Contacts of the helix formed by residues 373 - 391 (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 ASP 373 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B LEU* 2.7 19.1 + - + +
371B ALA 3.9 0.2 - - - -
372B GLU* 1.3 78.7 - - + +
374B MET* 1.3 67.9 + - - +
375B ALA* 3.1 4.9 - - + +
376B ALA* 3.0 18.3 + - + +
377B ALA 3.0 17.2 + - - -
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Residues in contact with MET 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLY* 3.1 30.1 - - - +
326B THR* 4.8 1.3 - - - +
327B ASP 5.5 0.2 - - - +
369B LEU 3.8 0.8 + - - -
370B LYS* 4.1 39.9 + - + +
373B ASP* 1.3 72.0 - - - +
375B ALA* 1.3 50.1 - - - +
377B ALA* 3.9 8.3 - - + -
378B ASN* 2.6 64.3 + - - +
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Residues in contact with ALA 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B VAL* 4.9 2.1 - - - +
373B ASP* 3.1 6.2 - - + +
374B MET* 1.3 80.1 - - - +
376B ALA* 1.3 63.1 + - - +
378B ASN* 3.1 20.1 + - - +
379B ALA* 3.1 14.0 + - - +
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Residues in contact with ALA 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ALA 4.7 0.5 - - - +
369B LEU* 3.9 25.7 - - + +
373B ASP* 3.0 15.3 + - + +
375B ALA* 1.3 75.8 - - - +
377B ALA* 1.3 61.2 + - - +
379B ALA* 3.2 7.8 + - - +
380B MET* 2.8 31.4 + - - +
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Residues in contact with ALA 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B THR* 5.3 1.1 - - - +
366B VAL* 4.1 9.1 - - + +
369B LEU* 3.7 36.0 - - + +
370B LYS* 3.8 13.9 - - + +
373B ASP 3.0 9.4 + - - +
374B MET* 3.3 19.1 - - + +
376B ALA* 1.3 76.1 - - - +
378B ASN* 1.3 54.6 + - - +
380B MET* 3.3 1.6 + - - +
381B ALA* 2.7 39.1 + - - +
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Residues in contact with ASN 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B THR* 4.4 11.3 + - - +
327B ASP* 3.8 21.1 + - - +
330B VAL* 3.6 31.4 - - + +
374B MET* 2.6 62.0 + - - +
375B ALA* 3.1 12.4 + - - +
377B ALA* 1.3 73.2 - - - +
379B ALA* 1.3 56.9 + - - +
381B ALA* 3.3 2.3 + - - +
382B SER* 2.9 31.0 + - - -
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Residues in contact with ALA 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B VAL* 3.9 6.2 - - + +
331B ALA 3.6 14.4 - - - +
333B ALA* 3.1 45.7 + - + +
375B ALA 3.1 9.2 + - - +
376B ALA* 3.7 9.9 - - - +
378B ASN* 1.3 78.4 - - - +
380B MET* 1.3 57.7 + - - +
382B SER* 3.4 2.9 + - - -
383B HIS* 2.9 21.5 + - - +
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Residues in contact with MET 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ALA 3.4 4.0 + - - +
334B GLY* 3.1 28.9 - - - +
335B GLY* 3.7 21.5 - - - -
338B PHE* 4.1 13.2 - - + -
362B MET* 3.8 15.9 - - + +
365B GLU* 4.1 16.4 - - + +
366B VAL* 3.6 19.3 - - + -
369B LEU* 3.9 24.7 - - + -
376B ALA 2.8 18.0 + - - +
377B ALA 3.7 3.1 - - - +
379B ALA* 1.3 75.3 - - - +
381B ALA* 1.3 59.5 + - - +
383B HIS* 3.0 4.4 + - - +
384B LEU* 2.8 27.4 + - - +
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Residues in contact with ALA 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LEU* 5.4 6.3 - - + -
326B THR* 3.2 40.6 - - + +
366B VAL* 3.9 19.4 - - + +
377B ALA 2.7 19.0 + - - +
378B ASN 3.6 0.2 - - - +
380B MET* 1.3 72.5 - - - +
382B SER* 1.3 62.5 + - - +
384B LEU* 3.1 7.2 + - - +
385B ARG* 3.0 22.2 + - - +
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Residues in contact with SER 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B THR* 4.8 1.7 - - - +
327B ASP 5.3 3.8 - - - -
328B LYS* 5.2 6.3 + - - +
330B VAL* 2.9 27.9 + - - -
331B ALA 4.2 0.4 - - - -
332B PRO* 3.1 24.4 - - - +
378B ASN 2.9 16.4 + - - -
379B ALA 3.5 6.3 - - - -
381B ALA* 1.3 78.9 - - - +
383B HIS* 1.3 59.8 + - - +
385B ARG* 3.3 8.9 + - - +
386B LYS* 3.1 20.6 + - - +
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Residues in contact with HIS 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B PRO* 4.0 10.0 - - + +
333B ALA* 3.8 19.1 - - - +
334B GLY 4.1 0.4 - - - -
335B GLY 3.2 34.5 - - - +
336B GLU* 3.8 13.4 + - - +
339B GLU* 3.0 39.9 + - + -
362B MET* 3.6 15.0 - - + +
379B ALA 2.9 12.8 + - - +
380B MET* 3.0 12.1 + - - +
382B SER* 1.3 74.4 - - - +
384B LEU* 1.3 65.8 + - - +
386B LYS* 3.2 17.5 + - + +
387B LEU* 3.2 22.5 + - + +
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Residues in contact with LEU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 5.3 5.2 - - + +
322B ALA* 5.6 1.8 - - + -
323B LEU* 5.9 5.8 - - + -
359B LEU* 3.7 30.3 - - + +
362B MET* 3.7 21.5 - - + +
363B ALA* 3.7 35.4 - - + +
366B VAL* 4.2 11.0 - - + -
380B MET 2.8 11.7 + - - +
381B ALA* 3.1 10.5 + - - +
383B HIS* 1.3 78.3 - - - +
385B ARG* 1.3 53.8 + - - +
387B LEU* 3.4 1.4 + - - +
388B SER* 2.7 49.0 + - - +
394B LEU* 4.2 15.7 - - + -
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Residues in contact with ARG 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ALA 3.0 12.4 + - - +
382B SER* 3.6 12.1 - - - +
383B HIS 3.2 0.2 - - - -
384B LEU* 1.3 75.8 - - - +
386B LYS* 1.3 64.1 + - - +
388B SER* 4.0 5.5 - - - -
389B ALA* 2.9 27.5 + - - +
393B LEU 4.9 0.9 - - - +
394B LEU* 4.9 15.5 - - + +
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Residues in contact with LYS 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PHE* 3.9 24.4 - - + -
332B PRO* 4.7 17.0 - - + +
339B GLU* 2.8 31.0 + - - -
382B SER 3.1 13.0 + - - +
383B HIS* 3.2 26.7 + - + +
385B ARG* 1.3 79.9 - - - +
387B LEU* 1.3 62.6 + - + +
389B ALA* 3.7 9.1 + - - +
390B VAL* 3.5 15.6 - - - +
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Residues in contact with LEU 387 (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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56B PHE* 4.0 17.0 - - + -
338B PHE* 4.2 2.2 - - + -
339B GLU* 3.6 54.3 - - + +
342B PHE* 3.5 34.9 - - + -
358B VAL* 5.3 0.9 - - + -
359B LEU* 4.0 13.5 - - + -
362B MET* 3.8 27.8 - - + -
383B HIS* 3.2 13.3 + - - +
384B LEU 4.0 4.3 - - - +
386B LYS* 1.3 80.6 - - + +
388B SER* 1.3 64.4 + - - +
390B VAL* 3.2 22.1 + - - +
391B LEU 3.9 0.9 + - - -
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Residues in contact with SER 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU* 3.7 19.0 - - - +
384B LEU* 2.7 29.7 + - - +
385B ARG 4.0 2.2 - - - -
387B LEU* 1.3 73.8 - - - +
389B ALA* 1.3 60.9 + - - +
391B LEU* 2.8 21.5 + - - +
393B LEU* 2.9 34.9 + - - -
394B LEU* 3.1 30.7 - - - +
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Residues in contact with ALA 389 (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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52B ARG* 3.2 18.5 + - - -
385B ARG 2.9 19.5 + - - +
386B LYS* 3.8 8.5 - - - +
387B LEU 3.2 0.2 - - - -
388B SER* 1.3 76.2 - - - +
390B VAL* 1.3 56.9 + - + +
392B GLY* 2.8 17.4 + - - +
393B LEU 3.7 8.0 + - - +
395B GLU* 4.4 18.2 - - + +
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 4.7 3.3 - - - +
52B ARG* 3.2 29.8 - - - +
53B TYR* 4.0 37.9 - - + +
56B PHE* 3.5 43.3 - - + -
342B PHE* 4.1 11.0 - - + -
346B MET* 5.4 0.2 - - + -
386B LYS 3.5 15.9 - - - +
387B LEU* 3.3 10.5 - - - +
388B SER 3.1 0.4 - - - -
389B ALA* 1.3 77.3 - - + +
391B LEU* 1.3 62.3 + - + +
392B GLY 3.2 0.4 - - - -
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 3.9 15.7 - - + -
290B ARG* 2.9 28.0 + - - +
294B MET* 3.1 21.3 - - + +
342B PHE* 3.9 20.6 - - + -
346B MET* 3.7 32.8 - - + -
352B THR* 4.3 7.2 - - + -
355B ALA* 4.3 6.7 - - + -
356B TYR* 3.9 23.6 - - + -
359B LEU* 3.8 27.4 - - + -
387B LEU 4.5 0.7 - - - +
388B SER 2.8 9.6 + - - +
390B VAL* 1.3 78.6 - - + +
392B GLY* 1.3 60.2 + - - +
393B LEU* 4.1 5.2 - - + -
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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
------------------------------------------------------------
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