Contacts of the helix formed by residues 257 - 280 (chain A) in PDB entry 1A9R
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 HIS 257 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PRO* 4.5 15.2 - - + +
200A PHE* 4.0 17.7 - - + -
256A ASN* 1.3 73.0 - - - +
258A GLU* 1.3 62.3 + - - +
260A VAL* 3.0 40.1 - - + +
261A LEU* 3.2 38.2 + - + +
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Residues in contact with GLU 258 (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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256A ASN* 3.4 13.2 - - + +
257A HIS* 1.3 78.5 - - - +
259A GLU* 1.3 64.9 + - - +
261A LEU* 3.0 19.6 + - - +
262A GLU* 3.0 39.1 + - + +
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Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A VAL* 5.5 2.6 - - - +
242A THR 4.2 3.9 - - - +
243A ASN* 3.6 25.2 - - + +
244A LYS 5.4 0.7 + - - +
254A LYS 4.0 1.6 - - - +
255A ALA* 3.4 11.3 - - - +
256A ASN* 2.7 60.5 + - - +
258A GLU* 1.3 74.7 - - - +
260A VAL* 1.3 68.3 + - + +
262A GLU* 3.1 11.9 + - - +
263A ALA* 3.0 23.6 + - - +
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ALA* 5.4 0.4 - - + -
200A PHE* 4.8 8.3 - - + -
242A THR* 3.5 30.5 - - + +
243A ASN* 3.4 29.4 - - - +
255A ALA* 6.2 0.2 - - + -
256A ASN 3.6 14.4 - - - +
257A HIS* 3.0 42.1 + - + +
259A GLU* 1.3 75.0 - - + +
261A LEU* 1.3 59.8 + - + +
263A ALA 3.4 0.5 + - - -
264A GLY* 3.0 23.7 + - - -
290A HPA 4.1 12.3 - - + +
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Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PRO* 4.8 13.9 - - + -
257A HIS* 3.2 49.1 - - + +
258A GLU* 3.0 12.4 + - - +
260A VAL* 1.3 81.7 - - + +
262A GLU* 1.3 65.8 + - - +
264A GLY* 3.1 3.5 + - - -
265A LYS* 2.9 33.5 + - - +
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Residues in contact with GLU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLU* 3.0 43.6 + - + +
259A GLU* 3.1 9.8 + - - +
261A LEU* 1.3 80.3 - - - +
263A ALA* 1.3 57.5 + - - +
265A LYS* 3.0 26.3 + - - +
266A GLN* 2.8 38.2 + - - +
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Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A VAL* 4.0 13.9 - - + -
127A GLY* 5.3 2.6 - - - +
240A LEU* 4.3 4.0 - - + -
241A ILE 4.8 1.1 - - - +
242A THR* 3.6 35.7 - - + +
259A GLU 3.0 7.2 + - - +
260A VAL 3.6 8.3 - - - +
262A GLU* 1.3 75.1 - - - +
264A GLY* 1.3 65.1 - - - +
266A GLN* 3.1 16.9 - - - +
267A ALA* 3.0 26.3 + - - +
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Residues in contact with GLY 264 (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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33A SER* 4.4 5.2 - - - -
34A GLY* 3.1 32.5 - - - -
240A LEU* 3.7 18.8 - - - +
242A THR* 5.0 0.2 - - - -
260A VAL 3.0 15.5 + - - -
261A LEU* 3.1 4.9 + - - -
263A ALA* 1.3 76.0 - - - +
265A LYS* 1.3 60.3 + - - +
267A ALA 4.2 0.2 - - - -
268A ALA* 3.3 11.4 + - - +
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Residues in contact with LYS 265 (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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261A LEU* 2.9 14.3 + - - +
262A GLU* 3.2 32.8 - - - +
264A GLY* 1.3 78.8 - - - +
266A GLN* 1.3 61.1 + - - +
267A ALA 3.5 0.3 + - - -
268A ALA* 3.6 6.7 - - - +
269A GLN* 3.5 17.5 + - - +
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Residues in contact with GLN 266 (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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126A VAL* 4.3 15.8 - - - +
127A GLY* 5.1 6.9 - - - -
262A GLU* 2.8 22.8 + - - +
263A ALA* 3.1 27.6 - - - +
265A LYS* 1.3 75.2 - - - +
267A ALA* 1.3 58.8 + - + +
268A ALA 3.5 0.2 - - - -
269A GLN* 3.4 20.0 + - - +
270A LYS* 5.1 1.4 + - - -
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Residues in contact with ALA 267 (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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127A GLY* 4.7 4.0 - - - +
240A LEU* 3.6 31.9 - - + -
263A ALA 3.0 12.8 + - - +
266A GLN* 1.3 77.2 - - + +
268A ALA* 1.3 66.1 + - - +
269A GLN 3.2 2.9 - - - -
270A LYS* 3.1 35.5 + - - +
271A LEU* 3.0 23.6 + - + +
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Residues in contact with ALA 268 (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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34A GLY* 3.3 27.8 - - - +
264A GLY 3.3 11.7 + - - +
265A LYS* 3.6 10.8 - - - +
266A GLN 3.5 1.4 - - - -
267A ALA* 1.3 75.1 - - - +
269A GLN* 1.3 75.2 + - - +
271A LEU* 3.2 1.3 + - - -
272A GLU* 3.0 40.3 + - - +
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Residues in contact with GLN 269 (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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265A LYS 3.5 14.9 + - - +
266A GLN* 3.4 23.1 + - - +
267A ALA 3.1 0.4 + - - -
268A ALA* 1.3 80.9 - - - +
270A LYS* 1.3 61.0 + - + +
272A GLU* 3.8 6.9 + - - +
273A GLN* 3.3 30.6 + - - +
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Residues in contact with LYS 270 (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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127A GLY* 3.4 28.5 + - - -
129A ILE* 4.1 18.6 - - + +
178A TRP* 4.3 16.6 - - + -
181A MET* 4.0 4.4 - - + +
183A GLU* 4.1 26.9 - - - +
266A GLN 5.1 0.6 + - - -
267A ALA* 3.1 28.9 + - - +
269A GLN* 1.3 77.9 - - + +
271A LEU* 1.3 67.4 + - - +
273A GLN* 3.3 16.9 - - + +
274A PHE* 3.0 26.7 + - - +
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Residues in contact with LEU 271 (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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33A SER* 3.6 24.2 - - - +
34A GLY* 3.7 22.7 - - - +
35A LEU* 4.0 13.0 - - + +
129A ILE* 3.6 26.0 - - + -
238A PHE* 3.5 31.9 - - + -
240A LEU* 3.8 21.5 - - + -
267A ALA* 3.0 22.0 + - + +
268A ALA* 3.6 4.0 - - - +
270A LYS* 1.3 77.6 - - - +
272A GLU* 1.3 58.7 + - - +
274A PHE* 3.3 6.0 + - + +
275A VAL* 3.0 33.8 + - - +
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Residues in contact with GLU 272 (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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34A GLY 3.4 21.0 - - - +
35A LEU* 4.1 6.1 - - + -
37A GLY* 3.8 27.1 - - - +
38A LEU* 3.8 29.9 - - + +
41A LYS* 4.1 19.1 - - + +
268A ALA* 3.0 29.5 + - - +
269A GLN* 4.0 5.2 - - - +
271A LEU* 1.3 77.0 - - - +
273A GLN* 1.3 57.5 + - - +
275A VAL 3.4 1.0 + - - -
276A SER* 2.7 33.6 + - - -
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Residues in contact with GLN 273 (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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41A LYS* 5.5 3.6 - - - +
181A MET* 3.3 25.5 - - + +
183A GLU* 5.2 2.8 + - - +
269A GLN* 3.3 23.2 + - - +
270A LYS* 3.3 24.2 - - - +
272A GLU* 1.3 78.3 - - - +
274A PHE* 1.3 56.2 + - - +
276A SER* 3.6 7.4 - - - -
277A LEU* 2.9 41.3 + - + +
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Residues in contact with PHE 274 (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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129A ILE* 4.5 22.0 - - + -
131A LEU* 4.6 4.7 - - + -
174A ALA* 3.6 39.7 - - + -
177A THR* 4.2 9.6 - - + -
178A TRP* 4.0 27.1 - + + -
181A MET* 3.7 24.9 - - + -
187A LEU* 4.2 9.9 - - + -
238A PHE* 4.4 26.7 - + - -
270A LYS 3.0 20.7 + - - +
271A LEU* 3.4 4.7 - - - +
273A GLN* 1.3 77.3 - - - +
275A VAL* 1.3 63.1 + - - +
277A LEU* 3.2 3.2 + - - +
278A LEU* 3.0 36.0 + - + +
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Residues in contact with VAL 275 (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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29A VAL* 5.0 8.1 - - + -
35A LEU* 3.8 17.9 - - + -
38A LEU* 3.7 24.9 - - + -
73A LEU* 4.4 2.0 - - + -
112A VAL* 5.1 5.4 - - + -
114A THR* 5.1 0.4 - - + -
238A PHE* 3.4 35.9 - - + -
271A LEU 3.0 18.4 + - - +
272A GLU 3.9 3.8 - - - +
274A PHE* 1.3 74.7 - - - +
276A SER* 1.3 61.8 + - - +
278A LEU* 3.3 10.5 + - + +
279A MET* 3.2 40.8 + - + +
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Residues in contact with SER 276 (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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38A LEU* 4.0 2.6 - - - +
41A LYS* 3.5 23.4 - - - -
73A LEU* 3.6 25.7 - - - +
74A ASN* 2.8 28.7 + - - +
272A GLU 2.7 23.9 + - - -
273A GLN* 3.6 8.5 - - - -
275A VAL* 1.3 77.5 - - - +
277A LEU* 1.3 63.5 + - - +
279A MET* 3.2 12.7 + - - +
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Residues in contact with LEU 277 (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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74A ASN* 4.1 8.1 - - - +
177A THR* 3.5 22.4 - - + +
180A GLN* 5.9 2.2 - - + -
181A MET* 3.5 36.1 - - + -
273A GLN* 2.9 31.5 + - + +
274A PHE 3.2 1.5 + - - +
276A SER* 1.3 77.0 - - - +
278A LEU* 1.3 63.0 + - - +
279A MET 3.2 0.9 + - - -
280A ALA* 3.3 19.8 + - - +
281A SER* 4.0 5.5 + - - -
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Residues in contact with LEU 278 (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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112A VAL* 6.3 0.2 - - + -
170A MET* 4.3 16.6 - - + -
173A LYS* 4.2 5.2 - - + -
174A ALA* 3.8 28.7 - - + +
177A THR* 4.0 12.1 - - - +
236A PHE* 3.5 35.0 - - + -
238A PHE* 4.8 1.6 - - + -
274A PHE* 3.0 40.1 + - + +
275A VAL* 3.6 13.7 - - + +
276A SER 3.3 0.4 - - - -
277A LEU* 1.3 74.3 - - - +
279A MET* 1.3 67.7 + - + +
281A SER* 2.9 18.0 + - - +
282A ILE* 3.2 18.1 + - + +
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Residues in contact with MET 279 (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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27A VAL* 4.1 17.9 - - + -
29A VAL* 4.4 9.4 - - + -
73A LEU* 3.7 40.6 - - + +
74A ASN* 4.2 3.4 - - + +
76A ARG* 2.8 53.3 + - + +
78A CYS* 5.0 5.6 - - - -
112A VAL* 4.6 5.6 - - + -
275A VAL* 3.2 36.7 + - + +
276A SER 3.3 10.5 - - - +
277A LEU 3.2 0.6 - - - -
278A LEU* 1.3 79.0 - - + +
280A ALA* 1.3 58.9 + - - +
281A SER 3.3 0.9 + - - -
282A ILE* 3.4 29.5 + - + +
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASN* 3.9 19.8 - - - +
76A ARG* 3.5 13.8 + - - +
277A LEU 3.3 12.4 + - - +
278A LEU 3.1 0.6 - - - -
279A MET* 1.3 79.3 - - - +
281A SER* 1.3 60.8 + - - +
282A ILE 4.5 0.3 - - - +
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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
------------------------------------------------------------
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