Contacts of the helix formed by residues 351 - 373 (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 ASN 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A HIS* 4.1 13.1 + - - +
345A ALA 3.2 24.8 + - - +
346A MET* 4.1 3.3 - - - +
348A ASP* 3.4 24.3 + - - +
349A ASP 3.3 1.5 - - - -
350A PHE* 1.3 73.1 - - - +
352A THR* 1.3 62.3 + - - +
353A PRO* 3.2 19.2 - - - +
354A GLU* 3.4 32.7 + - - +
355A ALA* 3.3 15.9 + - - +
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Residues in contact with THR 352 (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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49A VAL* 4.4 10.5 - - + -
294A MET* 2.9 38.9 + - + +
296A GLY 3.7 7.1 + - - -
297A HIS* 4.5 1.7 - - - -
298A TYR* 4.7 2.8 + - + +
346A MET* 4.1 20.6 - - + -
350A PHE* 2.8 18.0 + - + +
351A ASN* 1.3 72.2 - - - +
353A PRO* 1.4 68.9 - - - +
355A ALA* 2.8 20.2 + - - +
356A TYR* 2.9 19.4 + - - -
391A LEU* 4.2 11.7 - - + -
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Residues in contact with PRO 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A MET 4.2 0.8 - - - +
295A SER 3.4 25.6 - - - +
296A GLY* 3.8 0.9 - - - -
297A HIS* 3.7 23.6 - - + +
351A ASN* 3.2 18.2 - - - +
352A THR* 1.4 91.9 - - - +
354A GLU* 1.3 61.2 + - - +
356A TYR* 3.1 14.1 + - + +
357A SER* 3.1 19.9 + - - -
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Residues in contact with GLU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ARG 4.7 1.4 - - - +
344A GLU* 4.4 13.3 - - - +
345A ALA* 3.5 28.0 + - + +
348A ASP* 4.8 4.4 - - - +
351A ASN* 3.3 31.7 + - - +
352A THR 3.3 0.8 - - - -
353A PRO* 1.3 78.1 - - - +
355A ALA* 1.3 63.7 + - - +
357A SER* 3.0 20.7 + - - -
358A VAL* 3.1 16.7 + - + +
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Residues in contact with ALA 355 (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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342A PHE* 3.8 19.7 - - + -
345A ALA* 3.7 10.9 - - + +
346A MET* 3.7 29.4 - - - -
351A ASN 3.3 3.9 + - - +
352A THR* 2.8 13.1 + - - +
354A GLU* 1.3 79.9 - - - +
356A TYR* 1.3 60.4 + - - +
358A VAL* 3.0 10.3 + - - +
359A LEU* 3.0 25.3 + - - +
391A LEU* 4.5 5.6 - - + -
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Residues in contact with TYR 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A TYR* 2.7 74.0 + + - +
294A MET* 3.0 35.3 - - + +
295A SER* 3.7 20.2 - - - -
352A THR* 2.9 17.2 + - - -
353A PRO* 3.1 13.9 + - + +
355A ALA* 1.3 74.9 - - - +
357A SER* 1.3 63.6 + - - +
359A LEU* 3.0 19.8 + - + +
360A PHE* 3.0 22.7 + + + -
391A LEU* 3.7 27.1 - - + -
393A LEU* 4.0 9.2 - - + -
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Residues in contact with SER 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ARG* 5.1 3.0 + - - -
353A PRO 3.1 7.6 + - - -
354A GLU* 3.0 19.0 + - - -
356A TYR* 1.3 79.3 - - - +
358A VAL* 1.3 60.3 + - - +
360A PHE* 3.5 7.9 + - - +
361A ASP* 3.2 29.7 + - - +
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A PHE* 3.6 36.4 - - + +
341A ARG* 3.6 51.1 - - + +
342A PHE* 4.1 13.9 - - + +
345A ALA* 5.1 1.6 - - + -
354A GLU* 3.1 14.9 + - + +
355A ALA* 3.0 13.1 + - - +
357A SER* 1.3 75.8 - - - +
359A LEU* 1.3 67.9 + - - +
361A ASP* 3.1 4.3 + - - +
362A MET* 2.9 24.8 + - + +
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Residues in contact with LEU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 3.9 20.5 - - + +
342A PHE* 4.5 8.7 - - + -
355A ALA 3.0 15.5 + - - +
356A TYR* 3.0 17.1 + - + +
358A VAL* 1.3 76.6 - - + +
360A PHE* 1.3 58.6 + - + +
362A MET* 3.3 28.3 + - + +
363A ALA* 2.8 27.9 + - - +
384A LEU* 3.7 14.0 - - + +
387A LEU* 4.1 18.6 - - + -
388A SER* 4.0 20.4 - - - +
391A LEU* 4.0 25.6 - - + -
393A LEU* 4.8 7.2 - - + -
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Residues in contact with PHE 360 (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* 3.1 20.6 - + - -
315A ALA* 3.3 43.3 - - + -
318A ARG* 3.7 34.1 - - + -
319A LEU* 4.0 24.9 - - + -
356A TYR* 3.0 29.5 + + + -
357A SER* 3.8 9.9 - - - +
359A LEU* 1.3 74.2 - - - +
361A ASP* 1.3 68.9 + - - +
363A ALA* 3.2 3.5 + - + +
364A ARG* 2.9 24.1 + - - +
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Residues in contact with ASP 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A PHE* 3.7 7.9 - - + -
341A ARG* 2.8 41.0 + - - +
357A SER* 3.2 14.4 + - - +
358A VAL 3.1 6.1 + - - +
360A PHE* 1.3 78.6 - - - +
362A MET* 1.3 63.7 + - - +
364A ARG* 3.3 8.5 + - - +
365A GLU* 3.1 21.7 + - - +
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Residues in contact with MET 362 (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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335A GLY 5.1 1.1 - - - +
338A PHE* 3.5 45.5 - - + -
358A VAL* 2.9 11.4 + - + +
359A LEU* 3.5 24.7 - - + +
361A ASP* 1.3 79.1 - - - +
363A ALA* 1.3 56.9 + - - +
365A GLU* 3.3 3.8 + - - +
366A VAL* 3.0 30.6 + - + +
380A MET* 4.2 13.4 - - - +
383A HIS* 4.4 4.9 - - - -
384A LEU* 3.2 53.8 - - + -
387A LEU* 3.5 17.7 - - + -
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Residues in contact with ALA 363 (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 4.8 2.0 - - - +
319A LEU* 3.8 21.8 - - + -
322A ALA* 3.7 25.4 - - + +
359A LEU 2.8 17.9 + - - +
360A PHE* 3.2 6.7 + - + +
362A MET* 1.3 75.6 - - - +
364A ARG* 1.3 64.5 + - - +
366A VAL* 3.0 13.8 + - - +
367A ASN* 3.0 12.4 + - - +
384A LEU* 3.8 14.6 - - + +
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Residues in contact with ARG 364 (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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360A PHE 2.9 16.3 + - - +
361A ASP* 3.3 7.8 + - - +
363A ALA* 1.3 75.8 - - - +
365A GLU* 1.3 60.4 + - - +
367A ASN* 3.5 13.6 + - - +
368A ARG* 3.2 22.2 + - - +
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Residues in contact with GLU 365 (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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338A PHE* 4.0 27.1 - - + -
361A ASP 3.1 12.6 + - - +
362A MET 3.5 8.5 - - - +
363A ALA 3.1 0.2 - - - -
364A ARG* 1.3 75.5 - - - +
366A VAL* 1.3 65.6 + - - +
368A ARG* 3.4 10.4 + - - +
369A LEU* 3.1 48.0 + - + +
380A MET* 4.4 10.9 - - + +
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Residues in contact with VAL 366 (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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322A ALA* 3.5 27.6 - - + +
323A LEU* 5.1 0.4 - - + -
326A THR* 4.8 0.4 - - - +
362A MET 3.0 18.0 + - - +
363A ALA* 3.0 10.6 + - - +
365A GLU* 1.3 77.8 - - - +
367A ASN* 1.3 62.3 + - - +
369A LEU* 3.3 7.9 + - - +
370A LYS* 3.0 31.0 + - + +
377A ALA* 4.1 7.3 - - + +
380A MET* 3.8 28.5 - - + +
381A ALA* 3.9 27.8 - - + +
384A LEU* 4.1 12.8 - - + -
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Residues in contact with ASN 367 (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 5.3 2.6 + - - -
321A THR* 4.5 5.5 - - - +
322A ALA* 3.2 31.7 - - - +
363A ALA* 3.0 17.2 + - - +
364A ARG* 3.7 13.0 - - - +
365A GLU 3.3 0.2 - - - -
366A VAL* 1.3 76.4 - - - +
368A ARG* 1.3 64.0 + - - +
370A LYS* 2.8 35.7 + - - +
371A ALA* 3.7 2.9 + - - +
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Residues in contact with ARG 368 (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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364A ARG 3.2 11.2 + - - +
365A GLU* 3.7 20.0 - - - +
367A ASN* 1.3 79.6 - - - +
369A LEU* 1.3 63.3 + - + +
370A LYS 3.3 0.2 + - - -
371A ALA* 3.5 15.9 + - - +
372A GLU* 4.0 5.4 + - - +
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Residues in contact with LEU 369 (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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365A GLU* 3.1 33.5 + - - +
366A VAL 3.6 4.9 - - - +
368A ARG* 1.3 79.0 - - + +
370A LYS* 1.3 65.5 + - - +
371A ALA 3.2 0.3 + - - -
372A GLU* 4.7 6.1 - - + +
373A ASP* 2.9 34.6 + - + +
376A ALA* 3.8 29.2 - - + +
377A ALA* 3.8 13.7 - - + +
380A MET* 3.5 34.3 - - + -
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Residues in contact with LYS 370 (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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321A THR 4.0 4.9 + - - -
322A ALA 3.0 30.1 + - - -
324A ARG* 3.4 21.2 + - - +
326A THR* 4.3 8.5 - - - -
366A VAL* 3.0 26.0 + - - +
367A ASN* 2.8 27.8 + - - +
369A LEU* 1.3 77.0 - - - +
371A ALA* 1.3 61.3 + - - +
374A MET* 3.5 45.9 + - + +
377A ALA* 4.0 4.2 - - + +
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Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ASN 3.7 2.1 + - - +
368A ARG* 3.5 11.0 + - - +
369A LEU 3.2 0.6 - - - -
370A LYS* 1.3 82.5 - - - +
372A GLU* 1.3 62.3 + - + +
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Residues in contact with GLU 372 (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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368A ARG 4.0 6.2 + - - +
369A LEU* 3.2 10.5 + - + +
371A ALA* 1.3 83.5 - - + +
373A ASP* 1.3 64.7 + - + +
374A MET 4.1 1.1 + - - -
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Residues in contact with ASP 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LEU* 2.9 19.3 + - + +
372A GLU* 1.3 79.6 - - + +
374A MET* 1.3 57.6 + - - +
375A ALA* 2.9 28.0 + - - +
376A ALA* 3.2 27.5 + - + +
377A ALA 3.0 21.1 + - - -
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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
------------------------------------------------------------
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