Contacts of the helix formed by residues 145 - 164 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B SER* 3.6 1.3 - - - -
144B SER* 1.3 77.5 - - - +
146B VAL* 1.3 63.8 + - - +
147B GLN* 3.4 8.8 + - - +
148B GLU* 3.0 29.2 + - - +
149B ALA* 2.9 18.0 + - - +
176B THR* 3.6 15.7 - - - +
179B GLU* 6.0 1.8 - - - -
181B GLN* 6.6 0.4 - - - -
281B GLU* 3.7 26.5 - - - -
478B THR* 5.7 3.4 - - - -
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR 3.6 11.0 - - - +
9B ASP 3.6 10.5 - - - +
10B GLY* 3.6 17.9 - - - +
13B ALA* 3.8 10.4 - - + +
145B SER* 1.3 73.8 - - - +
147B GLN* 1.4 63.5 + - - +
149B ALA* 3.2 14.0 + - - +
150B HIS 3.4 8.1 + - - -
176B THR* 3.8 19.5 - - + +
179B GLU* 3.3 34.0 + - + +
181B GLN* 3.9 27.2 - - + +
183B ILE* 4.1 13.2 - - + +
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Residues in contact with GLN 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B SER* 3.3 7.2 + - - +
146B VAL* 1.4 78.4 - - - +
148B GLU* 1.3 64.0 + - + +
150B HIS* 3.2 11.3 + - - +
151B ASP* 3.3 12.8 + - - +
183B ILE* 3.4 25.8 - - + +
184B GLU* 2.9 44.7 + - - +
256B ARG* 3.4 46.0 + - - +
258B TYR* 4.6 2.0 - - - +
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B SER* 3.4 13.0 - - - -
144B SER* 2.5 44.4 + - - +
145B SER* 3.0 22.7 + - - +
147B GLN* 1.3 74.0 - - + +
149B ALA* 1.4 57.4 + - - +
151B ASP* 3.2 1.2 + - - -
152B MET* 2.7 42.1 + - + +
258B TYR* 3.6 30.9 - - + +
281B GLU* 4.9 4.2 - - - +
301B LYS* 4.8 5.5 + - - -
303B ARG* 3.1 34.2 + - - -
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Residues in contact with ALA 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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10B GLY* 4.1 10.1 - - - +
13B ALA* 4.7 0.2 - - + -
14B THR* 3.6 25.2 - - + +
143B SER* 3.5 18.6 - - - +
145B SER 2.9 12.7 + - - +
146B VAL* 3.4 12.8 - - - +
147B GLN 3.1 0.6 - - - -
148B GLU* 1.4 77.4 - - - +
150B HIS* 1.3 64.0 + - - +
153B ALA* 3.1 26.0 + - - +
169B HIS* 3.3 3.9 + - - +
171B PHE* 4.5 7.0 - - + -
176B THR* 4.6 0.9 - - + -
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Residues in contact with HIS 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA* 3.8 27.2 - - + +
16B HIS* 3.9 7.1 + - - -
17B VAL* 3.5 30.4 - - + +
146B VAL 3.4 3.0 + - - -
147B GLN* 3.2 12.6 + - - +
149B ALA* 1.3 82.8 - - - +
151B ASP* 1.3 86.3 + - - +
153B ALA 3.4 0.2 + - - -
154B LEU* 3.3 21.5 + - + +
183B ILE* 4.4 4.0 - - + -
184B GLU 4.2 4.7 + - - -
185B VAL* 3.5 27.1 - - + -
186B LEU* 3.1 48.1 + - + +
191B MET* 4.2 1.2 - - - +
250B VAL* 6.0 0.4 - - + -
256B ARG* 4.6 1.6 - - - -
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Residues in contact with ASP 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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147B GLN 3.3 9.0 + - - +
148B GLU 3.2 4.4 + - - +
150B HIS* 1.3 107.5 + - - +
152B MET* 1.3 59.1 + - - +
154B LEU* 3.3 7.4 + - - +
155B VAL* 3.0 31.2 + - + +
250B VAL* 4.6 13.8 - - + +
254B THR* 4.8 1.7 - - - +
256B ARG* 2.7 38.4 + - - +
258B TYR* 2.6 43.4 + - + +
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Residues in contact with MET 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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141B LEU* 3.4 31.1 - - + +
142B ALA 3.8 16.2 - - - +
143B SER* 3.8 4.3 - - - -
148B GLU* 2.7 27.1 + - - +
151B ASP* 1.3 71.8 - - - +
153B ALA* 1.3 66.6 + - - +
154B LEU 3.1 0.2 - - - -
155B VAL* 4.2 7.2 - - - -
156B ALA* 2.8 26.5 + - - +
169B HIS* 3.7 20.2 - - + +
247B MET* 4.0 9.0 - - - -
258B TYR* 3.5 39.0 - - + -
303B ARG* 3.5 33.2 - - + +
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Residues in contact with ALA 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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14B THR* 3.9 10.1 - - - +
17B VAL* 3.8 19.5 - - + -
110B HIS* 3.8 12.6 - - - +
149B ALA 3.1 21.1 + - - +
150B HIS 3.6 4.5 - - - +
152B MET* 1.3 77.0 - - - +
154B LEU* 1.3 63.4 + - - +
156B ALA* 3.3 2.2 + - - +
157B HIS* 3.1 28.8 + - - -
169B HIS* 3.7 22.9 + - + -
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 3.4 16.6 - - + -
21B MET* 4.2 11.9 - - + -
150B HIS* 3.3 14.6 + - + +
151B ASP* 3.4 9.2 - - - +
152B MET 3.1 0.2 - - - -
153B ALA* 1.3 79.3 - - - +
155B VAL* 1.3 65.1 + - - +
157B HIS* 3.4 1.7 + - - +
158B LEU* 3.0 45.9 + - + +
186B LEU* 3.8 26.5 - - + -
191B MET* 4.0 31.6 - - + -
194B LEU* 4.1 7.2 - - + -
250B VAL* 3.8 26.0 - - + -
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 4.0 16.8 - - + -
151B ASP* 3.0 18.3 + - + +
152B MET* 3.7 9.2 - - - +
154B LEU* 1.3 75.1 - - - +
156B ALA* 1.3 56.5 + - - +
158B LEU* 3.2 7.3 + - - +
159B ALA* 2.8 35.1 + - + +
243B VAL* 4.1 32.8 - - + +
246B TYR* 4.1 18.3 - - + +
247B MET* 4.2 14.1 - - + +
250B VAL* 4.1 22.4 - - + -
258B TYR* 6.0 2.7 - - + -
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Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B VAL* 4.2 8.3 - - + -
141B LEU* 4.1 7.4 - - + -
152B MET 2.8 17.6 + - - +
153B ALA 3.7 4.3 - - - +
155B VAL* 1.3 76.3 - - - +
157B HIS* 1.4 57.0 + - - +
160B ALA* 2.8 32.9 + - - +
167B PHE* 3.8 36.5 - - + -
169B HIS* 4.1 17.5 - - + -
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Residues in contact with HIS 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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17B VAL* 4.4 1.6 - - + -
18B ALA* 3.6 11.5 - - - -
21B MET* 3.4 42.7 + - + +
22B SER* 3.4 25.1 - - - -
81B THR 5.2 2.0 - - - -
82B THR* 3.9 4.0 - - + -
108B VAL* 3.5 29.0 - - + +
110B HIS* 2.9 32.1 - + - -
153B ALA 3.1 26.9 + - - -
154B LEU 3.8 5.8 - - - +
156B ALA* 1.4 75.7 - - - +
158B LEU* 1.3 65.6 + - - +
160B ALA* 3.4 1.4 + - - +
161B ILE* 3.2 31.2 + - + +
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Residues in contact with LEU 158 (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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21B MET* 3.8 22.0 - - + -
154B LEU* 3.0 38.1 + - + +
155B VAL* 3.8 2.2 - - - +
157B HIS* 1.3 77.0 - - - +
159B ALA* 1.3 61.7 + - - +
161B ILE* 3.5 6.8 + - + +
162B GLU* 3.2 17.8 + - - +
191B MET 4.3 2.5 - - - +
194B LEU* 3.7 51.1 - - + +
195B VAL* 3.8 11.2 - - + +
196B ASN* 5.9 0.5 + - - +
246B TYR* 3.6 38.4 + - + -
250B VAL* 4.3 8.3 - - + -
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Residues in contact with ALA 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 VAL* 2.8 22.2 + - + +
156B ALA 4.0 0.2 - - - +
158B LEU* 1.3 71.7 - - - +
160B ALA* 1.3 55.2 + - - +
163B SER* 2.7 42.7 + - - +
167B PHE* 3.7 24.0 - - + -
242B ILE* 3.8 24.4 - - + +
243B VAL* 3.9 12.3 - - + -
246B TYR* 3.9 5.4 - - + -
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Residues in contact with ALA 160 (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 PRO* 3.3 23.1 - - - +
107B GLY 4.0 4.0 - - - +
108B VAL* 3.8 21.1 - - + -
156B ALA 2.8 22.0 + - - +
157B HIS 3.9 1.3 - - - +
159B ALA* 1.3 73.9 - - - +
161B ILE* 1.3 58.5 + - + +
164B ASN* 2.9 26.3 + - - -
165B VAL 3.6 21.1 - - - +
167B PHE* 3.8 7.0 - - + -
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Residues in contact with ILE 161 (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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21B MET* 4.3 18.8 - - + +
80B LEU* 3.9 38.8 - - + -
106B PRO* 3.9 10.0 - - + +
157B HIS* 3.2 23.2 + - + +
158B LEU* 3.7 7.9 - - + +
160B ALA* 1.3 79.2 - - + +
162B GLU* 1.3 62.8 + - - +
164B ASN* 3.9 12.8 + - - +
195B VAL* 4.6 15.7 - - + -
196B ASN* 4.2 12.3 - - + +
199B ALA* 3.6 11.7 - - + +
200B LEU* 4.1 33.7 - - + +
203B PHE* 5.7 3.3 - - + +
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Residues in contact with GLU 162 (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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158B LEU 3.2 14.5 + - - +
159B ALA 4.1 1.3 - - - +
161B ILE* 1.3 82.2 - - - +
163B SER* 1.3 60.8 + - - +
164B ASN* 3.8 4.5 + - - +
196B ASN* 3.0 30.0 + - + +
199B ALA* 3.9 12.2 - - + +
242B ILE* 3.8 22.4 - - + +
245B GLU* 3.1 23.9 - - - +
246B TYR* 2.5 36.5 + - + +
249B LYS* 5.1 1.6 + - - -
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Residues in contact with SER 163 (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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159B ALA 2.7 28.4 + - - -
162B GLU* 1.3 74.5 - - - +
164B ASN* 1.3 64.9 + - - +
165B VAL* 3.0 27.7 + - - +
167B PHE* 3.9 5.2 - - - -
235B TYR* 3.6 20.9 - - - +
239B VAL* 4.3 20.2 - - - -
242B ILE* 3.5 23.6 - - - -
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Residues in contact with ASN 164 (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 LEU* 3.0 47.2 + - + +
105B LEU 3.5 2.4 + - - -
106B PRO* 3.9 17.3 - - - +
160B ALA 2.9 17.5 + - - -
161B ILE 4.2 9.7 + - - +
162B GLU 3.5 4.4 - - - +
163B SER* 1.3 73.2 - - - +
165B VAL* 1.3 60.2 + - - +
199B ALA* 5.6 3.3 + - - +
203B PHE* 4.4 10.7 - - - +
206B LYS* 3.0 33.6 - - - +
235B TYR* 4.7 12.6 - - + -
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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
------------------------------------------------------------
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