Contacts of the helix formed by residues 305 - 324 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ASP* 4.9 13.0 - - - +
303B ASN* 3.4 5.2 + - - -
304B TYR* 1.3 81.7 - - - +
306B GLU* 1.3 66.4 + - - +
307B GLU* 3.7 7.6 + - - +
308B ASN* 2.8 45.9 + - - +
309B LEU* 2.9 16.8 + - - +
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B TYR* 3.7 22.9 + - - +
304B TYR* 5.5 2.6 - - - -
305B SER* 1.3 70.6 - - - +
307B GLU* 1.3 61.5 + - - +
310B LYS* 3.0 26.7 + - - +
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B SER* 3.0 8.8 - - - +
306B GLU* 1.3 78.7 - - - +
308B ASN* 1.3 61.1 + - - +
310B LYS* 3.3 5.2 + - - +
311B GLN* 2.9 31.6 + - - +
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Residues in contact with ASN 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B PHE* 4.1 13.1 - - + -
303B ASN* 2.8 33.2 - - - +
305B SER* 2.8 30.9 + - - +
307B GLU* 1.3 77.0 - - - +
309B LEU* 1.3 58.3 + - - +
311B GLN* 3.3 7.5 + - - +
312B ALA* 2.9 26.2 + - - +
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B VAL* 4.0 6.3 - - + -
284B TYR* 3.4 52.9 - - + -
288B THR* 3.6 9.2 - - + +
289B VAL* 5.1 4.0 - - + -
292B PHE* 3.5 43.7 - - + -
304B TYR* 3.3 39.0 - - + +
305B SER 2.9 19.5 + - - +
306B GLU 4.2 0.2 - - - +
308B ASN* 1.3 70.4 - - - +
310B LYS* 1.3 61.5 + - - +
312B ALA* 3.0 7.8 - - - +
313B ARG* 2.8 25.6 + - - +
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Residues in contact with LYS 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B TYR* 4.3 7.1 - - + -
306B GLU 3.0 20.9 + - - +
307B GLU* 3.6 5.4 - - - +
309B LEU* 1.3 74.8 - - - +
311B GLN* 1.3 66.6 + - - +
313B ARG* 3.4 8.4 + - - +
314B ALA* 3.0 22.9 + - - +
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Residues in contact with GLN 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLU 2.9 18.5 + - - +
308B ASN* 3.7 9.2 - - - +
310B LYS* 1.3 76.0 - - - +
312B ALA* 1.3 58.0 + - - +
314B ALA* 3.7 6.4 - - - +
315B ALA* 2.8 31.2 + - - +
318B ARG* 5.2 0.3 + - - -
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B THR* 3.8 18.6 - - + +
291B TYR* 3.9 28.7 - - + -
292B PHE* 4.2 10.1 - - + -
295B SER* 6.3 0.2 - - - -
308B ASN 2.9 13.6 + - - +
309B LEU* 3.0 15.3 - - - +
311B GLN* 1.3 75.0 - - - +
313B ARG* 1.3 66.5 + - - +
315B ALA* 3.1 4.2 + - - +
316B LEU* 2.9 23.8 + - - +
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Residues in contact with ARG 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B TYR* 5.7 3.8 - - + -
285B ASP* 2.9 32.3 + - - +
288B THR* 3.3 18.1 - - + +
309B LEU 2.8 14.8 + - - +
310B LYS* 3.6 11.2 - - - +
312B ALA* 1.3 71.6 - - - +
314B ALA* 1.3 63.4 + - - +
316B LEU* 3.2 5.4 + - - +
317B GLU* 3.0 48.0 + - - +
401B PHE* 3.2 53.3 + - - -
402B LEU* 4.2 9.5 - - - +
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Residues in contact with ALA 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LYS 3.0 17.0 + - - +
311B GLN* 3.7 7.9 - - - +
313B ARG* 1.3 75.2 - - - +
315B ALA* 1.3 57.6 + - - +
317B GLU* 2.6 47.6 + - - +
318B ARG* 3.2 19.5 + - - +
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TYR* 3.6 28.3 - - + +
311B GLN 2.8 21.0 + - - +
312B ALA 3.5 4.7 - - - +
314B ALA* 1.3 72.9 - - - +
316B LEU* 1.3 61.8 + - - +
317B GLU 3.2 0.9 + - - -
318B ARG* 3.3 33.3 + - - +
319B LEU* 3.5 2.8 + - - +
360B PHE* 3.3 25.8 - - + -
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLU* 3.6 33.0 - - + +
288B THR* 3.6 40.8 - - - +
291B TYR* 3.9 23.7 - - + -
312B ALA 2.9 11.7 + - - +
313B ARG 3.4 9.9 - - - +
315B ALA* 1.3 73.1 - - - +
317B GLU* 1.3 62.9 + - - +
319B LEU* 3.7 8.6 + - + +
320B TYR* 3.2 28.0 + - + -
393B LEU* 4.5 3.4 - - + -
394B LEU* 4.2 15.7 - - + -
401B PHE* 3.8 17.7 - - + -
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Residues in contact with GLU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ARG* 3.0 51.4 + - - +
314B ALA* 2.6 33.5 + - - +
316B LEU* 1.3 69.4 - - - +
318B ARG* 1.3 52.4 + - + +
320B TYR* 3.2 3.1 + - - +
321B THR* 2.7 44.4 + - - +
401B PHE* 4.2 10.8 - - + -
402B LEU* 6.4 0.7 - - - -
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Residues in contact with ARG 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B GLN 5.2 0.6 + - - -
314B ALA* 3.2 24.4 + - - +
315B ALA* 3.3 34.6 - - - +
317B GLU* 1.3 78.1 - - + +
319B LEU* 1.3 62.6 + - - +
321B THR* 3.3 6.9 + - - -
322B ALA* 3.1 24.1 + - - +
360B PHE* 3.8 23.5 - - + -
363B ALA* 5.0 1.3 - - - +
367B ASN* 5.1 1.4 + - - -
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TYR* 4.3 16.4 - - + -
315B ALA 3.5 2.6 + - - +
316B LEU* 3.9 18.2 - - + +
317B GLU 3.2 0.4 - - - -
318B ARG* 1.3 76.9 - - - +
320B TYR* 1.3 62.4 + - - +
322B ALA* 3.3 13.2 + - - +
323B LEU* 3.4 12.3 + - - +
359B LEU* 4.2 16.6 - - + +
360B PHE* 3.7 54.1 - - + +
363B ALA* 3.8 23.3 - - + +
384B LEU* 5.3 3.5 - - + +
393B LEU* 5.5 3.6 - - + -
394B LEU* 3.9 31.1 - - + +
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Residues in contact with TYR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B GLU* 2.7 37.5 + - - -
316B LEU* 3.2 21.1 + - + +
317B GLU* 3.9 2.5 - - - +
319B LEU* 1.3 79.1 - - - +
321B THR* 1.3 61.1 + - - +
323B LEU* 3.3 6.3 + - + +
324B ARG* 3.3 16.8 + - - +
394B LEU* 3.2 30.8 - - + -
396B GLN* 3.0 51.1 + - + +
398B PRO* 3.6 37.7 - - + +
401B PHE* 3.3 41.7 - + + -
402B LEU* 5.4 4.5 - - + +
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Residues in contact with THR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B GLU* 2.7 31.7 + - - +
318B ARG* 3.6 7.8 - - - -
320B TYR* 1.3 68.6 - - - +
322B ALA* 1.3 66.5 + - - +
323B LEU 3.0 2.8 + - - -
324B ARG* 3.2 21.5 + - + +
367B ASN* 4.4 3.5 - - - +
370B LYS* 4.0 6.6 + - - -
402B LEU* 5.9 3.1 - - - +
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B ARG 3.1 15.9 + - - +
319B LEU 3.3 6.3 + - - +
321B THR* 1.3 76.3 - - - +
323B LEU* 1.3 58.7 + - - +
326B THR* 4.3 0.2 + - - -
363B ALA* 3.6 26.9 - - + +
366B VAL* 3.4 18.6 - - + +
367B ASN* 3.2 35.4 - - - +
370B LYS* 3.2 17.2 + - - +
384B LEU* 5.6 2.0 - - + -
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Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU 3.4 9.0 + - - +
320B TYR* 3.3 14.9 + - + +
321B THR 3.0 1.0 - - - -
322B ALA* 1.3 79.6 - - - +
324B ARG* 1.3 63.6 + - - +
325B GLY 3.4 0.2 + - - -
326B THR* 3.1 30.0 + - + +
366B VAL* 5.2 1.3 - - - -
381B ALA* 5.4 5.2 - - + -
384B LEU* 5.9 5.6 - - + -
394B LEU* 6.1 5.6 - - + -
398B PRO* 3.6 19.1 - - + +
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Residues in contact with ARG 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B TYR 3.3 8.3 + - - +
321B THR* 3.2 18.3 + - + +
323B LEU* 1.3 75.6 - - - +
325B GLY* 1.3 59.8 + - - +
370B LYS* 3.3 25.8 + - - -
398B PRO* 3.8 16.6 - - + -
399B GLU 5.6 1.1 - - - +
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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