Contacts of the helix formed by residues 248 - 268 (chain A) in PDB entry 1LU9
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 GLY 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A ASP* 3.5 3.4 - - - -
232A ILE* 4.2 9.2 - - - +
233A ASP 3.8 11.9 - - - -
234A ALA* 3.1 17.0 - - - -
236A ASP* 2.7 17.5 + - - +
247A PHE* 1.3 73.9 - - - +
249A ALA* 1.3 65.6 + - - -
251A GLY* 3.1 2.8 + - - -
252A ILE* 3.0 24.3 + - - +
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Residues in contact with ALA 249 (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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220A ASP* 3.0 21.7 + - - +
221A TYR* 3.5 10.8 - - - +
222A ASN 3.4 8.4 + - - +
223A ALA* 3.4 39.0 - - + +
234A ALA* 3.3 4.0 + - - +
248A GLY* 1.3 71.2 - - - -
250A LEU* 1.3 60.4 + - - +
252A ILE* 3.8 4.7 - - - +
253A GLY* 2.8 23.9 + - - -
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Residues in contact with LEU 250 (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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223A ALA* 4.1 19.7 - - + +
234A ALA* 2.8 35.2 + - + +
235A THR* 4.1 19.7 - - + -
249A ALA* 1.3 72.3 - - - +
251A GLY* 1.3 61.7 - - - +
253A GLY* 3.7 2.9 - - - +
254A GLY* 2.9 27.2 + - - -
88C PHE* 6.2 5.4 - - + -
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Residues in contact with GLY 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 4.2 2.2 - - - +
234A ALA 3.2 6.3 + - - -
235A THR* 4.0 9.7 - - - +
236A ASP 3.8 14.4 - - - -
237A LYS* 3.9 30.9 + - - +
247A PHE* 5.8 0.4 - - - -
248A GLY 3.1 7.2 + - - -
250A LEU* 1.3 78.2 - - - +
252A ILE* 1.3 61.9 + - - +
254A GLY* 3.6 5.9 + - - -
255A LEU 3.9 5.9 + - - -
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Residues in contact with ILE 252 (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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102A THR* 3.9 14.6 - - + +
105A ALA* 3.7 2.8 - - + +
106A GLY* 3.6 34.8 - - - +
109A LEU* 3.9 11.9 - - + -
219A ALA* 4.3 7.6 - - + -
220A ASP 3.7 24.0 - - - +
221A TYR* 4.0 23.1 - - + -
247A PHE* 4.0 24.5 - - + +
248A GLY 3.0 17.5 + - - +
249A ALA* 3.8 4.5 - - - +
251A GLY* 1.3 76.3 - - - +
253A GLY* 1.3 60.2 + - - +
255A LEU* 3.2 7.3 + - - +
256A LYS* 2.9 23.0 + - + +
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Residues in contact with GLY 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A THR* 6.4 0.9 - - - -
249A ALA 2.8 19.8 + - - -
250A LEU* 3.2 5.5 + - - -
252A ILE* 1.3 75.3 - - - +
254A GLY* 1.3 62.9 + - - +
256A LYS* 3.5 11.6 - - - +
257A LEU* 3.0 32.0 + - - +
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Residues in contact with GLY 254 (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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237A LYS* 5.5 2.0 - - - -
250A LEU 2.9 15.3 + - - -
251A GLY* 3.6 3.3 + - - -
252A ILE 3.2 0.6 - - - -
253A GLY* 1.3 75.6 - - - +
255A LEU* 1.3 63.4 + - - +
257A LEU* 3.5 8.5 + - - +
258A LYS* 3.4 30.4 + - - +
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Residues in contact with LEU 255 (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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105A ALA* 3.7 20.4 - - + +
108A ALA* 5.0 1.3 - - + -
109A LEU* 3.6 36.6 - - + -
237A LYS* 4.9 10.8 - - - +
251A GLY 3.9 5.3 + - - +
252A ILE 3.2 8.6 + - - +
254A GLY* 1.3 74.6 - - - +
256A LYS* 1.3 55.3 + - - +
258A LYS* 3.1 9.6 + - + +
259A LEU* 2.8 39.8 + - + +
284A ALA* 4.7 5.2 - - + +
287A MET* 4.1 38.1 - - + +
288A ALA* 4.0 19.1 - - + +
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Residues in contact with LYS 256 (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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18A PHE* 4.0 24.7 - - - -
95A ASP* 3.7 3.0 + - - -
98A GLY* 4.1 7.4 - - - +
101A THR* 2.7 28.5 + - - -
102A THR* 3.4 38.4 - - + +
105A ALA* 3.7 15.8 - - + +
252A ILE* 2.9 14.2 + - + +
253A GLY* 3.5 15.5 - - - +
255A LEU* 1.3 76.1 - - - +
257A LEU* 1.3 67.0 + - + +
259A LEU* 3.7 2.8 - - - +
260A HIS* 2.8 56.0 + - - +
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Residues in contact with LEU 257 (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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18A PHE* 4.0 26.5 - - + -
22A VAL* 4.1 19.1 - - + -
253A GLY 3.0 20.2 + - - +
254A GLY* 3.9 7.4 - - - +
255A LEU 3.2 0.2 - - - -
256A LYS* 1.3 83.0 - - + +
258A LYS* 1.3 63.1 - - - +
260A HIS* 3.9 2.2 - - - +
261A ARG* 3.1 47.6 + - - +
51C TYR 3.9 17.3 - - - +
52C THR 4.1 18.6 - - - +
53C ARG 6.2 0.2 - - - -
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Residues in contact with LYS 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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254A GLY* 3.4 17.0 + - - +
255A LEU* 3.1 13.9 + - + +
257A LEU* 1.3 78.0 - - + +
259A LEU* 1.3 58.0 + - - +
261A ARG* 3.7 21.8 - - - +
262A ALA* 3.0 29.5 + - - +
287A MET* 3.7 18.7 - - + +
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Residues in contact with LEU 259 (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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101A THR* 3.7 24.0 - - + +
104A ALA* 4.0 2.2 - - + -
105A ALA* 4.2 4.9 - - - +
255A LEU* 2.8 24.6 + - + +
256A LYS* 3.7 3.4 - - - +
258A LYS* 1.3 69.6 - - - +
260A HIS* 1.3 68.1 + - - +
262A ALA* 3.1 1.9 + - - -
263A CYS* 2.9 39.4 + - - -
280A ILE* 3.7 26.0 - - + +
283A LEU* 3.8 13.5 - - + -
284A ALA* 3.5 45.3 - - + +
287A MET* 4.0 11.8 - - - +
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Residues in contact with HIS 260 (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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18A PHE* 4.6 1.6 - + - -
19A ASP* 3.8 26.3 + - - -
22A VAL* 3.4 36.7 - - + +
64A PHE* 3.7 18.1 - + - -
93A MET* 3.9 13.0 - - + -
95A ASP* 3.8 9.6 + - - -
98A GLY 6.1 0.2 - - - -
101A THR* 3.8 18.2 - - + -
256A LYS* 2.8 46.2 + - - +
257A LEU* 3.9 2.4 - - - +
259A LEU* 1.3 73.7 - - - +
261A ARG* 1.3 62.8 + - - +
263A CYS* 3.2 3.8 + - - +
264A ILE* 3.2 27.1 + - + +
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Residues in contact with ARG 261 (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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22A VAL* 3.7 26.6 - - + +
25A ASP* 3.9 29.4 + - + +
26A GLY* 3.5 19.5 - - - +
257A LEU* 3.1 36.4 + - - +
258A LYS* 3.7 26.5 - - - +
260A HIS* 1.3 75.1 - - - +
262A ALA* 1.3 63.7 + - - +
264A ILE* 3.1 15.0 + - - +
265A ALA* 3.1 10.8 + - - +
52C THR 3.2 25.7 + - - -
53C ARG* 4.8 4.6 - - - +
54C GLY 5.5 1.6 - - - +
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Residues in contact with ALA 262 (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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258A LYS 3.0 17.9 + - - +
259A LEU 3.1 4.2 + - - +
261A ARG* 1.3 77.0 - - - +
263A CYS* 1.3 62.0 + - - +
265A ALA* 3.3 9.1 + - - +
266A LYS* 3.0 27.8 + - - +
283A LEU* 4.1 9.9 - - + -
287A MET* 3.9 23.8 - - + -
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Residues in contact with CYS 263 (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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93A MET* 3.5 23.6 - - + -
259A LEU* 2.9 40.1 + - - -
260A HIS 3.5 7.9 - - - +
262A ALA* 1.3 74.5 - - - +
264A ILE* 1.3 66.0 + - - +
266A LYS* 3.1 15.7 + - - +
267A LEU* 3.1 18.5 + - - +
275A PHE* 4.0 10.7 - - + -
280A ILE* 3.9 28.5 - - - -
283A LEU* 4.0 12.6 - - - -
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Residues in contact with ILE 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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6A LEU* 4.1 20.4 - - + -
19A ASP 5.8 0.4 - - - +
22A VAL 4.5 2.0 - - - +
23A GLY* 3.6 34.3 - - - +
26A GLY* 3.9 10.1 - - - +
28A ALA 4.4 0.7 - - - +
64A PHE* 4.0 29.4 - - + -
93A MET* 4.1 7.6 - - - -
260A HIS* 3.2 23.3 + - + +
261A ARG 3.1 7.8 + - - +
263A CYS* 1.3 77.7 - - - +
265A ALA* 1.3 63.9 + - - +
267A LEU* 3.0 27.7 + - + +
268A PHE* 3.5 23.0 - - + -
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Residues in contact with ALA 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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26A GLY* 3.4 18.3 + - - +
261A ARG 3.1 7.4 + - - +
262A ALA* 3.4 12.8 - - - +
264A ILE* 1.3 80.8 - - - +
266A LYS* 1.3 62.6 - - + +
268A PHE* 3.1 18.3 + - - +
269A GLU* 3.8 18.7 + - - +
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Residues in contact with LYS 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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91A SER* 4.9 0.5 + - - -
262A ALA* 3.0 20.7 + - - +
263A CYS 3.1 8.2 + - - +
265A ALA* 1.3 76.6 - - - +
267A LEU* 1.3 56.5 + - - +
269A GLU* 2.8 52.7 + - - +
270A SER* 4.0 4.5 + - - -
275A PHE* 3.4 35.9 - - + -
283A LEU* 4.1 27.3 - - + +
286A GLU* 5.6 2.4 + - - -
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Residues in contact with LEU 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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6A LEU* 4.1 19.5 - - + -
59A GLN 3.7 4.7 - - - +
61A THR 4.8 0.2 - - - +
62A ALA* 3.7 17.0 - - + +
63A ILE 4.1 11.0 - - - +
64A PHE* 5.2 0.4 - - + -
91A SER* 3.2 20.1 + - - -
92A CYS 3.7 21.8 - - - +
93A MET* 3.8 21.3 - - + -
263A CYS 3.4 9.9 - - - +
264A ILE* 3.0 27.0 + - + +
266A LYS* 1.3 76.8 - - - +
268A PHE* 1.3 59.0 + - + +
269A GLU 3.3 0.4 - - - -
270A SER 3.2 17.3 - - - +
275A PHE* 3.7 28.7 - - + -
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Residues in contact with PHE 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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4A LYS* 3.7 41.7 - - + +
5A LEU 3.5 42.4 - - - -
6A LEU* 4.0 11.9 - - + -
27A GLY 5.0 1.1 - - - -
28A ALA* 4.0 20.9 - - + -
59A GLN* 3.2 38.2 + - - +
60A SER* 3.7 8.4 + - - -
61A THR 4.2 0.2 - - - -
62A ALA* 3.7 21.3 - - + -
264A ILE* 3.5 29.2 - - + -
265A ALA* 3.1 9.4 + - - +
266A LYS 2.9 1.4 + - - -
267A LEU* 1.3 77.8 - - + +
269A GLU* 1.3 62.1 + - - +
270A SER 3.5 1.8 - - - -
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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