Contacts of the helix formed by residues 305 - 324 (chain A) in PDB entry 1LI5
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 SER 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A VAL* 6.1 0.2 - - - -
263A ASP* 5.3 4.0 - - - -
303A ASN* 3.6 12.4 + - - -
304A TYR* 1.3 89.5 - - - +
306A GLU* 1.3 66.2 + - - +
307A GLU* 3.6 8.2 + - - +
308A ASN* 3.2 28.8 + - - +
309A LEU* 3.0 26.7 + - - +
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Residues in contact with GLU 306 (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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284A TYR* 3.7 21.8 + - - +
304A TYR* 5.0 3.4 - - - -
305A SER* 1.3 72.9 - - - +
307A GLU* 1.3 57.1 + - - +
309A LEU* 3.3 3.1 + - - +
310A LYS* 2.8 30.8 + - - +
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A SER* 3.2 9.1 + - - +
306A GLU* 1.3 77.6 - - - +
308A ASN* 1.3 58.6 + - - +
310A LYS* 3.0 8.9 + - - +
311A GLN* 2.8 43.6 + - + +
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Residues in contact with ASN 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A PHE* 4.0 21.5 - - + -
303A ASN* 2.9 28.4 + - - +
305A SER* 3.2 18.7 + - - +
307A GLU* 1.3 82.0 - - - +
309A LEU* 1.3 53.5 + - - +
311A GLN* 3.3 13.1 + - - +
312A ALA* 2.7 34.5 + - - +
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Residues in contact with LEU 309 (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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280A VAL* 4.7 0.4 - - + -
284A TYR* 3.7 43.1 - - + -
288A THR* 3.5 14.2 - - + +
289A VAL* 4.5 16.6 - - + -
292A PHE* 3.4 52.3 - - + -
304A TYR* 3.8 26.2 - - + -
305A SER 3.0 19.1 + - - +
306A GLU 3.7 4.0 - - - +
308A ASN* 1.3 74.5 - - - +
310A LYS* 1.3 64.6 + - - +
312A ALA* 4.0 2.5 - - - -
313A ARG* 3.1 18.5 + - - +
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Residues in contact with LYS 310 (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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284A TYR* 4.7 6.2 - - + -
306A GLU 2.8 15.0 + - - +
307A GLU* 3.0 11.6 + - - +
309A LEU* 1.3 73.6 - - - +
311A GLN* 1.3 67.1 + - - +
313A ARG* 3.2 8.1 + - - +
314A ALA* 3.0 27.9 + - - +
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Residues in contact with GLN 311 (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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307A GLU* 2.8 27.2 + - + +
308A ASN* 3.5 15.3 - - - +
310A LYS* 1.3 79.2 - - - +
312A ALA* 1.3 56.8 + - - +
314A ALA* 3.0 10.1 + - - +
315A ALA* 2.7 36.0 + - - +
318A ARG* 5.4 4.7 + - - -
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Residues in contact with ALA 312 (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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288A THR* 3.7 25.8 - - + +
291A TYR* 3.7 26.9 - - + -
292A PHE* 3.8 14.8 - - + -
308A ASN 2.7 21.6 + - - +
309A LEU 3.6 6.7 - - - +
311A GLN* 1.3 72.6 - - - +
313A ARG* 1.3 61.7 + - - +
315A ALA* 3.4 2.4 + - - +
316A LEU* 3.1 23.9 + - - +
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Residues in contact with ARG 313 (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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284A TYR* 5.6 4.0 - - + -
285A ASP* 2.8 25.0 + - - +
288A THR* 3.5 21.3 - - + +
309A LEU 3.1 14.1 + - - +
310A LYS* 3.4 11.0 - - - +
311A GLN 3.1 0.2 - - - -
312A ALA* 1.3 77.5 - - - +
314A ALA* 1.3 58.2 + - - +
316A LEU* 3.4 2.5 + - - +
317A GLU* 2.5 56.4 + - - +
401A PHE* 3.2 49.8 + - - -
402A LEU* 4.3 6.5 - - - +
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Residues in contact with ALA 314 (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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310A LYS 3.0 13.6 + - - +
311A GLN* 3.6 14.4 - - - +
313A ARG* 1.3 74.1 - - - +
315A ALA* 1.3 66.3 + - - +
317A GLU* 3.2 15.5 + - - +
318A ARG* 3.1 42.4 + - - +
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Residues in contact with ALA 315 (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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291A TYR* 3.5 35.9 - - + +
311A GLN 2.7 21.0 + - - +
312A ALA 3.6 0.2 - - - +
314A ALA* 1.3 74.3 - - - +
316A LEU* 1.3 62.8 + - - +
318A ARG* 3.2 22.7 + - - +
319A LEU* 3.3 10.5 + - - +
360A PHE* 3.3 25.3 - - + -
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Residues in contact with LEU 316 (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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287A GLU* 3.4 50.5 - - + +
288A THR* 3.7 11.0 - - - +
291A TYR* 3.8 26.0 - - + -
312A ALA 3.1 13.6 + - - +
313A ARG 3.7 4.5 - - - +
315A ALA* 1.3 76.3 - - - +
317A GLU* 1.3 58.7 + - - +
319A LEU* 3.1 9.2 + - + +
320A TYR* 2.9 38.6 + - + +
393A LEU* 4.4 3.6 - - + -
394A LEU* 3.9 25.8 - - + -
401A PHE* 3.8 21.1 - - + -
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Residues in contact with GLU 317 (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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313A ARG* 2.5 56.8 + - - +
314A ALA* 3.2 15.9 + - - +
316A LEU* 1.3 77.4 - - - +
318A ARG* 1.3 54.9 + - + +
321A THR* 2.6 39.6 + - - +
401A PHE* 4.0 7.8 - - + -
402A LEU* 3.7 23.0 - - + +
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Residues in contact with ARG 318 (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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311A GLN* 5.4 4.6 + - - -
314A ALA* 3.1 33.7 + - - +
315A ALA* 3.6 23.2 - - - +
316A LEU 3.2 0.4 - - - -
317A GLU* 1.3 76.1 - - + +
319A LEU* 1.3 63.8 + - - +
321A THR* 3.7 5.5 + - - -
322A ALA* 3.4 19.8 + - - +
360A PHE* 3.7 24.2 - - + -
363A ALA* 4.8 2.9 - - - +
367A ASN* 5.3 2.9 + - - -
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A TYR* 4.3 9.6 - - + -
315A ALA 3.3 10.5 + - - +
316A LEU* 3.1 20.3 + - + +
318A ARG* 1.3 75.8 - - - +
320A TYR* 1.3 65.5 + - - +
322A ALA* 3.2 14.0 + - - +
323A LEU* 3.3 16.9 + - - +
359A LEU* 3.9 32.3 - - + +
360A PHE* 4.0 28.3 - - + -
363A ALA* 3.8 25.4 - - + +
384A LEU* 5.1 1.9 - - + +
393A LEU* 5.5 1.8 - - + -
394A LEU* 3.8 34.5 - - + +
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Residues in contact with TYR 320 (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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287A GLU* 2.9 36.1 + - - -
316A LEU* 2.9 23.3 + - + +
317A GLU 4.2 0.9 - - - +
319A LEU* 1.3 74.6 - - - +
321A THR* 1.3 65.4 + - - +
323A LEU* 3.2 8.8 + - + +
324A ARG* 3.0 19.1 + - - +
394A LEU* 3.0 38.5 - - + -
396A GLN* 3.1 42.4 + - + +
398A PRO* 3.6 31.9 - - + +
401A PHE* 3.4 41.3 - + + -
402A LEU* 4.1 12.8 - - + -
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Residues in contact with THR 321 (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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317A GLU* 2.6 27.7 + - - +
318A ARG* 3.9 7.1 - - - -
319A LEU 3.2 0.2 - - - -
320A TYR* 1.3 77.1 - - - +
322A ALA* 1.3 64.1 + - - +
324A ARG* 3.2 19.3 + - + +
367A ASN* 4.5 5.1 - - - +
370A LYS* 4.0 5.9 + - - -
402A LEU* 3.9 20.3 - - + +
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Residues in contact with ALA 322 (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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318A ARG 3.4 10.5 + - - +
319A LEU 3.2 10.7 + - - +
320A TYR 3.2 0.2 - - - -
321A THR* 1.3 79.5 - - - +
323A LEU* 1.3 58.8 + - + +
363A ALA* 3.7 31.0 - - + +
366A VAL* 3.5 11.6 - - + +
367A ASN* 3.2 25.5 - - - +
370A LYS* 3.0 29.6 + - - -
384A LEU* 5.2 0.9 - - + -
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Residues in contact with LEU 323 (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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319A LEU 3.3 11.2 + - - +
320A TYR* 3.2 17.1 + - + +
322A ALA* 1.3 76.9 - - - +
324A ARG* 1.3 65.9 + - - +
325A GLY 3.2 0.5 + - - -
326A THR* 3.0 25.0 + - - +
366A VAL* 5.1 0.9 - - + -
381A ALA* 3.7 34.5 - - + +
384A LEU* 3.9 19.1 - - + -
385A ARG* 3.7 34.1 - - + +
394A LEU* 4.0 29.6 - - + +
396A GLN 5.9 0.2 - - - +
398A PRO* 3.9 17.3 - - + +
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Residues in contact with ARG 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TYR 3.0 11.2 + - - +
321A THR* 3.2 20.7 + - + +
323A LEU* 1.3 77.2 - - - +
325A GLY* 1.3 61.8 + - - +
370A LYS* 3.4 19.6 + - - +
398A PRO* 3.9 14.4 - - + -
399A GLU 6.0 0.2 - - - +
402A LEU* 4.7 7.9 - - + -
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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
------------------------------------------------------------
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