Contacts of the helix formed by residues 240 - 260 (chain A) in PDB entry 3L3N
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 LEU 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A LEU 3.5 10.2 + - - +
237A PHE 3.1 11.2 + - - +
239A GLU* 1.3 79.4 - - - +
241A GLN* 1.3 58.9 + - - +
242A PRO 3.5 1.1 - - - -
243A LEU* 3.5 11.5 + - + +
244A TYR* 3.0 29.3 + - + +
455A ILE* 3.5 33.7 - - + -
458A ILE* 4.2 24.2 - - + -
528A ILE* 3.5 32.3 - - + -
589A ALA* 4.1 9.4 - - + -
592A MET* 3.5 24.5 - - + -
593A LEU* 4.4 14.4 - - + -
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Residues in contact with GLN 241 (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 PHE* 3.5 39.0 + - + +
238A GLN* 3.3 31.3 + - - +
240A LEU* 1.3 74.5 - - - +
242A PRO* 1.3 76.6 - - + +
244A TYR* 4.4 18.6 - - - +
245A LEU* 2.8 55.5 + - + +
492A TYR 4.9 2.4 + - - -
616A TRP* 5.7 0.8 - - - -
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Residues in contact with PRO 242 (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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238A GLN 3.9 4.3 - - - +
239A GLU* 3.7 13.7 - - - +
241A GLN* 1.3 94.3 - - + +
243A LEU* 1.3 56.5 + - - +
245A LEU* 4.2 4.9 - - + +
246A ASN* 2.7 40.1 + - - +
593A LEU* 6.6 0.2 - - + -
600A LEU* 4.1 8.3 - - + -
604A ARG* 3.9 26.0 - - - +
614A LEU* 6.3 0.9 - - + -
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Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 3.5 15.0 + - + +
241A GLN 3.2 0.6 - - - -
242A PRO* 1.3 78.2 - - + +
244A TYR* 1.3 63.4 + - - +
246A ASN* 4.3 0.7 - - - +
247A LEU* 3.3 20.5 + - + +
455A ILE* 3.7 27.4 - - + +
593A LEU* 4.3 26.2 - - + +
596A PHE* 3.5 34.3 - - + +
599A LEU* 5.0 4.9 - - + -
600A LEU* 3.9 40.8 - - + +
603A LEU* 4.4 11.2 - - + -
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Residues in contact with TYR 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A PHE* 6.2 0.2 - + - -
240A LEU* 3.0 19.2 + - + +
241A GLN* 3.9 14.6 - - - +
243A LEU* 1.3 76.8 - - - +
245A LEU* 1.3 64.7 + - - +
247A LEU* 2.9 5.6 + - + +
248A HIS* 2.8 35.8 + + + +
283A TRP* 3.3 37.6 - + - -
455A ILE* 3.7 29.6 - - + +
456A ALA* 3.8 12.5 + - - -
458A ILE* 6.0 2.0 - - + -
459A PRO* 3.6 23.9 - - + +
492A TYR 3.7 17.0 - - - -
493A GLN* 2.6 35.2 + - - +
616A TRP* 4.2 10.5 - + - -
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Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLN* 2.8 53.7 + - + +
242A PRO* 4.2 4.7 - - + +
244A TYR* 1.3 73.2 - - + +
246A ASN* 1.3 57.5 + - - +
248A HIS* 3.6 6.3 + - - +
249A ALA* 3.0 29.3 + - - +
614A LEU* 3.8 28.1 - - + +
615A GLY* 4.1 14.5 + - - +
616A TRP* 3.7 34.3 - - + -
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Residues in contact with ASN 246 (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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242A PRO* 2.7 32.4 + - - +
243A LEU 4.3 1.6 - - - +
244A TYR 3.1 0.4 - - - -
245A LEU* 1.3 74.0 - - - +
247A LEU* 1.3 66.5 + - - +
250A TYR* 3.1 14.2 + - - +
600A LEU* 4.0 7.3 - - + +
603A LEU* 3.9 18.2 - - + +
604A ARG* 3.9 37.2 - - - +
607A ASN* 2.9 40.5 + - - +
614A LEU* 3.7 26.6 - - - +
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Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 3.3 13.5 + - + +
244A TYR* 2.9 9.7 + - + +
246A ASN* 1.3 77.6 - - - +
248A HIS* 1.3 57.9 + - - +
250A TYR* 3.2 2.5 + - + +
251A VAL* 2.9 42.7 + - + +
283A TRP* 4.2 21.5 - - + -
448A MET* 3.6 35.9 - - + -
451A ALA* 3.6 34.3 - - + +
452A LEU* 4.1 4.5 - - + -
455A ILE* 3.9 17.9 - - + -
456A ALA* 4.0 7.4 - - - +
603A LEU* 4.0 12.5 - - + +
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Residues in contact with HIS 248 (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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244A TYR* 2.8 31.4 + - + +
245A LEU* 3.6 9.7 + - - +
247A LEU* 1.3 77.4 - - - +
249A ALA* 1.3 58.8 + - - +
251A VAL 3.4 0.3 + - - -
252A ARG* 2.9 54.9 + - - +
268A GLY 4.1 3.4 - - - -
270A ILE* 3.4 32.2 - - + +
283A TRP* 4.1 11.8 - + - -
493A GLN 3.4 19.7 - - - -
494A GLY 3.0 22.8 + - - -
495A LEU* 5.2 0.4 - - + -
615A GLY 4.7 1.6 + - - -
616A TRP* 3.4 30.6 - + + -
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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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245A LEU 3.0 18.5 + - - +
246A ASN 3.9 2.9 - - - +
248A HIS* 1.3 76.7 + - - +
250A TYR* 1.3 62.8 + - - +
252A ARG* 3.5 28.3 + - - +
253A ARG* 3.2 22.7 + - - +
607A ASN* 4.0 6.7 - - - +
612A GLU* 4.1 17.4 - - + +
614A LEU* 3.8 21.5 - - + -
615A GLY 5.4 0.2 - - - +
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Residues in contact with TYR 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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246A ASN 3.1 18.4 + - - +
247A LEU* 3.2 2.7 + - + +
249A ALA* 1.3 77.8 - - - +
251A VAL* 1.3 68.2 + - + +
253A ARG* 3.3 10.9 + - + +
254A ALA* 3.2 20.4 + - + +
257A ARG* 4.9 13.4 + - - -
290A VAL* 2.7 39.9 + - + -
291A VAL 3.7 2.9 + - - -
292A PRO* 3.6 16.5 - - - +
448A MET* 3.5 28.3 - - + -
602A TRP* 3.5 23.9 - + - -
603A LEU* 3.6 13.2 - - + -
606A GLU* 3.7 30.3 - - + -
607A ASN* 3.6 10.7 + - - +
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Residues in contact with VAL 251 (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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247A LEU* 2.9 25.8 + - + +
248A HIS 3.9 2.7 - - - +
250A TYR* 1.3 77.1 - - + +
252A ARG* 1.3 67.0 + - - +
254A ALA* 3.2 7.5 + - - +
255A LEU* 2.9 34.5 + - + +
270A ILE* 4.7 1.8 - - + -
275A LEU* 4.2 4.0 - - + -
283A TRP* 3.8 22.7 - - + -
286A ILE* 3.9 26.5 - - + -
290A VAL* 4.3 8.7 - - + -
452A LEU* 3.8 27.4 - - + -
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Residues in contact with ARG 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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248A HIS* 2.9 32.3 + - - +
249A ALA* 3.7 24.0 + - - +
251A VAL* 1.3 77.8 - - - +
253A ARG* 1.3 56.1 + - - +
255A LEU* 3.4 5.7 + - - +
256A HIS* 3.0 27.3 + - - +
264A ILE* 3.5 19.6 - - + +
265A ASN 3.3 17.9 - - - -
266A LEU* 3.0 27.5 + - + +
267A GLU 3.8 0.8 - - - -
268A GLY 2.9 27.5 + - - +
269A PRO 5.3 0.7 - - - -
270A ILE* 4.0 18.8 - - + +
612A GLU* 5.1 3.0 + - - -
613A LYS 3.0 27.7 + - - +
615A GLY 2.8 22.8 + - - +
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Residues in contact with ARG 253 (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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249A ALA 3.2 10.5 + - - +
250A TYR* 3.5 12.1 - - + +
251A VAL 3.2 0.2 - - - -
252A ARG* 1.3 76.0 - - - +
254A ALA* 1.3 63.2 + - - +
256A HIS* 3.1 14.9 + - - +
257A ARG* 3.0 42.1 + - - +
266A LEU* 3.4 42.4 - - - +
610A HIS* 3.6 31.2 + - + +
611A GLY 5.2 1.2 + - - -
612A GLU* 2.7 47.0 + - - +
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Residues in contact with ALA 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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250A TYR* 3.2 13.8 + - + +
251A VAL 3.2 7.6 + - - +
253A ARG* 1.3 75.8 - - - +
255A LEU* 1.3 58.1 + - - +
257A ARG* 3.3 25.9 + - - +
258A HIS* 3.1 27.4 + - - +
289A LEU* 3.4 27.5 - - + +
290A VAL* 3.6 20.9 - - + -
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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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251A VAL* 2.9 34.3 + - + +
252A ARG* 3.7 6.1 - - - +
254A ALA* 1.3 74.8 - - + +
256A HIS* 1.3 60.4 + - - +
258A HIS* 4.5 0.7 - - - +
259A TYR* 2.8 63.0 + - + +
264A ILE* 3.8 14.6 - - + +
270A ILE* 3.5 32.1 - - + -
274A LEU* 3.8 28.3 - - + +
275A LEU* 4.5 2.7 - - + -
286A ILE* 4.2 6.7 - - + -
289A LEU* 4.0 15.7 - - + -
290A VAL* 5.9 0.2 - - + -
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Residues in contact with HIS 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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252A ARG 3.0 14.8 + - - +
253A ARG* 3.2 19.0 + - - +
255A LEU* 1.3 77.4 - - - +
257A ARG* 1.3 65.5 + - - +
260A GLY* 3.1 23.4 + - - -
261A ALA* 3.3 40.4 + - + +
264A ILE* 3.6 28.7 - - + +
266A LEU* 3.7 36.9 - - + +
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Residues in contact with ARG 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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250A TYR* 4.9 12.7 + - - -
253A ARG* 3.0 29.6 + - - +
254A ALA* 3.3 36.0 + - - +
255A LEU 3.3 0.2 - - - -
256A HIS* 1.3 82.4 + - - +
258A HIS* 1.3 60.1 + - + +
260A GLY* 4.6 1.7 + - - -
289A LEU 3.5 22.4 + - - -
290A VAL* 4.9 4.4 - - - +
291A VAL 5.7 1.6 + - - -
606A GLU* 5.8 1.8 + - - -
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Residues in contact with HIS 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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173A ARG* 3.3 34.0 + - + +
254A ALA 3.1 13.4 + - - +
255A LEU 4.1 1.3 - - - +
257A ARG* 1.3 83.0 - - - +
259A TYR* 1.3 92.5 + + + +
260A GLY 3.6 0.4 + - - -
289A LEU* 3.4 34.3 - - + +
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Residues in contact with TYR 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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173A ARG* 3.3 43.7 - - - -
175A TYR* 3.8 35.7 - + + -
178A LEU* 3.3 19.1 - - - +
255A LEU* 2.8 49.0 + - + +
258A HIS* 1.3 91.9 - + - +
260A GLY* 1.3 56.9 + - - +
263A HIS* 2.9 32.0 - - + -
264A ILE* 4.8 4.5 - - + -
274A LEU* 3.8 30.0 + - + -
286A ILE* 6.0 0.5 - - - +
289A LEU* 4.1 5.4 - - + +
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Residues in contact with GLY 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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255A LEU 4.0 0.2 + - - -
256A HIS 3.1 18.3 + - - +
257A ARG 4.6 1.5 + - - -
258A HIS 3.6 1.8 - - - -
259A TYR* 1.3 79.8 - - - +
261A ALA* 1.3 62.8 + - - -
262A GLN* 2.9 8.5 - - - -
263A HIS* 2.9 14.4 + - - +
264A ILE* 3.4 12.5 + - - +
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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