Contacts of the helix formed by residues 275 - 286 (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 ASP 275 (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 3.6 20.0 - - - +
241A THR* 3.5 8.8 - - + +
242A GLN* 2.9 63.1 + - - +
273A THR* 3.4 3.5 - - - +
274A PRO* 1.3 80.1 - - + +
276A GLU* 1.3 56.7 + - - +
277A VAL 2.9 11.1 + - - -
278A VAL* 3.2 8.7 + - + +
279A ARG* 3.0 27.2 + - - +
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Residues in contact with GLU 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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242A GLN* 5.1 2.3 - - - +
274A PRO 3.0 6.2 + - - +
275A ASP* 1.3 71.6 + - - +
277A VAL* 1.3 65.3 + - + +
279A ARG* 3.5 34.1 + - - +
280A LEU* 3.2 18.2 + - - +
305A VAL* 3.6 22.7 - - + +
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Residues in contact with VAL 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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242A GLN* 3.4 41.5 - - + +
245A HIS* 4.7 17.3 - - + +
275A ASP* 2.9 2.2 + - - -
276A GLU* 1.3 76.2 - - + +
278A VAL* 1.3 67.9 + - - +
280A LEU* 3.4 6.9 + - - +
281A GLU* 3.2 20.4 + - + +
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Residues in contact with VAL 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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237A LEU* 4.3 6.1 - - + +
240A LEU* 3.1 43.5 - - + +
241A THR 3.5 26.0 - - - +
242A GLN* 3.9 1.8 - - - +
245A HIS* 3.9 15.0 - - + -
249A ILE* 5.2 4.5 - - + -
273A THR* 4.0 13.2 - - + -
275A ASP* 3.2 13.1 + - - +
277A VAL* 1.3 75.5 - - - +
279A ARG* 1.3 61.8 + - - +
281A GLU* 3.0 13.6 + - - +
282A ILE* 2.8 31.9 + - + +
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Residues in contact with ARG 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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270A PHE* 4.3 13.7 - - + -
272A PHE* 3.7 15.6 - - - -
273A THR* 2.9 39.8 + - - +
274A PRO* 3.3 16.4 + - - +
275A ASP 3.0 13.5 + - - +
276A GLU* 3.6 29.6 + - - +
278A VAL* 1.3 76.2 - - - +
280A LEU* 1.3 60.7 + - - +
282A ILE* 2.7 26.2 - - - +
283A VAL* 3.0 13.7 + - - +
301A SER* 2.8 50.7 + - - +
302A VAL* 4.4 2.7 - - + +
304A SER* 5.2 4.2 + - - -
305A VAL* 3.9 16.7 - - + +
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Residues in contact with LEU 280 (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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276A GLU 3.2 14.8 + - - +
277A VAL* 3.8 6.3 - - - +
279A ARG* 1.3 78.9 - - - +
281A GLU* 1.3 62.8 + - - +
283A VAL* 3.1 19.2 + - + +
284A LYS* 3.1 39.9 + - - +
305A VAL* 3.9 36.5 - - + +
306A MET* 4.8 4.7 - - - -
336A GLU* 4.5 11.0 - - - +
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Residues in contact with GLU 281 (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 HIS* 2.6 42.8 + - + +
246A GLY* 5.7 0.5 - - - -
249A ILE* 3.0 40.9 - - + +
253A ARG* 4.5 12.1 + - - +
277A VAL* 3.2 11.8 + - + +
278A VAL* 3.0 11.0 + - - +
280A LEU* 1.3 81.7 - - - +
282A ILE* 1.3 56.9 + - - +
284A LYS* 3.3 9.2 + - - +
285A LEU* 3.0 25.1 + - - +
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Residues in contact with ILE 282 (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* 3.9 30.5 - - + -
238A HIS 5.7 0.2 - - - +
249A ILE* 5.8 4.7 - - + +
268A LEU* 3.3 34.8 - - + -
270A PHE* 3.1 35.2 - - + -
271A ALA 5.8 0.4 - - - +
273A THR* 4.6 8.3 - - + +
278A VAL* 2.8 23.9 + - + +
279A ARG* 2.7 31.0 - - - +
281A GLU* 1.3 70.5 - - - +
283A VAL* 1.3 65.2 + - - +
285A LEU* 3.1 20.7 + - + +
286A LEU* 3.2 13.5 + - - +
289A PHE* 6.0 0.2 - - + -
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Residues in contact with VAL 283 (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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270A PHE* 3.7 11.2 - - + -
279A ARG 3.0 21.5 + - - +
280A LEU* 3.1 13.7 + - + +
282A ILE* 1.3 77.5 - - - +
284A LYS* 1.3 58.1 + - - +
286A LEU* 3.0 32.1 - - - +
302A VAL* 3.5 28.3 - - + -
305A VAL* 4.3 8.3 - - + -
306A MET* 3.5 34.5 - - + -
333A LEU* 4.4 4.3 - - + -
336A GLU* 3.7 10.8 - - - +
337A THR* 3.2 16.1 - - + +
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Residues in contact with LYS 284 (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* 6.1 2.2 - - - +
280A LEU* 3.1 34.0 + - + +
281A GLU* 3.8 9.6 - - - +
282A ILE 3.3 0.2 - - - -
283A VAL* 1.3 72.5 - - - +
285A LEU* 1.3 62.1 + - - +
286A LEU 3.0 6.1 + - - -
287A LYS* 2.7 46.6 + - + +
288A HIS* 4.5 1.0 + - - -
336A GLU* 4.0 25.8 - - + +
337A THR* 4.7 1.8 - - - -
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Residues in contact with LEU 285 (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* 4.2 15.9 - - + -
249A ILE* 4.5 20.0 - - + -
252A VAL* 4.0 23.6 - - + -
253A ARG* 3.8 43.3 - - + +
256A LEU* 3.9 15.9 - - + -
281A GLU 3.0 14.2 + - - +
282A ILE* 3.1 16.6 + - + +
284A LYS* 1.3 76.8 - - - +
286A LEU* 1.3 55.9 + - - +
288A HIS* 2.9 31.6 + - - +
289A PHE* 3.7 16.8 - - + -
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Residues in contact with LEU 286 (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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268A LEU* 4.2 17.3 - - + -
270A PHE* 4.1 16.4 - - + -
282A ILE 3.2 10.2 + - - +
283A VAL* 3.0 27.7 + - - +
284A LYS 3.0 0.6 - - - -
285A LEU* 1.3 72.6 - - - +
287A LYS* 1.3 56.1 + - - +
288A HIS 2.9 6.1 - - - -
289A PHE* 2.9 43.6 + - + +
292A VAL* 3.8 33.2 - - + -
333A LEU* 3.9 29.4 - - + -
337A THR* 3.8 11.2 - - + +
339A VAL* 4.0 10.9 - - + +
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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