79.6 - - - +
148A GLU* 1.4 64.5 + - + +
150A HIS* 3.3 6.1 + - - +
151A ASP* 3.2 19.0 + - - +
181A GLN* 5.9 0.2 - - - +
183A ILE* 3.5 21.5 - - + +
184A GLU* 2.9 46.1 + - - +
256A ARG* 3.3 45.8 + - - +
258A TYR* 4.5 2.2 - - - +
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Residues in contact with GLU 148 (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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142A ALA 4.6 1.0 - - - +
143A SER* 3.5 13.7 - - - -
144A SER* 2.5 41.6 + - - +
145A SER* 3.0 17.3 + - - +
147A GLN* 1.4 81.1 - - + +
149A ALA* 1.3 56.9 + - - +
151A ASP* 3.7 0.9 - - - +
152A MET* 2.7 41.2 + - + +
258A TYR* 3.4 31.3 - - + +
281A GLU* 5.0 2.9 - - - +
301A LYS* 4.9 5.0 + - - -
303A ARG* 3.0 35.6 + - - -
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLY* 4.1 10.1 - - - +
13A ALA* 4.6 0.4 - - + -
14A THR* 3.5 25.1 - - + +
143A SER* 3.4 18.4 - - - +
145A SER 3.0 13.4 + - - +
146A VAL* 3.4 14.1 - - - +
147A GLN 3.2 0.2 - - - -
148A GLU* 1.3 73.8 - - - +
150A HIS* 1.4 65.1 + - - +
153A ALA* 3.0 27.2 + - - +
169A HIS* 3.3 4.4 + - - -
171A PHE* 4.5 7.0 - - + -
176A THR* 4.6 1.1 - - + -
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Residues in contact with HIS 150 (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 ALA* 3.8 25.4 - - + +
16A HIS* 3.8 7.1 + - - -
17A VAL* 3.5 27.3 - - + +
146A VAL 3.4 2.8 + - - -
147A GLN* 3.3 12.9 + - - +
148A GLU 3.2 0.6 - - - -
149A ALA* 1.4 81.4 - - - +
151A ASP* 1.3 86.9 + - - +
153A ALA* 3.5 2.9 - - - +
154A LEU* 3.2 20.7 + - + +
183A ILE* 4.4 4.0 - - + -
184A GLU 4.1 7.1 + - - -
185A VAL* 3.7 24.2 - - + -
186A LEU* 3.0 49.1 + - + +
191A MET* 4.3 1.4 - - - +
250A VAL* 6.0 0.4 - - + -
254A THR* 5.2 0.2 - - + -
256A ARG* 4.4 2.2 - - - -
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Residues in contact with ASP 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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147A GLN* 3.2 10.9 + - - +
148A GLU 3.3 2.9 + - - +
150A HIS* 1.3 107.9 + - - +
152A MET* 1.3 64.1 + - - +
154A LEU* 3.2 6.7 + - - +
155A VAL* 3.1 25.2 + - + +
250A VAL* 4.7 13.9 - - + +
254A THR* 4.6 1.0 - - - +
256A ARG* 2.7 36.4 + - - +
258A TYR* 2.6 44.2 + - + +
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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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141A LEU* 3.3 30.5 - - + +
142A ALA 3.8 16.6 - - - +
143A SER* 4.0 5.4 - - - -
148A GLU* 2.7 27.9 + - + +
151A ASP* 1.3 70.6 - - + +
153A ALA* 1.3 58.9 + - - +
155A VAL* 3.7 6.7 - - - +
156A ALA* 2.9 30.5 + - - +
169A HIS* 3.7 19.5 + - + +
247A MET* 3.9 9.9 - - + -
258A TYR* 3.6 38.1 - - + -
303A ARG* 3.4 36.1 - - + +
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Residues in contact with ALA 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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14A THR* 3.9 14.6 - - - +
17A VAL* 3.8 17.7 - - + -
110A HIS* 4.0 9.9 - - - +
149A ALA 3.0 21.3 + - - +
150A HIS 3.5 5.4 - - - +
152A MET* 1.3 74.4 - - - +
154A LEU* 1.4 61.7 + - - +
156A ALA* 3.3 2.7 + - - +
157A HIS* 3.1 28.9 + - - -
169A HIS* 3.7 23.2 + - + +
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Residues in contact with LEU 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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17A VAL* 3.6 14.1 - - + +
21A MET* 4.3 12.8 - - + -
150A HIS* 3.2 13.4 + - + +
151A ASP* 3.5 8.7 - - - +
152A MET 3.1 0.6 - - - -
153A ALA* 1.4 76.7 - - - +
155A VAL* 1.4 66.9 + - - +
156A ALA 3.3 0.2 + - - -
157A HIS* 3.3 1.8 + - - -
158A LEU* 3.1 41.6 + - + +
186A LEU* 3.8 29.2 - - + -
191A MET* 4.0 32.8 - - + -
194A LEU* 4.4 7.6 - - + -
250A VAL* 3.9 23.3 - - + -
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Residues in contact with VAL 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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141A LEU* 4.0 14.8 - - + -
151A ASP* 3.1 15.5 + - + +
152A MET* 3.9 9.9 - - - +
154A LEU* 1.4 76.2 - - - +
156A ALA* 1.4 56.5 + - - +
158A LEU* 3.9 2.2 - - - +
159A ALA* 2.7 38.9 + - + +
243A VAL* 4.0 34.5 - - + +
246A TYR* 4.1 20.3 - - + +
247A MET* 4.2 15.5 - - + -
250A VAL* 4.0 22.9 - - + -
258A TYR* 5.8 2.7 - - + -
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Residues in contact with ALA 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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108A VAL* 4.2 9.0 - - + -
141A LEU* 4.1 5.8 - - + -
152A MET 2.9 18.3 + - - +
153A ALA 3.5 5.2 - - - +
154A LEU 3.2 0.2 - - - -
155A VAL* 1.4 78.3 - - - +
157A HIS* 1.3 57.7 + - - +
160A ALA* 2.9 32.6 + - - +
167A PHE* 3.8 34.3 - - + -
169A HIS* 4.1 17.7 - - + -
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Residues in contact with HIS 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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17A VAL* 4.2 7.2 - - + -
18A ALA* 3.7 6.7 - - - -
21A MET* 3.4 41.5 + - + +
22A SER* 3.4 24.7 - - - -
81A THR 5.3 2.0 - - - -
82A THR* 3.9 4.3 - - + -
108A VAL* 3.7 27.0 - - + +
110A HIS* 2.9 32.9 - + - -
153A ALA 3.1 27.5 + - - +
154A LEU 3.9 3.1 - - - +
156A ALA* 1.3 80.5 - - - +
158A LEU* 1.3 63.5 + - - +
160A ALA* 3.7 1.4 - - - +
161A ILE* 3.1 31.9 + - + +
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Residues in contact with LEU 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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21A MET* 3.8 8.7 - - + -
154A LEU* 3.1 40.8 + - + +
155A VAL* 3.9 1.3 - - - +
157A HIS* 1.3 76.9 - - - +
159A ALA* 1.3 64.4 + - - +
161A ILE* 3.3 6.9 + - + +
162A GLU* 3.1 18.5 + - - +
191A MET 4.2 2.2 - - - +
194A LEU* 3.7 24.5 - - + +
195A VAL* 3.7 46.0 - - + +
246A TYR* 3.6 41.8 + - + -
250A VAL* 4.3 7.9 - - + -
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Residues in contact with ALA 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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155A VAL 2.7 22.7 + - - +
156A ALA 4.1 0.2 - - - +
158A LEU* 1.3 74.9 - - - +
160A ALA* 1.3 49.1 + - - +
163A SER* 2.7 44.4 + - - -
167A PHE* 3.6 25.4 - - + -
242A ILE* 3.8 22.9 - - + +
243A VAL* 4.0 13.5 - - + -
246A TYR* 4.0 5.3 - - + -
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Residues in contact with ALA 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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106A PRO* 3.5 23.4 - - - +
107A GLY 4.0 3.1 - - - +
108A VAL* 3.6 22.9 - - + -
156A ALA 2.9 19.3 + - - +
157A HIS 3.7 2.2 - - - +
159A ALA* 1.3 74.5 - - - +
161A ILE* 1.4 63.2 + - + +
164A ASN* 3.0 22.3 + - - -
165A VAL 3.5 20.9 - - - +
167A PHE* 3.8 6.2 - - + -
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Residues in contact with ILE 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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21A MET* 4.3 19.1 - - + +
80A LEU* 4.0 35.9 - - + -
106A PRO* 4.0 10.4 - - + +
157A HIS* 3.1 25.9 + - + +
158A LEU* 3.3 9.8 + - + +
160A ALA* 1.4 77.4 - - + +
162A GLU* 1.3 62.0 + - - +
164A ASN* 4.1 12.0 + - - +
195A VAL* 4.5 16.2 - - + -
196A ASN* 4.3 11.9 - - + +
199A ALA* 3.7 11.7 - - + +
200A LEU* 4.2 33.2 - - + +
203A PHE* 5.7 4.1 - - + +
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Residues in contact with GLU 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 LEU 3.1 15.3 + - - +
159A ALA 4.1 1.1 - - - +
161A ILE* 1.3 79.0 - - - +
163A SER* 1.3 61.6 + - - +
164A ASN* 3.7 5.5 + - - +
196A ASN* 2.9 29.8 + - + +
199A ALA* 3.9 13.5 - - + +
242A ILE* 3.6 21.8 - - + +
245A GLU* 2.9 25.5 - - - +
246A TYR* 2.6 37.4 + - + +
249A LYS* 4.8 1.7 + - - -
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Residues in contact with SER 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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159A ALA 2.7 28.3 + - - -
162A GLU* 1.3 75.8 - - - +
164A ASN* 1.3 65.4 + - - +
165A VAL* 3.0 28.6 + - - +
167A PHE* 4.0 4.0 - - - -
235A TYR* 3.7 20.4 - - - +
239A VAL* 4.1 20.9 - - - -
242A ILE* 3.7 24.7 - - - -
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Residues in contact with ASN 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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104A LEU* 3.0 46.8 + - + +
105A LEU 3.4 2.4 + - - -
106A PRO* 3.9 15.5 - - - +
160A ALA 3.0 12.6 + - - -
161A ILE 4.5 9.2 + - - +
162A GLU 3.5 6.5 - - - +
163A SER* 1.3 77.9 - - - +
165A VAL* 1.3 62.1 + - - +
199A ALA* 5.9 1.2 - - - +
203A PHE* 4.7 6.7 - - - +
206A LYS* 3.1 32.3 - - - +
235A TYR* 4.4 15.7 - - + -
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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