Contacts of the helix formed by residues 245 - 262 (chain A) in PDB entry 1L2L
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 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A LEU* 4.2 8.7 - - + -
241A THR 3.0 16.6 + - - +
242A GLN* 2.9 34.9 + - - -
244A ASN* 1.3 78.8 + - - +
246A GLY* 1.3 79.9 + - - +
248A PRO* 3.5 6.7 - - - -
249A ILE* 3.1 28.5 + - + +
277A VAL* 4.7 17.1 - - + +
278A VAL* 3.9 15.0 - - + +
281A GLU* 2.6 41.5 + - - +
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Residues in contact with GLY 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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243A GLU 5.1 1.4 + - - -
244A ASN* 3.3 3.6 - - - +
245A HIS* 1.3 94.9 - - - +
247A LYS* 1.3 63.3 + - - +
249A ILE* 4.0 1.6 - - - +
250A LYS* 3.3 18.5 + - - +
281A GLU* 5.7 0.7 - - - -
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Residues in contact with LYS 247 (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 ASN 4.5 0.4 + - - -
246A GLY* 1.3 72.5 - - - +
248A PRO* 1.3 72.8 - - + +
250A LYS* 3.2 29.8 + - + +
251A LEU* 3.0 37.7 + - + +
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Residues in contact with PRO 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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211A ILE 3.6 23.3 - - - +
212A LEU* 3.8 23.3 - - + +
240A LEU* 3.9 9.6 - - + -
244A ASN 3.0 26.0 - - - +
245A HIS* 3.2 16.2 - - - +
247A LYS* 1.3 94.3 - - + +
249A ILE* 1.3 55.4 + - - +
251A LEU* 3.0 13.7 + - + +
252A VAL* 2.8 34.2 + - - +
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Residues in contact with ILE 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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237A LEU* 4.4 17.3 - - + -
240A LEU* 3.8 20.4 - - + -
245A HIS* 3.1 23.6 + - + +
246A GLY 4.0 1.3 - - - +
248A PRO* 1.3 76.3 - - - +
250A LYS* 1.3 58.9 + - - +
252A VAL* 3.3 3.9 + - + +
253A ARG* 2.8 47.8 + - - +
278A VAL* 5.2 5.8 - - + -
281A GLU* 3.0 44.0 - - + +
282A ILE* 5.8 5.2 - - + -
285A LEU* 4.5 21.0 - - + +
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Residues in contact with LYS 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 GLY 3.3 10.7 + - - +
247A LYS* 3.2 31.4 + - + +
249A ILE* 1.3 79.4 - - - +
251A LEU* 1.3 64.2 + - + +
253A ARG* 3.4 10.0 + - - +
254A GLU* 3.1 43.7 + - + +
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Residues in contact with LEU 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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212A LEU 5.6 0.4 - - - +
214A VAL* 4.0 28.5 - - + +
219A ILE* 4.1 39.7 - - + -
247A LYS* 3.0 29.7 + - + +
248A PRO* 3.0 14.4 + - + +
250A LYS* 1.3 80.5 - - + +
252A VAL* 1.3 61.5 + - + +
254A GLU* 3.0 26.0 + - - +
255A HIS* 2.9 35.1 + - + +
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Residues in contact with VAL 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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32A TYR* 3.7 38.1 - - + +
212A LEU* 4.0 7.6 - - + -
234A ILE* 4.6 12.8 - - + -
237A LEU* 4.0 20.2 - - + -
248A PRO 2.8 21.4 + - - +
249A ILE* 3.7 6.5 - - - +
251A LEU* 1.3 75.3 - - + +
253A ARG* 1.3 57.5 + - - +
255A HIS* 3.2 2.9 + - + +
256A LEU* 2.9 46.8 + - + +
285A LEU* 4.0 15.0 - - + -
289A PHE* 5.0 0.9 - - + -
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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 ILE* 2.8 38.3 + - - +
250A LYS* 3.6 9.0 - - - +
251A LEU 3.2 0.2 - - - -
252A VAL* 1.3 76.2 - - - +
254A GLU* 1.3 61.6 + - - +
256A LEU* 3.4 5.1 + - - +
257A LYS* 3.1 54.8 + - + +
281A GLU* 4.5 16.6 + - - +
284A LYS* 6.1 1.8 - - - +
285A LEU* 3.8 27.6 - - + +
288A HIS* 4.5 19.6 - - - +
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Residues in contact with GLU 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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219A ILE* 5.6 2.3 - - - +
250A LYS* 3.1 50.2 + - + +
251A LEU* 3.0 26.5 + - - +
253A ARG* 1.3 79.2 - - + +
255A HIS* 1.3 68.2 + - - +
257A LYS* 3.6 12.1 + - + +
258A ILE* 3.3 29.3 + - + +
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Residues in contact with HIS 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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32A TYR* 2.7 33.2 - + - +
214A VAL* 4.3 15.4 - - - +
218A TRP* 3.2 29.1 + + - +
219A ILE* 4.5 7.4 - - - -
222A PHE* 3.3 47.8 - + + +
234A ILE* 6.1 2.0 - - + -
251A LEU* 2.9 26.1 + - + +
252A VAL* 3.6 6.3 - - + +
254A GLU* 1.3 80.9 - - + +
256A LEU* 1.3 60.1 + - + +
258A ILE* 3.2 5.6 + - + +
259A LEU* 2.8 34.6 + - + +
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Residues in contact with LEU 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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234A ILE* 4.6 6.7 - - + -
252A VAL* 2.9 25.8 + - + +
253A ARG* 3.7 4.9 - - - +
255A HIS* 1.3 77.4 - - + +
257A LYS* 1.3 52.9 + - - +
259A LEU* 3.1 10.9 + - + +
260A ASN* 2.7 36.9 + - - +
266A ALA* 3.9 27.8 - - + -
285A LEU* 3.9 18.8 - - + -
288A HIS* 3.8 35.7 - - + +
289A PHE* 3.4 41.3 - - + -
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Residues in contact with LYS 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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253A ARG* 3.1 40.3 + - - +
254A GLU* 3.7 10.4 - - + +
256A LEU* 1.3 76.3 - - - +
258A ILE* 1.3 58.7 + - + +
260A ASN* 3.2 7.5 + - - +
261A ASP* 2.9 39.2 + - - +
288A HIS* 4.6 24.7 - - + -
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Residues in contact with ILE 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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222A PHE* 3.9 35.9 - - + -
223A GLU* 4.0 29.2 - - + +
254A GLU* 3.3 18.1 + - + +
255A HIS* 3.2 9.5 + - - +
257A LYS* 1.3 78.2 - - + +
259A LEU* 1.3 62.6 + - - +
261A ASP* 3.1 11.3 + - - +
262A LEU* 3.1 40.9 + - + +
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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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29A LEU* 4.1 9.2 - - + -
222A PHE* 3.9 14.8 - - + -
226A ALA* 4.0 25.6 - - + -
229A SER* 4.8 0.2 - - - +
232A ALA* 3.6 22.4 - - + -
234A ILE* 5.0 7.6 - - + -
255A HIS* 2.8 18.7 + - + +
256A LEU* 3.4 15.9 - - + +
258A ILE* 1.3 75.8 - - - +
260A ASN* 1.3 61.9 + - - +
262A LEU* 3.1 8.4 + - - -
264A ILE* 2.9 60.7 + - + +
266A ALA* 3.8 17.3 - - + -
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Residues in contact with ASN 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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256A LEU 2.7 19.5 + - - +
257A LYS* 3.6 7.6 - - - +
259A LEU* 1.3 73.8 - - - +
261A ASP* 1.3 68.1 + - - +
263A GLY* 3.2 13.3 + - - +
264A ILE 4.2 5.6 + - - +
288A HIS* 5.3 6.9 + - - +
290A TYR* 6.3 0.4 - - - -
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Residues in contact with ASP 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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257A LYS* 2.9 26.2 + - - +
258A ILE* 3.1 10.0 + - + +
260A ASN* 1.3 83.9 - - - +
262A LEU* 1.3 63.3 + - + +
263A GLY 3.4 0.4 + - - -
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Residues in contact with LEU 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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223A GLU* 4.2 10.8 - - + +
226A ALA* 3.8 28.7 - - + -
227A LYS* 3.8 39.0 - - + -
258A ILE* 3.1 27.6 + - + +
259A LEU 3.6 7.0 - - - +
260A ASN 3.1 0.4 - - - -
261A ASP* 1.3 81.4 - - + +
263A GLY* 1.3 61.8 + - - +
264A ILE* 3.2 21.9 + - + +
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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