Contacts of the helix formed by residues 351 - 373 (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 ASN 351 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B HIS* 4.2 12.5 + - - +
345B ALA* 3.3 23.1 + - - +
346B MET* 4.1 3.3 - - - +
348B ASP* 3.3 27.1 + - + +
350B PHE* 1.3 70.7 - - - +
352B THR* 1.3 61.2 + - - +
353B PRO* 3.1 13.7 - - - +
354B GLU* 3.0 35.6 + - + +
355B ALA* 3.1 17.2 + - - +
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Residues in contact with THR 352 (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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49B VAL* 4.1 22.0 - - + -
294B MET* 2.7 38.2 + - + +
296B GLY 3.6 6.6 + - - -
297B HIS* 4.7 1.0 - - - -
298B TYR 5.0 1.2 + - - -
346B MET* 4.0 15.5 - - + -
350B PHE* 2.9 17.6 + - + +
351B ASN* 1.3 69.2 - - - +
353B PRO* 1.3 74.0 - - - +
355B ALA* 3.0 7.4 + - - +
356B TYR* 2.8 33.2 + - - -
391B LEU* 4.3 7.9 - - + -
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Residues in contact with PRO 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B MET 4.5 0.4 - - - +
295B SER 3.7 20.2 - - - +
296B GLY* 3.8 1.1 - - - -
297B HIS* 3.6 29.8 - - + +
351B ASN* 3.1 15.0 - - - +
352B THR* 1.3 97.3 - - - +
354B GLU* 1.3 60.1 + - - +
356B TYR* 3.1 25.6 - - + +
357B SER* 3.2 10.3 + - - -
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Residues in contact with GLU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ALA* 3.8 16.2 - - + -
351B ASN* 3.0 33.7 + - + +
353B PRO* 1.3 76.2 - - - +
355B ALA* 1.3 64.3 + - - +
357B SER* 3.0 34.4 + - - -
358B VAL* 3.3 14.9 + - + +
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Residues in contact with ALA 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B PHE* 3.9 20.0 - - + -
345B ALA* 3.7 10.0 - - + +
346B MET* 3.6 32.3 - - + -
351B ASN 3.1 6.8 + - - +
352B THR* 3.0 9.1 + - - +
354B GLU* 1.3 76.7 - - - +
356B TYR* 1.3 63.6 + - - +
358B VAL* 3.3 8.4 + - - +
359B LEU* 3.0 26.5 + - - +
391B LEU* 4.3 6.1 - - + -
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Residues in contact with TYR 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TYR* 2.7 75.4 + + - +
294B MET* 3.2 27.4 - - + +
295B SER* 3.8 20.2 - - - -
352B THR* 2.8 22.2 + - - -
353B PRO* 3.1 17.5 - - + +
355B ALA* 1.3 75.3 - - - +
357B SER* 1.3 64.0 + - - +
359B LEU* 3.1 10.7 + - + +
360B PHE* 3.0 33.3 + + + -
391B LEU* 3.9 25.8 - - + -
393B LEU* 4.2 8.5 - - + -
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Residues in contact with SER 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ARG* 5.2 4.9 - - - -
353B PRO 3.2 7.9 + - - -
354B GLU* 3.0 29.5 + - - -
356B TYR* 1.3 78.9 - - - +
358B VAL* 1.3 64.2 + - - +
360B PHE* 3.4 6.5 + - - +
361B ASP* 3.1 23.6 + - - +
364B ARG* 4.8 2.0 + - - +
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Residues in contact with VAL 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B PHE* 3.5 40.4 - - + +
341B ARG* 3.8 50.0 - - + +
342B PHE* 3.9 13.2 - - + +
345B ALA* 4.9 1.8 - - + -
354B GLU* 3.3 15.2 + - + +
355B ALA* 3.4 9.0 - - - +
356B TYR 3.2 0.4 - - - -
357B SER* 1.3 77.0 - - - +
359B LEU* 1.3 64.9 + - - +
361B ASP* 3.2 4.3 + - - +
362B MET* 2.9 21.2 + - + +
387B LEU* 5.3 2.7 - - + -
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Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 4.2 16.6 - - + +
342B PHE* 4.2 11.2 - - + -
355B ALA 3.0 17.2 + - - +
356B TYR* 3.1 14.8 + - + +
358B VAL* 1.3 76.9 - - + +
360B PHE* 1.3 58.7 + - + +
362B MET* 3.1 7.8 + - - +
363B ALA* 2.8 28.2 + - - +
384B LEU* 3.7 16.4 - - + +
387B LEU* 4.0 24.7 - - + -
388B SER* 3.7 29.4 - - - +
391B LEU* 3.8 27.8 - - + -
393B LEU* 4.9 8.3 - - + -
394B LEU* 5.7 0.4 - - + -
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Residues in contact with PHE 360 (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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291B TYR* 3.1 29.2 - + - -
315B ALA* 3.3 35.7 - - + -
318B ARG* 3.8 31.4 - - + -
319B LEU* 3.7 32.8 - - + -
356B TYR* 3.0 34.6 + + + +
357B SER* 3.9 4.9 - - - +
359B LEU* 1.3 76.5 - - + +
361B ASP* 1.3 57.6 + - - +
363B ALA* 3.0 4.1 + - + +
364B ARG* 2.8 53.2 + - - +
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Residues in contact with ASP 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B PHE* 3.3 11.6 - - - -
341B ARG* 2.6 33.6 + - - +
357B SER 3.1 16.2 + - - +
358B VAL 3.7 0.4 - - - +
360B PHE* 1.3 76.4 - - - +
362B MET* 1.3 60.9 + - - +
364B ARG* 3.2 30.0 + - - +
365B GLU* 3.3 19.6 + - - +
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Residues in contact with MET 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B GLY* 3.9 5.8 - - - +
338B PHE* 3.7 46.4 - - + -
358B VAL* 2.9 13.5 + - - +
359B LEU* 3.3 11.2 - - - +
361B ASP* 1.3 76.0 - - - +
363B ALA* 1.3 63.9 + - - +
365B GLU* 3.2 4.2 + - - +
366B VAL* 3.1 21.7 + - - +
380B MET* 3.8 19.1 - - + -
383B HIS* 3.6 36.3 - - + +
384B LEU* 3.7 34.5 - - + +
387B LEU* 3.8 13.0 - - + -
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Residues in contact with ALA 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ARG 5.0 1.1 - - - +
319B LEU* 3.8 24.7 - - + -
322B ALA* 3.6 24.9 - - + +
359B LEU 2.8 13.7 + - - +
360B PHE* 3.5 8.5 - - + +
362B MET* 1.3 74.3 - - - +
364B ARG* 1.3 66.2 + - - +
366B VAL* 3.0 14.0 + - - +
367B ASN* 3.1 10.9 + - - +
384B LEU* 3.7 17.2 - - + +
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Residues in contact with ARG 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B SER 4.8 1.8 + - - -
360B PHE* 2.8 30.1 + - - +
361B ASP* 3.2 48.4 + - - +
363B ALA* 1.3 75.9 - - - +
365B GLU* 1.3 63.1 + - - +
367B ASN* 3.2 21.1 + - - +
368B ARG* 3.3 12.5 + - - +
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Residues in contact with GLU 365 (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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338B PHE* 4.0 17.3 - - + -
361B ASP 3.3 9.8 + - - +
362B MET 3.2 10.0 + - - +
363B ALA 3.1 0.6 - - - -
364B ARG* 1.3 77.1 - - - +
366B VAL* 1.3 65.5 + - - +
368B ARG* 3.4 10.0 + - - +
369B LEU* 3.1 46.5 + - + +
380B MET* 4.1 26.3 - - + +
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Residues in contact with VAL 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ALA* 3.4 25.6 - - + +
323B LEU* 5.2 0.2 - - - -
326B THR* 4.6 0.9 - - - +
362B MET 3.1 14.3 + - - +
363B ALA* 3.0 9.9 + - - +
365B GLU* 1.3 77.9 - - - +
367B ASN* 1.3 59.1 + - - +
369B LEU* 3.3 7.7 + - - +
370B LYS* 2.8 35.3 + - + +
377B ALA* 4.1 6.7 - - + +
380B MET* 3.6 24.2 - - + +
381B ALA* 3.9 32.8 - - + +
384B LEU* 4.2 13.7 - - + -
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Residues in contact with ASN 367 (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 5.1 1.6 + - - -
321B THR* 4.4 4.6 - - - +
322B ALA* 3.2 40.0 - - - +
363B ALA* 3.1 13.7 + - - +
364B ARG* 3.2 11.5 + - - +
366B VAL* 1.3 77.4 - - - +
368B ARG* 1.3 61.8 + - - +
370B LYS* 3.1 34.5 + - - +
371B ALA* 3.6 4.7 + - - +
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Residues in contact with ARG 368 (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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364B ARG 3.3 9.4 + - - +
365B GLU* 3.9 16.2 - - - +
366B VAL 3.3 0.4 - - - -
367B ASN* 1.3 77.6 - - - +
369B LEU* 1.3 62.0 + - - +
370B LYS 3.3 0.2 + - - -
371B ALA* 3.3 15.0 + - - +
372B GLU* 3.3 13.0 + - - +
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Residues in contact with LEU 369 (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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365B GLU* 3.1 40.6 + - - +
366B VAL 3.7 4.5 - - - +
368B ARG* 1.3 76.0 - - - +
370B LYS* 1.3 61.5 + - - +
372B GLU* 4.4 7.2 - - + +
373B ASP* 2.7 39.3 + - + +
376B ALA* 3.9 28.0 - - + +
377B ALA* 3.7 13.2 - - - +
380B MET* 3.9 38.6 - - + -
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Residues in contact with LYS 370 (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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321B THR 4.0 4.2 + - - -
322B ALA 3.2 26.0 + - - +
324B ARG 3.3 24.6 + - - -
325B GLY* 5.2 2.2 - - - -
326B THR* 4.6 6.7 - - - +
366B VAL* 2.8 30.6 + - + +
367B ASN* 3.1 27.2 + - - +
369B LEU* 1.3 78.6 - - - +
371B ALA* 1.3 61.6 + - - +
372B GLU 3.5 0.3 + - - -
373B ASP 4.3 1.6 + - - -
374B MET* 4.1 36.3 + - + +
377B ALA* 3.8 9.2 - - + +
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Residues in contact with ALA 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ASN 3.6 4.4 + - - +
368B ARG* 3.3 10.0 + - - +
369B LEU 3.2 0.4 - - - -
370B LYS* 1.3 81.2 - - - +
372B GLU* 1.3 58.2 + - + +
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Residues in contact with GLU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ARG 3.3 11.1 + - - +
369B LEU* 3.2 9.9 + - + +
370B LYS 4.6 0.4 - - - -
371B ALA* 1.3 81.7 - - + +
373B ASP* 1.3 64.2 + - + +
374B MET 4.3 0.2 - - - -
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Residues in contact with ASP 373 (chain B).
Click here for Legend to table.
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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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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