Contacts of the helix formed by residues 397 - 413 (chain N) in PDB entry 5LN3
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 397 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363N SER* 4.4 22.2 - - - +
366N HIS* 4.5 0.2 - - - -
396N ALA* 1.4 74.0 - - - +
398N ASN* 1.4 61.1 + - - +
399N TRP* 3.4 27.9 - - + -
400N ALA* 3.0 21.0 + - + +
401N LYS* 2.8 34.8 + - - +
169V VAL* 5.2 8.6 - - + +
170V LEU* 4.5 9.3 - - + +
190V GLN* 4.9 8.3 - - - -
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Residues in contact with ASN 398 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397N THR* 1.4 73.1 + - - +
399N TRP* 1.4 86.1 + - + +
401N LYS* 3.2 19.9 + - - +
402N PHE 3.2 6.1 + - - -
435N SER* 4.8 7.1 + - - +
437N TYR* 3.2 43.9 + - + -
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Residues in contact with TRP 399 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397N THR* 3.4 25.6 - - + -
398N ASN* 1.4 90.0 - - - +
400N ALA* 1.4 61.5 + - - +
402N PHE* 3.4 7.0 + - - +
403N THR* 3.0 24.9 + - - -
437N TYR* 3.5 39.2 + + - -
772N TRP* 4.4 19.8 - + - -
773N PHE* 4.4 30.1 - + + +
774N PRO* 5.2 2.6 - - - +
166V ASN* 3.6 31.2 - - + -
167V MET* 4.9 14.7 - - + +
169V VAL* 5.6 0.9 - - + -
170V LEU* 3.6 27.8 - - + -
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Residues in contact with ALA 400 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363N SER* 5.9 0.2 - - - -
366N HIS* 3.3 37.5 - - + +
367N THR* 4.4 10.1 - - + +
392N TRP* 5.5 1.1 - - + -
396N ALA* 3.9 4.5 - - + -
397N THR* 3.0 25.7 + - + +
399N TRP* 1.4 62.5 - - - +
401N LYS* 1.4 54.4 + - - +
403N THR* 3.2 8.8 + - - -
404N ALA* 2.9 30.5 + - - +
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Residues in contact with LYS 401 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393N LEU* 3.5 35.9 + - + +
394N ALA* 5.5 0.8 - - - +
396N ALA* 4.3 11.9 - - + +
397N THR 2.8 19.3 + - - +
398N ASN* 3.2 14.5 + - - +
400N ALA* 1.4 71.4 - - - +
402N PHE* 1.4 65.0 + - - +
404N ALA* 3.4 16.0 + - + +
405N THR* 3.4 19.6 + - + +
435N SER* 5.2 2.7 - - - +
437N TYR* 4.5 4.5 - - + -
438N GLN* 3.9 38.4 + - + +
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Residues in contact with PHE 402 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398N ASN 3.2 3.4 + - - -
399N TRP* 3.4 11.9 - - - +
401N LYS* 1.4 77.9 - - - +
403N THR* 1.4 61.6 + - - +
405N THR* 3.1 16.1 + - - -
406N ALA* 3.7 4.5 + - - +
437N TYR* 2.9 47.9 - + + +
440N GLY* 3.4 27.8 - - - -
441N GLY* 3.4 16.2 - - - -
444N TYR* 3.8 24.5 - + + -
472N ILE* 3.8 23.3 - - + -
475N HIS* 4.2 13.0 - + - -
476N GLY* 3.9 13.5 - - - -
479N LEU* 5.1 2.7 - - + -
772N TRP* 4.4 13.9 - + + +
774N PRO* 4.6 11.9 - - + -
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Residues in contact with THR 403 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367N THR* 4.0 27.2 - - + +
370N VAL* 5.0 5.2 - - + -
371N ILE* 4.3 8.1 - - + -
399N TRP 3.0 14.7 + - - -
400N ALA* 3.2 10.1 + - - -
402N PHE* 1.4 75.1 - - - +
404N ALA* 1.4 62.1 + - - +
406N ALA* 3.4 10.2 + - - +
407N SER* 3.1 24.8 + - - +
444N TYR* 6.3 0.2 - - - -
773N PHE* 5.8 0.7 - - - +
774N PRO* 3.9 33.0 - - + +
777N HIS* 4.1 16.0 - - + +
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Residues in contact with ALA 404 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370N VAL* 5.0 1.3 - - - -
386N LEU* 5.1 1.8 - - + +
392N TRP* 4.0 28.0 - - + -
393N LEU* 4.2 13.5 - - + -
400N ALA 2.9 17.1 + - - +
401N LYS* 3.4 13.2 + - + +
403N THR* 1.4 73.9 - - - +
405N THR* 1.4 57.8 + - + +
407N SER* 3.1 29.2 + - - -
408N LEU* 3.6 12.9 + - - +
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Residues in contact with THR 405 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401N LYS* 3.4 11.7 + - + +
402N PHE 3.1 12.6 + - - -
404N ALA* 1.4 73.8 - - + +
406N ALA* 1.4 57.6 + - - +
408N LEU* 3.2 37.3 + - + +
409N GLY 3.8 2.4 + - - -
423N MET* 3.9 12.5 - - - +
426N TYR* 5.3 12.6 - - + +
438N GLN* 3.7 30.1 + - + +
441N GLY* 3.3 21.3 - - - -
442N GLY* 3.6 4.2 + - - -
445N ALA* 4.4 0.2 - - - +
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Residues in contact with ALA 406 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402N PHE 3.7 6.5 + - - +
403N THR* 3.4 13.6 + - - +
405N THR* 1.4 78.1 + - - +
407N SER* 1.4 59.7 + - - +
409N GLY* 3.4 10.4 + - - -
410N VAL* 3.7 13.6 - - - +
441N GLY 3.8 12.8 + - - +
444N TYR* 4.1 21.8 - - + -
445N ALA* 3.9 17.9 - - + +
448N LEU* 6.1 0.7 - - - +
777N HIS* 5.4 12.8 + - + +
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Residues in contact with SER 407 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370N VAL* 3.3 25.2 - - - +
371N ILE* 5.9 0.3 - - - +
374N SER* 3.6 20.3 + - - -
386N LEU* 5.5 7.6 - - - -
392N TRP* 6.0 0.4 - - - -
403N THR* 3.1 16.6 + - - +
404N ALA* 3.1 14.7 + - - -
406N ALA* 1.4 73.0 - - - +
408N LEU* 1.4 65.0 + - - +
410N VAL* 3.4 20.5 + - - +
411N ILE* 3.7 13.4 + - - +
777N HIS* 5.7 4.3 + - - -
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Residues in contact with LEU 408 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383N ASP* 4.9 7.0 - - - +
386N LEU* 3.8 33.7 - - + -
404N ALA 3.8 13.2 - - - +
405N THR* 3.2 24.6 + - + +
407N SER* 1.4 78.5 - - - +
409N GLY* 1.4 54.6 + - - +
411N ILE* 3.4 6.1 + - - +
412N HIS* 3.0 42.4 + - + +
423N MET* 4.0 11.0 - - - -
426N TYR* 4.3 37.5 - - + -
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Residues in contact with GLY 409 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405N THR 3.8 3.6 + - - -
406N ALA 3.4 8.5 + - - -
407N SER 3.3 1.4 - - - -
408N LEU* 1.4 76.0 - - - +
410N VAL* 1.4 58.6 + - - +
412N HIS* 3.6 6.6 - - - -
413N LYS* 2.9 23.7 + - - +
423N MET* 4.5 6.8 - - - -
445N ALA* 4.4 12.3 - - - -
449N ILE* 3.0 29.3 - - - +
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Residues in contact with VAL 410 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374N SER* 3.9 20.2 - - - +
375N PHE* 6.6 0.2 - - + -
377N HIS 5.0 0.2 - - - -
378N CYS* 3.5 38.5 - - + -
379N GLY 3.5 13.2 + - - -
406N ALA 3.7 16.2 - - - +
407N SER* 3.6 11.4 - - - +
408N LEU 3.3 0.2 - - - -
409N GLY* 1.4 75.0 - - - +
411N ILE* 1.3 65.3 + - + +
413N LYS* 3.5 13.1 + - - +
448N LEU* 5.2 12.3 - - + -
449N ILE* 5.2 0.9 - - - -
777N HIS* 5.6 8.3 - - + +
780N SER* 4.9 12.1 - - - +
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Residues in contact with ILE 411 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374N SER* 5.8 3.1 - - - +
377N HIS* 4.4 20.4 - - + -
379N GLY* 4.2 7.1 - - - -
381N THR* 3.8 15.4 + - + +
382N SER 3.5 39.9 - - - +
383N ASP* 3.4 43.1 - - - +
386N LEU* 3.8 17.0 - - + -
407N SER* 3.7 14.8 + - - +
408N LEU* 3.4 9.8 + - - +
410N VAL* 1.3 80.4 - - + +
412N HIS* 1.3 64.4 + - - +
413N LYS 3.4 6.8 + - - +
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Residues in contact with HIS 412 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381N THR* 6.1 1.7 - - + +
383N ASP* 3.7 24.2 - - - -
408N LEU* 3.0 32.6 + - + +
409N GLY* 3.6 7.9 - - - +
410N VAL 3.4 0.2 - - - -
411N ILE* 1.3 82.7 - - - +
413N LYS* 1.3 62.5 + - - +
414N GLY 3.2 3.5 + - - -
415N HIS* 4.1 9.4 + - - -
419N ALA* 3.7 23.1 - - + +
422N LEU* 3.5 48.7 + - + +
423N MET* 3.8 27.5 - - + -
426N TYR* 4.6 9.4 - + - -
449N ILE* 5.3 2.7 - - + -
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Residues in contact with LYS 413 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335N ILE* 4.9 18.3 - - - +
339N LEU* 5.3 0.2 - - - +
379N GLY* 3.6 24.3 - - - +
409N GLY 2.9 15.6 + - - +
410N VAL* 3.8 8.7 - - - +
411N ILE 3.3 2.8 - - - +
412N HIS* 1.3 73.8 - - - +
414N GLY* 1.3 63.4 + - - +
415N HIS 4.0 17.8 + - - +
416N GLU* 4.9 6.7 - - - +
419N ALA* 5.2 0.9 - - - -
449N ILE* 3.0 42.9 + - + +
450N HIS* 5.0 3.6 + - + +
451N ALA 5.7 0.2 + - - -
453N HIS* 4.8 15.9 + - - -
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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
------------------------------------------------------------
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