Contacts of the helix formed by residues 243 - 264 (chain B) in PDB entry 5LDH
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 LYS 243 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ARG* 5.4 13.7 - - - +
102B GLN* 6.2 1.3 - - - +
105B GLU* 4.5 17.3 + - - +
239B VAL 4.6 2.9 - - - +
240B ILE* 3.8 11.1 + - - +
241B LYS 3.4 19.4 + - - +
242B LEU* 1.3 80.8 - - - +
244B GLY* 1.3 54.7 + - - +
245B TYR* 2.8 6.8 - - - +
246B THR* 2.5 45.4 + - + +
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Residues in contact with GLY 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLN* 4.4 16.5 - - - +
101B ARG* 5.8 1.8 - - - -
243B LYS* 1.3 77.6 - - - +
245B TYR* 1.3 67.3 + - - +
246B THR* 3.1 4.5 - - - -
247B ASN* 2.6 44.0 + - - +
248B TRP* 3.3 1.2 + - - -
332B LNC 4.5 9.0 - - - -
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Residues in contact with TYR 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLY* 5.6 1.2 - - - -
58A LYS* 3.0 33.3 - - + +
61A GLY 3.2 19.1 - - - +
62A GLU* 1.5 58.5 - - + -
64A MET* 6.1 0.4 - - - -
65A ASP* 1.5 52.1 + - + +
31B GLN* 5.7 3.4 - - - -
239B VAL* 6.0 0.9 - - + -
242B LEU* 3.4 34.3 - - + +
243B LYS 2.5 4.9 + - - +
244B GLY* 1.3 83.5 - - - +
246B THR* 1.3 54.0 + - - +
248B TRP* 2.6 36.6 - + + -
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Residues in contact with THR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP* 2.6 10.6 - - - +
68A HIS* 6.4 0.2 - - - -
101B ARG* 6.1 2.2 - - - +
102B GLN* 4.5 3.4 - - - +
171B ARG* 4.7 1.8 + - - +
236B ALA 4.8 5.9 + - - -
239B VAL* 5.7 7.3 + - - +
242B LEU 5.4 1.3 + - - -
243B LYS* 2.5 17.7 + - + +
244B GLY* 5.3 0.4 - - - -
245B TYR 1.3 76.6 - - - +
247B ASN* 1.3 56.0 - - + +
249B ALA* 3.7 2.6 - - - +
250B ILE* 2.6 31.3 + - + +
332B LNC 2.5 68.3 + - + +
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Residues in contact with ASN 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP* 2.6 2.5 - - - -
31B GLN* 3.5 16.4 + - - +
32B VAL* 2.8 21.6 - - + +
35B ALA* 2.3 38.4 - - - +
244B GLY* 2.6 29.7 + - - +
246B THR* 1.3 78.2 - - - +
248B TRP* 1.3 83.3 + - - +
250B ILE* 2.3 34.2 - - + +
251B GLY* 2.5 3.8 + - - -
332B LNC 3.9 13.7 - - - +
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Residues in contact with TRP 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN* 6.0 1.1 - - - -
34A MET* 2.8 44.0 - - + -
35A ALA* 4.3 1.6 - - - -
38A ILE* 3.1 42.8 - - + -
62A GLU* 2.9 13.8 + - - -
65A ASP* 1.9 41.7 + - + -
66A LEU* 4.4 6.5 - - + +
247A ASN* 6.4 0.2 - - - -
248A TRP* 5.0 17.0 - + - -
35B ALA* 4.3 14.9 - - + +
244B GLY 3.3 3.5 + - - -
245B TYR* 2.6 57.8 - + + -
247B ASN* 1.3 91.8 - - - +
249B ALA* 1.3 53.4 + - - -
251B GLY* 3.7 0.3 - - - -
252B LEU* 2.8 34.7 + - + +
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Residues in contact with ALA 249 (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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65A ASP* 0.9 82.9 + - - +
68A HIS* 3.9 19.1 - - + +
69A GLY* 4.1 4.0 - - - +
72A PHE* 4.2 0.2 - - - -
167B LEU* 4.8 8.3 - - + -
171B ARG* 5.5 1.8 - - - +
246B THR* 3.7 2.5 - - - +
248B TRP* 1.3 60.3 - - - +
250B ILE* 1.3 57.6 + - - +
252B LEU* 2.9 9.7 + - - +
253B SER* 2.6 40.0 + - - +
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Residues in contact with ILE 250 (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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32B VAL* 3.5 19.7 - - + -
138B VAL* 4.2 4.9 - - + -
163B SER* 5.2 0.2 - - - +
167B LEU* 3.9 13.2 - - + +
246B THR* 2.6 19.6 + - + +
247B ASN* 2.3 38.4 - - - +
249B ALA* 1.3 74.5 - - - +
251B GLY* 1.3 88.5 + - - +
253B SER* 3.0 3.5 + - - -
254B VAL* 2.9 40.3 + - + -
332B LNC 3.0 59.2 + - + +
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Residues in contact with GLY 251 (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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35B ALA* 4.5 5.6 - - - -
36B CYS* 3.9 30.4 - - - -
39B SER* 4.9 1.3 - - - -
247B ASN 2.5 10.6 + - - -
248B TRP 3.7 0.7 - - - -
250B ILE* 1.3 85.0 - - - +
252B LEU* 1.3 54.0 + - - -
254B VAL* 2.9 7.1 + - - +
255B ALA* 2.6 37.1 + - - +
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 4.6 16.6 - - + -
65A ASP 5.0 2.7 - - - +
66A LEU* 5.3 7.6 - - + +
69A GLY* 3.6 24.2 - - - -
72A PHE* 3.6 22.2 - - + -
73A LEU* 5.3 11.0 - - + -
35B ALA* 5.4 2.4 + - + +
39B SER* 3.8 22.6 + - - +
43B LYS* 4.7 3.1 + - - +
248B TRP* 2.8 41.6 + - + +
249B ALA* 3.2 11.4 - - - +
251B GLY* 1.3 68.9 - - - +
253B SER* 1.3 56.6 + - - +
255B ALA* 2.7 25.1 + - - +
256B ASP* 2.8 12.3 + - - +
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Residues in contact with SER 253 (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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72A PHE* 2.6 35.4 - - - -
163B SER* 6.1 0.9 - - - -
166B ASN* 3.2 23.9 + - - +
167B LEU* 3.8 22.5 - - - +
170B ALA* 5.6 0.5 - - - +
249B ALA* 2.6 14.4 + - - +
250B ILE 3.1 9.2 - - - -
252B LEU* 1.3 71.0 - - - +
254B VAL* 1.3 58.8 + - - -
256B ASP* 2.9 8.8 + - - +
257B LEU* 2.8 27.8 + - - +
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Residues in contact with VAL 254 (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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36B CYS* 4.6 16.6 - - + -
95B VAL* 4.8 21.1 - - + -
136B ILE* 4.8 14.8 - - + -
138B VAL* 4.8 11.0 - - + -
163B SER* 4.7 11.9 - - - +
250B ILE* 2.9 39.2 + - + +
251B GLY* 2.9 10.1 + - - +
253B SER* 1.3 73.2 - - - +
255B ALA* 1.3 55.5 + - - +
257B LEU* 3.2 11.1 + - + +
258B ILE* 2.8 36.6 + - + +
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Residues in contact with ALA 255 (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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36B CYS* 5.4 2.5 - - - +
39B SER* 3.6 28.9 - - - +
40B ILE* 4.9 6.7 - - + +
43B LYS* 4.1 15.0 - - + +
251B GLY 2.6 14.7 + - - +
252B LEU 2.7 13.0 + - - +
254B VAL* 1.3 73.5 - - - +
256B ASP* 1.3 52.4 + - - +
258B ILE* 2.5 31.4 - - - +
259B GLU* 2.7 18.3 + - - +
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Residues in contact with ASP 256 (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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71A LEU* 5.9 0.3 - - - +
72A PHE* 3.5 41.7 - - + -
43B LYS* 4.1 9.4 - - - +
166B ASN* 5.0 2.4 - - - +
252B LEU 2.8 8.1 + - - +
253B SER 3.1 10.4 - - - +
255B ALA* 1.3 77.6 - - - +
257B LEU* 1.3 66.9 + - - +
259B GLU* 3.2 9.2 + - - +
260B SER* 2.7 34.7 + - - -
267B ARG* 4.6 5.7 + - - -
269B HIS* 3.0 34.4 + - - -
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Residues in contact with LEU 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ILE* 2.8 45.3 - - + -
161B ILE* 4.3 9.4 - - + -
163B SER* 5.2 9.0 - - - +
166B ASN* 5.0 7.0 - - - +
253B SER 2.8 11.4 + - - +
254B VAL* 3.4 12.8 - - + +
256B ASP* 1.3 84.9 + - - +
258B ILE* 1.3 50.3 + - - +
260B SER* 2.8 9.9 + - - +
261B MET* 2.5 35.4 + - + +
269B HIS* 4.9 7.4 - - + -
271B VAL* 4.2 21.1 - - + -
293B LEU* 3.7 34.5 - - + -
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Residues in contact with ILE 258 (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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24B ILE* 5.4 4.3 - - + -
40B ILE* 5.2 14.4 - - + -
45B LEU* 3.3 28.7 - - + -
93B ILE* 3.0 41.3 - - + -
136B ILE* 4.5 4.9 - - + -
254B VAL* 2.8 18.3 + - + +
255B ALA* 2.5 38.8 - - + +
257B LEU* 1.3 71.5 - - - +
259B GLU* 1.3 66.4 + - + +
261B MET* 3.0 1.7 + - - +
262B LEU* 2.4 57.0 + - + +
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Residues in contact with GLU 259 (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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43B LYS* 4.9 16.2 - - + -
45B LEU* 4.2 21.8 - - + -
255B ALA 2.7 16.0 + - - +
256B ASP* 3.3 8.4 - - - +
258B ILE* 1.3 86.4 - - + +
260B SER* 1.3 67.2 + - - +
262B LEU* 4.5 0.2 - - - -
263B LYS* 2.9 43.7 + - + +
265B LEU* 3.4 7.5 - - - +
267B ARG* 2.8 33.4 + - - -
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Residues in contact with SER 260 (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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256B ASP 2.7 17.2 + - - -
257B LEU* 2.8 15.1 + - - -
259B GLU* 1.3 84.6 + - - +
261B MET* 1.3 60.0 + - - -
264B ASN* 3.4 15.1 + - - -
265B LEU* 3.5 12.1 + - - +
267B ARG* 3.1 28.9 + - - +
269B HIS* 3.8 17.2 + - - -
293B LEU* 4.3 19.3 + - - +
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Residues in contact with MET 261 (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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92B LYS* 5.6 1.4 + - - -
93B ILE* 2.7 45.1 - - + -
134B ILE* 2.7 43.5 - - + +
135B ILE 5.3 0.4 - - - +
136B ILE* 4.3 15.3 - - + -
161B ILE* 4.4 11.9 - - + -
257B LEU* 2.5 18.2 + - + +
258B ILE* 3.7 1.8 - - - +
260B SER* 1.3 75.2 + - - +
262B LEU* 1.3 74.3 + - - +
263B LYS 3.3 0.2 + - - -
264B ASN* 3.3 16.1 + - - +
293B LEU* 4.2 24.0 - - + -
294B ASN 4.1 11.1 - - - +
295B ALA* 4.8 2.2 - - - -
296B ARG 5.0 0.2 - - - -
297B GLY* 4.3 18.2 - - - -
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Residues in contact with LEU 262 (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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22B ASN* 5.0 15.0 - - + +
23B LYS 5.8 1.8 - - - +
24B ILE* 5.8 5.2 - - + -
45B LEU* 4.3 19.1 - - + +
92B LYS* 4.4 30.7 + - + +
93B ILE* 4.4 17.3 - - + -
258B ILE* 2.4 52.9 + - + +
259B GLU 3.7 2.2 - - - +
261B MET* 1.3 74.5 - - - +
263B LYS* 1.3 78.8 + - + +
264B ASN* 3.3 7.8 - - - +
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Residues in contact with LYS 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B SER* 3.9 21.8 + - - -
45B LEU* 4.6 13.5 + - + +
259B GLU* 2.9 37.5 + - + +
262B LEU* 1.3 91.9 - - + +
264B ASN* 1.3 71.2 + - - +
265B LEU* 4.1 10.3 - - + -
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Residues in contact with ASN 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LYS* 4.5 2.9 + - - +
260B SER 3.4 3.7 + - - -
261B MET 3.3 8.3 + - - +
262B LEU 3.3 13.4 - - - +
263B LYS* 1.3 82.2 - - - +
265B LEU* 1.3 64.6 + - - +
266B SER* 3.3 7.8 + - - -
294B ASN* 4.1 6.3 - - + +
295B ALA* 2.7 56.7 + - - +
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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
------------------------------------------------------------
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