Contacts of the helix formed by residues 364 - 377 (chain N) in PDB entry 5L4K
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 VAL 364 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363N SER* 1.3 79.0 - - - +
365N CYS* 1.3 71.2 + - - +
366N HIS 3.0 0.2 - - - -
367N THR* 2.8 24.9 + - + +
368N ALA* 3.2 6.1 + - - +
724N VAL* 4.2 34.5 - - + +
725N MET* 5.9 1.3 - - + -
728N PHE* 3.9 28.0 - - + -
773N PHE* 6.2 6.1 - - + -
177V THR* 5.4 5.7 - - + +
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Residues in contact with CYS 365 (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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360N VAL* 4.0 26.5 - - + +
362N ASN* 3.1 21.5 - - - +
363N SER 2.9 1.0 + - - -
364N VAL* 1.3 87.7 - - - +
366N HIS* 1.3 63.5 + - - +
368N ALA* 2.9 20.4 + - - +
369N THR* 3.0 16.4 + - - +
724N VAL* 4.5 12.6 - - - -
727N LYS* 4.3 31.6 - - - -
728N PHE* 5.4 1.6 - - - +
731N ILE* 4.0 7.5 - - + +
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Residues in contact with HIS 366 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361N ARG* 4.2 30.3 - - + +
362N ASN 4.3 0.6 + - - -
363N SER 3.0 14.2 + - - +
364N VAL 2.9 0.2 + - - -
365N CYS* 1.3 78.3 - - - +
367N THR* 1.3 62.3 + - - +
369N THR* 3.0 17.4 + - - -
370N VAL* 3.3 17.6 + - + +
392N TRP* 3.3 43.4 + + + -
395N ARG* 4.5 6.8 + - + -
396N ALA* 3.4 34.2 - - + -
397N THR* 4.7 4.4 + - + +
400N ALA* 3.5 25.5 - - + +
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Residues in contact with THR 367 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364N VAL* 2.8 21.4 + - + +
366N HIS* 1.3 77.2 + - - +
368N ALA* 1.3 69.1 + - - +
370N VAL* 2.9 21.9 + - - +
371N ILE* 3.0 17.2 + - + +
397N THR* 5.6 0.2 + - - -
399N TRP 5.5 0.4 - - - -
400N ALA* 4.1 17.7 + - - +
403N THR* 3.7 29.2 - - + +
728N PHE* 4.9 9.2 - - + -
773N PHE* 5.7 7.2 - - + +
774N PRO* 6.1 1.3 - - + -
776N SER* 5.6 1.3 - - - +
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Residues in contact with ALA 368 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364N VAL 3.2 2.2 + - - -
365N CYS* 2.9 13.7 + - - +
367N THR* 1.3 76.7 - - - +
369N THR* 1.3 61.8 + - - +
371N ILE* 2.7 35.3 + - + +
372N ALA 3.0 5.4 + - - -
728N PHE* 3.7 29.7 - - + +
731N ILE* 3.4 34.7 - - + +
732N LEU* 5.6 0.4 - - + -
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Residues in contact with THR 369 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353N LEU* 5.0 4.2 - - + +
356N THR* 3.5 45.8 - - + +
357N LYS* 4.2 12.2 - - + +
360N VAL 4.1 10.6 + - - +
361N ARG* 5.1 3.1 - - - +
365N CYS 3.0 10.4 + - - -
366N HIS* 3.0 20.4 + - - -
368N ALA* 1.3 74.6 - - - +
370N VAL* 1.3 59.7 + - - +
372N ALA* 2.9 24.9 + - + +
373N ASN* 3.3 14.3 + - - -
731N ILE* 4.0 13.2 - - + -
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Residues in contact with VAL 370 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366N HIS* 3.3 38.5 + - + +
367N THR* 2.9 21.6 + - - +
369N THR* 1.3 78.1 - - - +
371N ILE* 1.3 59.4 + - + +
373N ASN* 4.5 10.7 - - - +
374N SER* 4.1 2.5 + - - -
385N PHE* 5.3 5.7 - - + -
392N TRP* 4.0 35.7 - - + +
400N ALA* 5.1 1.6 - - + +
403N THR* 4.0 22.4 - - - +
404N ALA* 5.6 0.4 - - - -
407N SER* 3.8 22.6 - - - +
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Residues in contact with ILE 371 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367N THR* 3.0 17.0 + - + +
368N ALA* 2.7 36.9 + - - +
370N VAL* 1.3 83.4 - - - +
372N ALA* 1.3 63.3 + - - +
373N ASN 3.3 1.3 - - - -
374N SER* 2.9 21.1 + - - -
375N PHE* 3.2 14.7 + - + -
403N THR* 4.7 6.5 - - - -
728N PHE* 4.0 12.6 - - + -
732N LEU* 3.7 28.7 - - + -
776N SER* 3.3 41.3 - - - +
777N HIS* 3.7 18.4 - - + +
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Residues in contact with ALA 372 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353N LEU* 3.9 23.6 - - + -
368N ALA 3.0 10.1 + - - +
369N THR* 2.9 11.1 + - - +
371N ILE* 1.3 75.4 - - - +
373N ASN* 1.3 51.7 + - - +
375N PHE* 2.9 5.7 + - - +
376N MET* 2.6 37.3 + - - +
731N ILE* 4.1 16.4 - - + +
732N LEU* 4.4 4.9 - - + +
735N GLY* 3.8 22.8 - - - +
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Residues in contact with ASN 373 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353N LEU* 3.0 31.3 - - - +
357N LYS* 6.2 2.4 - - - +
369N THR* 3.3 15.8 + - - +
370N VAL* 4.7 5.1 - - - +
371N ILE 3.3 0.4 - - - -
372N ALA* 1.3 72.2 - - - +
374N SER* 1.3 54.3 + - - +
375N PHE 2.7 16.0 + - - -
376N MET* 2.9 15.2 + - - +
377N HIS* 3.0 35.5 + - - +
384N GLN* 4.9 0.3 + - - -
385N PHE* 3.9 35.2 - - + +
411N ILE* 3.8 21.8 - - + +
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Residues in contact with SER 374 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370N VAL 4.1 5.6 + - - -
371N ILE* 2.9 25.4 + - - +
373N ASN* 1.3 76.0 - - - +
375N PHE* 1.3 63.5 + - - +
378N CYS* 4.2 3.6 - - - +
407N SER* 4.2 8.2 - - - -
410N VAL* 2.9 36.9 - - - +
411N ILE* 3.9 15.5 - - - +
777N HIS* 3.1 30.6 + - - -
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Residues in contact with PHE 375 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371N ILE* 3.5 14.1 - - + -
372N ALA 2.9 2.7 + - - +
373N ASN 2.7 3.6 + - - -
374N SER* 1.3 89.3 - - - +
376N MET* 1.3 52.6 + - - +
377N HIS 3.2 2.4 + - - -
378N CYS* 3.6 7.4 + - - +
410N VAL* 4.8 2.2 - - + -
732N LEU* 3.9 21.8 - - + -
735N GLY 3.2 17.3 - - - +
736N ILE* 3.8 21.1 - - + -
739N ALA* 2.9 6.5 - - - +
740N GLY 2.7 30.5 + - - -
766N PHE* 4.6 6.3 - + - -
776N SER* 3.1 31.2 - - - -
777N HIS 4.2 7.6 - - - -
779N LEU* 3.6 35.7 - - + -
780N SER 4.3 0.7 - - - -
783N TYR* 3.5 28.7 - + - +
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Residues in contact with MET 376 (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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346N ASN* 4.4 0.7 + - - -
348N THR* 4.2 15.3 - - + +
349N ASP 3.6 23.8 - - - +
350N LEU* 4.0 9.2 - - + -
352N ILE* 5.9 2.5 - - - -
353N LEU* 3.8 42.4 - - + -
372N ALA 2.6 19.5 + - - +
373N ASN* 2.9 7.4 + - - -
375N PHE* 1.3 73.4 - - - +
377N HIS* 1.3 86.0 + - + +
378N CYS 3.6 0.7 - - - -
734N GLN 5.8 1.6 - - - +
735N GLY* 3.8 6.0 + - - +
738N ASP* 3.9 33.7 - - + +
739N ALA* 4.0 1.1 - - - +
740N GLY 3.8 0.4 - - - -
741N GLY 3.5 18.9 + - - -
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Residues in contact with HIS 377 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346N ASN* 4.0 17.3 - - - -
348N THR* 4.5 0.4 - - + -
350N LEU* 3.3 25.5 - - + +
353N LEU* 5.1 0.2 - - + -
373N ASN* 3.0 41.9 + - - +
376N MET* 1.3 99.1 - - + +
378N CYS* 1.3 61.1 + - - +
379N GLY 3.2 3.6 + - - -
380N THR* 3.2 22.9 + - - +
382N SER* 4.1 18.9 + - - -
384N GLN* 3.7 25.9 + - - -
385N PHE* 4.8 1.8 - + - -
411N ILE* 3.3 30.3 - - + +
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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