Contacts of the helix formed by residues 379 - 398 (chain A) in PDB entry 5LLU
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 MET 379 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A THR* 3.8 4.2 - - - +
345A SER* 5.3 0.2 - - - +
374A GLY 5.0 0.2 - - - +
375A ALA 3.2 26.5 - - - +
376A THR 3.5 3.8 - - - +
377A ILE 3.2 5.1 + - - -
378A ASN* 1.3 77.4 - - - +
380A ASP* 1.3 59.4 + - - +
382A THR* 3.8 8.7 - - - -
383A ALA* 3.0 17.7 + - - +
417A SER* 2.7 32.6 + - - +
420A ALA* 3.4 26.5 - - - +
421A ALA 3.6 3.4 - - - +
422A GLY* 3.6 21.3 - - - +
463A ASN* 3.3 30.3 - - + +
601A NA 2.7 27.6 - - - -
602A ASP* 4.1 5.4 - - - +
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Residues in contact with ASP 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A TYR* 5.1 0.2 + - - -
130A THR* 3.1 40.9 + - - -
131A THR* 3.3 5.0 + - - +
134A ALA* 3.4 17.4 - - + +
308A HIS* 3.5 24.9 - - + +
313A LEU* 4.2 6.2 - - - +
378A ASN* 3.2 18.6 + - - +
379A MET* 1.3 68.4 - - - +
381A GLY* 1.3 60.4 + - - +
383A ALA* 3.5 0.8 + - - -
384A LEU* 3.2 24.6 + - - +
462A VAL* 4.4 7.2 - - + +
463A ASN* 3.4 3.3 + - - +
466A GLY* 3.6 26.7 - - - -
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Residues in contact with GLY 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LEU* 3.7 26.2 - - - +
380A ASP* 1.3 72.9 - - - +
382A THR* 1.3 62.3 + - - +
384A LEU* 4.6 0.2 - - - -
385A TYR* 3.3 21.3 + - - +
459A ARG* 3.4 23.2 - - - +
462A VAL* 4.0 9.3 - - - +
463A ASN* 2.8 13.5 + - - -
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Residues in contact with THR 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A MET* 3.8 14.3 - - - +
380A ASP 3.3 0.2 - - - -
381A GLY* 1.3 74.4 - - - +
383A ALA* 1.4 53.4 + - - +
385A TYR* 3.1 4.5 + - + +
386A GLU* 2.8 58.1 + - + +
417A SER* 4.6 5.8 - - - -
420A ALA* 4.4 19.7 - - + -
427A GLY* 4.4 3.8 - - - -
459A ARG* 3.9 9.2 - - - +
463A ASN* 2.9 21.3 + - - -
602A ASP* 2.7 30.5 + - - +
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Residues in contact with ALA 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A THR* 3.9 22.7 - - - +
134A ALA* 4.6 2.7 - - + -
135A VAL* 3.9 13.1 - - + +
379A MET 3.0 18.8 + - - +
380A ASP* 3.5 8.5 + - - +
382A THR* 1.4 75.3 - - - +
384A LEU* 1.4 59.5 + - - +
386A GLU* 3.7 3.1 + - - +
387A ALA* 3.4 22.9 + - - +
413A ALA* 4.1 10.7 - - - +
414A THR* 4.9 0.2 - - - -
417A SER* 3.7 19.5 - - - +
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ALA* 3.4 30.2 - - + +
137A LEU* 4.2 8.3 - - + -
138A GLY* 4.1 10.9 - - - +
141A LEU* 5.7 0.2 - - + -
301A VAL* 3.9 17.7 - - + +
304A GLY* 3.4 41.3 - - - +
305A LEU* 3.9 16.4 - - + +
308A HIS* 4.0 18.4 - - + -
380A ASP 3.2 16.3 + - - +
381A GLY 3.9 4.0 - - - +
383A ALA* 1.4 73.5 - - - +
385A TYR* 1.4 60.9 + - - +
387A ALA* 3.5 3.9 + - - +
388A VAL* 3.2 33.4 + - + +
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Residues in contact with TYR 385 (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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297A TYR* 3.1 23.6 - - - -
301A VAL* 4.2 30.2 - - + +
381A GLY 3.3 13.7 + - - +
382A THR* 3.1 10.4 + - - +
384A LEU* 1.4 76.8 - - - +
386A GLU* 1.4 60.2 + - + +
388A VAL* 3.9 0.9 - - - +
389A ALA* 2.9 37.4 + - - +
427A GLY* 3.9 23.1 - - - -
428A LEU* 4.3 2.9 - - - +
431A MET* 4.1 15.6 - - - -
448A ILE* 3.5 18.5 - - - +
452A ASP* 2.7 20.0 + - - -
455A LEU* 4.1 11.2 - - + -
459A ARG* 3.3 44.4 - - - -
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Residues in contact with GLU 386 (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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382A THR* 2.8 37.7 + - + +
383A ALA 3.7 5.8 - - - +
385A TYR* 1.4 75.0 - - - +
387A ALA* 1.3 61.3 + - - +
389A ALA* 4.2 2.9 - - - +
390A ALA* 3.2 26.3 + - - +
413A ALA* 3.8 28.3 - - + +
416A ALA* 4.0 11.3 - - + +
417A SER 5.0 0.4 - - - +
427A GLY* 2.9 19.9 - - - +
430A THR* 2.9 25.8 + - - +
431A MET* 3.3 32.1 - - - +
434A VAL* 3.6 12.9 - - + +
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL* 3.8 26.0 - - + +
138A GLY 4.6 0.4 - - - -
139A ILE* 3.8 24.5 - - + +
142A VAL* 4.9 0.7 - - - -
383A ALA 3.4 13.4 + - - +
384A LEU 3.8 4.7 - - - +
385A TYR 3.3 0.6 - - - -
386A GLU* 1.3 77.5 - - - +
388A VAL* 1.4 62.6 + - - +
390A ALA* 3.7 1.0 + - - +
391A ILE* 3.4 31.8 + - - +
409A ILE* 4.5 7.2 - - + -
413A ALA* 4.2 4.9 - - + +
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Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLY* 3.4 28.7 - - - +
141A LEU* 5.5 0.7 - - + -
142A VAL* 3.7 17.8 - - + +
297A TYR* 4.1 10.1 - - + -
300A THR* 3.8 28.3 - - + +
301A VAL* 3.7 30.3 - - + -
384A LEU* 3.2 24.4 + - + +
385A TYR 4.0 0.4 - - - +
387A ALA* 1.4 74.4 - - - +
389A ALA* 1.3 52.4 + - - +
391A ILE 3.4 1.7 + - - -
392A PHE* 2.8 32.6 + - - +
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Residues in contact with ALA 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A TYR* 3.4 33.8 - - + +
385A TYR* 2.9 20.5 + - + +
386A GLU 4.3 0.4 - - - +
388A VAL* 1.3 73.8 - - - +
390A ALA* 1.3 62.8 + - - +
392A PHE* 4.1 1.6 - - - +
393A ILE* 3.3 29.6 + - - +
431A MET* 3.6 32.9 - - + +
448A ILE* 4.7 2.0 - - + +
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Residues in contact with ALA 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A GLU 3.2 19.7 + - - +
387A ALA 4.0 4.0 - - - +
388A VAL 3.4 0.2 - - - -
389A ALA* 1.3 75.8 - - - +
391A ILE* 1.4 59.6 + - + +
393A ILE* 3.4 19.1 - - - +
394A ALA* 3.5 1.2 + - - +
409A ILE* 4.5 12.8 - - + -
431A MET* 4.8 1.9 - - - +
434A VAL* 4.1 29.2 - - + +
435A LEU* 4.2 16.2 - - + -
438A VAL* 5.6 0.7 - - + -
440A LEU* 3.4 16.7 - - + +
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Residues in contact with ILE 391 (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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139A ILE* 3.7 28.9 - - + -
142A VAL* 3.7 32.5 - - + +
143A LEU* 4.9 15.5 - - + -
387A ALA 3.4 19.9 + - - +
390A ALA* 1.4 75.3 - - - +
392A PHE* 1.4 60.4 + - - +
393A ILE 3.3 0.7 - - - -
394A ALA* 3.2 10.8 + - + +
395A GLN* 2.9 31.4 + - + +
406A ILE* 3.9 22.4 - - + -
409A ILE* 4.3 19.7 - - + -
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Residues in contact with PHE 392 (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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142A VAL* 4.2 6.5 - - + +
294A LEU* 3.3 36.8 - - + -
296A MET* 4.2 17.0 - - + -
297A TYR* 3.6 44.6 - + + -
388A VAL 2.8 18.5 + - - +
389A ALA 4.1 3.4 - - - +
390A ALA 3.5 0.4 - - - -
391A ILE* 1.4 77.1 - - - +
393A ILE* 1.4 61.4 + - - +
395A GLN* 3.2 35.1 + - + +
396A VAL* 3.7 19.3 + - + +
447A LEU* 6.3 0.7 - - + -
448A ILE* 3.8 27.1 - - + -
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Residues in contact with ILE 393 (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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389A ALA 3.3 14.1 + - - +
390A ALA 3.4 15.7 - - - +
392A PHE* 1.4 75.8 - - + +
394A ALA* 1.4 55.4 + - - +
396A VAL* 3.3 7.0 + - - +
397A ASN* 2.9 34.6 + - - +
431A MET* 5.0 5.6 - - + -
435A LEU* 3.7 15.0 - - + -
440A LEU* 3.7 34.3 - - + -
441A PRO* 4.3 2.7 - - + +
444A ASP* 3.6 44.6 - - + +
447A LEU* 5.7 2.7 - - + -
448A ILE* 3.6 26.7 - - + -
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Residues in contact with ALA 394 (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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390A ALA 3.5 12.3 + - - +
391A ILE* 3.2 19.6 + - + +
393A ILE* 1.4 77.4 - - - +
395A GLN* 1.4 58.7 + - - +
396A VAL 3.2 0.7 - - - -
398A ASN* 2.9 39.3 + - - +
440A LEU* 3.8 20.4 - - + -
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Residues in contact with GLN 395 (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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142A VAL* 3.0 32.9 + - - +
145A ILE 3.1 18.9 + - - -
296A MET* 3.3 26.5 - - - +
391A ILE* 2.9 19.8 + - + +
392A PHE* 3.2 25.8 + - + +
394A ALA* 1.4 76.5 - - - +
396A VAL* 1.3 61.2 + - + +
398A ASN* 5.2 3.5 + - - +
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Residues in contact with VAL 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A PHE* 3.7 28.7 - - + +
393A ILE* 3.3 7.5 + - - +
395A GLN* 1.3 82.0 - - + +
397A ASN* 1.4 68.7 + - - +
398A ASN* 3.7 9.6 + - - -
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Residues in contact with ASN 397 (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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393A ILE* 2.9 20.9 + - - +
396A VAL* 1.4 81.0 - - - +
398A ASN* 1.4 78.2 + - - +
440A LEU* 4.1 15.3 - - + -
441A PRO* 4.2 15.5 - - + +
444A ASP* 3.0 31.0 + - - +
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Residues in contact with ASN 398 (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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394A ALA* 2.9 33.4 + - - +
395A GLN 5.2 3.2 + - - +
396A VAL 3.7 10.5 + - - -
397A ASN* 1.4 91.8 + - - +
440A LEU* 5.0 9.2 - - - +
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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