Contacts of the helix formed by residues 396 - 413 (chain A) in PDB entry 1LMU
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 THR 396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A LYS* 3.9 8.7 + - - -
394A HIS* 4.8 4.0 - - - -
395A LEU* 1.3 78.1 - - - +
397A GLU* 1.3 78.3 + - + +
398A ASN* 3.8 15.9 - - + +
399A GLU* 2.8 27.0 + - - +
400A ALA* 2.9 19.5 + - - +
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Residues in contact with GLU 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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396A THR* 1.3 79.5 - - + +
398A ASN* 1.3 60.7 + - - +
400A ALA* 3.3 7.7 + - - +
401A LYS* 2.9 57.7 + - + +
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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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307A LEU* 4.3 26.7 - - + +
311A ASN* 4.7 6.7 + - - +
315A ILE* 3.9 21.6 - - + +
396A THR* 3.2 11.0 - - + +
397A GLU* 1.3 77.6 - - - +
399A GLU* 1.3 67.1 + - - +
401A LYS* 3.0 29.8 + - - +
402A VAL* 3.0 25.1 + - - +
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Residues in contact with GLU 399 (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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315A ILE* 3.7 13.2 - - + +
318A LYS* 3.0 33.1 + - - +
319A LEU* 3.5 18.0 - - + +
323A HIS* 2.9 25.1 + - - -
394A HIS 3.7 0.9 - - - +
395A LEU* 2.9 34.0 - - + +
396A THR* 2.8 37.4 + - - +
398A ASN* 1.3 78.4 - - - +
400A ALA* 1.3 56.0 + - - +
402A VAL* 2.9 10.1 - - - +
403A TYR* 2.8 32.0 + - - +
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Residues in contact with ALA 400 (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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354A HIS 5.8 4.9 - - - +
395A LEU* 4.5 11.7 - - + +
396A THR 2.9 14.0 + - - +
397A GLU* 3.5 11.7 - - + +
399A GLU* 1.3 76.7 - - - +
401A LYS* 1.3 57.4 + - + +
403A TYR* 3.2 7.4 + - - +
404A THR* 2.8 37.6 + - - +
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Residues in contact with LYS 401 (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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305A PHE* 3.2 65.3 + - + +
307A LEU* 5.2 4.0 - - + +
397A GLU* 2.9 46.6 + - + +
398A ASN* 3.0 27.0 + - - +
400A ALA* 1.3 76.4 - - + +
402A VAL* 1.3 65.2 + - + +
404A THR* 3.2 6.7 + - - -
405A LEU* 3.1 20.8 + - - +
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Residues in contact with VAL 402 (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 LEU* 4.5 5.6 - - + +
301A ALA* 4.8 6.3 - - + -
305A PHE* 5.4 1.3 - - + -
307A LEU* 4.2 17.0 - - + -
312A VAL* 3.6 31.6 - - + -
315A ILE* 3.0 34.3 - - + -
316A CYS* 5.4 1.3 - - - +
319A LEU* 3.4 10.8 - - + -
398A ASN 3.0 10.4 + - - +
399A GLU 2.9 19.3 - - - +
401A LYS* 1.3 76.5 - - + +
403A TYR* 1.3 61.4 + - - +
405A LEU* 3.1 9.3 + - - +
406A ILE* 3.0 29.6 + - + +
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Residues in contact with TYR 403 (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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319A LEU* 4.1 9.6 - - + -
325A LEU* 3.6 44.8 + - + +
326A ILE* 3.8 12.8 - - + -
350A ALA* 4.3 2.6 - - - +
351A ILE* 3.8 14.9 + - - +
354A HIS* 3.2 42.7 + + + +
355A ALA* 4.1 12.3 - - + -
386A PRO* 3.4 26.2 - - + +
387A THR 4.7 0.5 + - - -
395A LEU* 4.7 7.2 - - + -
399A GLU 2.8 18.3 + - - +
400A ALA* 3.6 7.4 - - - +
402A VAL* 1.3 76.1 - - - +
404A THR* 1.3 63.6 + - - +
406A ILE* 3.0 6.9 + - - +
407A ALA* 2.8 38.3 + - + -
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Residues in contact with THR 404 (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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304A ARG* 5.0 8.7 - - - +
355A ALA* 4.2 10.4 - - - +
357A ASP* 4.3 8.0 + - - +
358A LEU* 3.3 32.3 - - + +
400A ALA* 2.8 26.3 + - - +
401A LYS* 3.5 7.4 - - - -
403A TYR* 1.3 80.2 - - - +
405A LEU* 1.3 54.6 + - - +
407A ALA* 3.1 4.8 + - - +
408A ARG* 2.7 38.7 + - + +
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Residues in contact with LEU 405 (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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292A PHE* 3.4 20.3 - - + -
297A LEU* 3.0 28.3 - - + -
300A GLU* 3.3 44.4 - - + -
301A ALA* 3.8 15.0 - - + +
304A ARG* 3.8 19.0 - - - +
305A PHE* 4.9 3.8 - - + -
401A LYS 3.1 8.9 + - - +
402A VAL* 3.1 11.3 + - - +
404A THR* 1.3 78.9 - - - +
406A ILE* 1.3 63.1 + - - +
408A ARG* 3.7 25.6 - - - +
409A GLN 3.1 18.5 + - - -
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Residues in contact with ILE 406 (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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292A PHE* 4.4 8.5 - - + -
297A LEU* 4.1 26.2 - - + -
316A CYS* 5.1 4.0 - - - -
319A LEU* 4.5 7.2 - - + -
326A ILE* 3.8 25.8 - - + -
384A ILE* 3.4 36.9 - - + +
385A ILE* 3.7 4.9 - - - -
386A PRO* 3.3 25.8 - - + -
402A VAL* 3.0 19.2 + - + +
403A TYR* 3.0 7.7 + - - +
405A LEU* 1.3 76.9 - - - +
407A ALA* 1.3 62.5 + - - +
409A GLN* 3.4 3.1 + - - +
410A TYR* 3.2 19.8 + - - +
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Residues in contact with ALA 407 (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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351A ILE* 3.8 29.0 - - + +
355A ALA* 4.8 3.1 - - + -
358A LEU* 4.8 1.8 - - + -
386A PRO* 3.5 20.4 - - + +
403A TYR* 2.8 24.4 + - + +
404A THR* 3.6 9.0 - - - +
406A ILE* 1.3 77.4 - - - +
408A ARG* 1.3 61.6 + - - +
410A TYR* 3.1 5.9 + - - +
411A LEU* 2.9 25.7 + - - +
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Residues in contact with ARG 408 (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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292A PHE* 5.7 0.4 - - - -
300A GLU* 4.2 14.6 + - - -
304A ARG* 4.1 15.6 - - - +
358A LEU* 3.8 25.1 - - + +
404A THR* 2.7 26.0 + - + +
405A LEU* 3.7 29.1 - - - +
407A ALA* 1.3 72.5 - - - +
409A GLN* 1.3 67.5 + - - +
411A LEU* 3.0 6.4 + - - +
412A MET* 2.9 33.7 + - + +
449A LEU* 3.4 37.8 + - + -
450A LEU* 3.4 28.1 - - - +
451A GLY 4.3 0.8 - - - +
454A GLU* 3.1 25.5 + - - -
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Residues in contact with GLN 409 (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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289A PRO* 3.3 26.9 + - - +
290A LEU 2.7 30.8 + - - +
291A PRO* 3.7 7.9 - - + -
292A PHE* 3.0 57.2 - - + +
334A ARG* 5.0 2.0 - - - +
405A LEU 3.1 7.5 + - - +
406A ILE 3.8 2.9 - - - +
408A ARG* 1.3 79.4 + - - +
410A TYR* 1.3 56.8 + - - +
412A MET* 3.2 29.5 + - - +
413A GLN* 2.6 29.5 + - - +
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Residues in contact with TYR 410 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A PRO* 5.5 3.1 - - + +
336A LEU* 5.1 0.9 - - + -
340A HIS 4.9 1.0 + - - -
344A ARG* 3.6 27.5 + - - +
347A VAL* 3.6 28.5 - - + +
348A MET* 4.9 2.7 - - + -
351A ILE* 3.9 18.4 - - + -
373A TRP* 3.6 28.0 - + - -
385A ILE* 3.6 44.0 - - + +
386A PRO* 4.0 11.9 - - + -
406A ILE 3.2 9.6 + - - +
407A ALA* 3.1 10.0 + - - +
409A GLN* 1.3 79.1 - - - +
411A LEU* 1.3 65.4 + - + +
413A GLN* 3.0 23.5 + - + +
414A PHE* 3.4 33.7 - + - -
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Residues in contact with LEU 411 (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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348A MET* 4.4 16.8 - - + -
351A ILE* 3.7 23.8 - - + -
358A LEU* 3.8 27.8 - - + +
359A LEU* 3.1 35.4 - - + -
364A VAL* 4.3 23.5 - - + +
407A ALA 2.9 15.4 + - - +
408A ARG* 3.0 8.2 + - - +
410A TYR* 1.3 78.4 - - + +
412A MET* 1.3 62.8 + - - +
414A PHE* 2.9 25.7 + - + +
415A CYS* 3.7 8.3 + - - -
449A LEU* 4.4 12.1 - - + -
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Residues in contact with MET 412 (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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288A ALA* 3.7 20.4 - - + +
289A PRO* 4.4 6.5 - - - -
408A ARG* 2.9 51.8 + - + +
409A GLN* 3.4 35.4 - - - +
410A TYR 3.1 0.6 - - - -
411A LEU* 1.3 76.8 - - - +
413A GLN* 1.3 59.2 + - - +
415A CYS* 2.8 35.9 + - - +
446A TRP* 3.9 28.9 - - + -
449A LEU* 4.3 12.3 - - + -
450A LEU* 3.5 23.3 - - + -
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Residues in contact with GLN 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ALA* 4.7 3.5 - - - +
289A PRO 2.7 30.7 + - - -
290A LEU* 3.7 1.6 - - - +
291A PRO* 3.2 26.2 - - + +
368A THR* 4.4 8.7 - - - +
370A ASN* 3.2 52.4 - - - +
372A CYS* 3.7 16.6 - - - -
373A TRP* 4.9 3.1 - - + +
409A GLN 2.6 24.8 + - - +
410A TYR* 3.0 20.7 - - + +
411A LEU 3.1 0.8 + - - -
412A MET* 1.3 78.3 - - - +
414A PHE* 1.3 66.8 + - + +
415A CYS 3.3 4.2 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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