Contacts of the helix formed by residues 414 - 427 (chain s) in PDB entry 3J7Y
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 414 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399s LYS* 5.8 1.9 - - - +
400s PRO* 3.6 21.8 - - - +
401s LEU* 2.8 24.4 + - - +
402s TYR* 5.3 0.4 - - - -
412s GLY 4.1 0.8 + - - -
413s PHE* 1.3 78.9 - - - +
415s ASP* 1.3 65.5 + - - +
416s ASP* 3.3 32.6 + - - +
417s VAL* 3.8 16.7 + - + +
418s LEU* 3.9 7.3 + - - +
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Residues in contact with ASP 415 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143s ARG* 5.1 24.1 + - - +
413s PHE* 3.6 7.4 + - - +
414s ASN* 1.3 72.3 - - - +
416s ASP* 1.3 59.1 + - - +
417s VAL 3.2 0.7 - - - -
418s LEU* 3.1 21.6 + - - +
419s LEU* 2.9 44.3 + - + +
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Residues in contact with ASP 416 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399s LYS* 6.1 3.8 - - + +
414s ASN* 3.3 20.5 + - - +
415s ASP* 1.3 76.7 - - - +
417s VAL* 1.3 64.1 + - + +
419s LEU* 3.2 19.5 + - - +
420s GLN* 3.0 38.0 + - - +
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Residues in contact with VAL 417 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367s PHE* 3.8 24.7 - - + +
369s PHE* 3.5 9.4 - - + -
399s LYS* 4.1 24.5 - - + +
400s PRO 3.9 8.7 - - - +
401s LEU* 3.8 41.5 - - + -
414s ASN* 3.8 16.1 + - + +
415s ASP 3.2 0.2 - - - -
416s ASP* 1.3 77.2 - - + +
418s LEU* 1.3 63.8 + - - +
420s GLN* 3.2 16.5 + - - +
421s ILE* 3.1 22.2 + - + +
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Residues in contact with LEU 418 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142s LEU* 4.5 5.2 - - + +
143s ARG* 3.7 25.4 - - + +
146s ALA* 3.9 19.3 - - + -
180s LEU* 4.9 7.9 - - + -
184s LEU* 5.3 9.0 - - + -
401s LEU* 4.4 9.0 - - + -
413s PHE* 3.4 37.9 - - + -
414s ASN 3.9 2.9 + - - +
415s ASP* 3.1 20.8 + - - +
417s VAL* 1.3 80.2 - - - +
419s LEU* 1.3 57.0 + - - +
421s ILE* 3.2 23.4 + - + +
422s VAL* 2.9 35.8 + - + +
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Residues in contact with LEU 419 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415s ASP* 2.9 37.7 + - - +
416s ASP* 3.3 23.8 - - - +
418s LEU* 1.3 77.0 - - - +
420s GLN* 1.3 56.6 + - + +
422s VAL* 3.2 13.2 + - + +
423s HIS* 2.9 45.8 + - + +
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Residues in contact with GLN 420 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118s LEU* 4.5 20.2 - - + -
369s PHE* 3.1 37.9 - - + -
396s THR* 4.4 10.4 + - - +
399s LYS* 4.4 22.5 + - - +
416s ASP* 3.0 34.5 + - - +
417s VAL* 3.4 10.0 - - - +
419s LEU* 1.3 75.7 - - + +
421s ILE* 1.3 57.9 + - - +
423s HIS* 3.2 11.4 + - + +
424s PHE* 2.9 38.3 + - + -
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Residues in contact with ILE 421 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180s LEU* 5.5 4.9 - - + -
184s LEU* 3.9 17.5 - - + -
297s THR* 6.0 0.4 - - + -
299s PHE* 4.8 15.9 - - + -
360s VAL* 5.0 3.4 - - + -
367s PHE* 4.5 11.9 - - + -
369s PHE* 3.4 26.0 - - + -
401s LEU* 4.4 7.6 - - + -
417s VAL* 3.1 22.8 + - + +
418s LEU* 3.3 29.6 - - + +
420s GLN* 1.3 75.3 - - - +
422s VAL* 1.3 58.4 + - + +
424s PHE* 3.2 6.5 + - + +
425s LEU* 2.9 47.0 + - + +
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Residues in contact with VAL 422 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142s LEU* 4.1 31.0 - - + -
184s LEU* 4.9 8.7 - - + -
188s LEU* 4.1 22.9 - - + -
191s HIS* 6.5 0.7 - - + -
418s LEU* 2.9 22.6 + - + +
419s LEU* 3.2 17.2 + - + +
421s ILE* 1.3 78.0 - - + +
423s HIS* 1.3 54.6 + - + +
425s LEU* 3.2 4.2 + - - +
426s LEU* 2.7 56.0 + - + +
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Residues in contact with HIS 423 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118s LEU* 6.4 1.8 - - + -
419s LEU* 2.9 36.6 + - + +
420s GLN* 3.4 12.8 - - + +
422s VAL* 1.3 78.3 - - + +
424s PHE* 1.3 65.7 + - + +
426s LEU* 3.3 22.0 + - + +
427s ASN* 3.3 16.6 + - - +
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Residues in contact with PHE 424 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118s LEU* 3.6 28.5 - - + -
296s HIS* 3.4 6.6 - - - -
297s THR* 3.8 14.1 - - + -
358s GLN* 2.7 54.5 + - + +
359s ALA 3.7 23.3 - - - -
360s VAL* 5.5 0.9 - - + -
369s PHE* 3.7 29.4 - + + -
370s PHE 4.1 3.4 - - - -
371s CYS* 3.3 35.0 - - - -
420s GLN 2.9 27.0 + - - +
421s ILE* 3.5 11.0 - - - +
423s HIS* 1.3 81.3 - - + +
425s LEU* 1.3 64.4 + - - +
427s ASN* 3.4 3.5 + - - -
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Residues in contact with LEU 425 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181s VAL* 5.4 0.7 - - - +
184s LEU* 3.9 29.8 - - + -
185s VAL* 4.5 5.2 - - + -
188s LEU* 3.9 20.9 - - + -
195s LEU* 3.6 26.2 - - + +
241s ILE* 3.4 32.8 - - + -
296s HIS* 3.2 20.0 + - - -
297s THR* 4.3 5.6 - - + +
299s PHE* 4.2 14.4 - - + -
421s ILE* 2.9 36.5 + - + +
422s VAL* 3.5 7.4 - - - +
424s PHE* 1.3 76.7 - - - +
426s LEU* 1.3 61.6 + - - +
427s ASN 3.3 2.3 + - - +
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Residues in contact with LEU 426 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188s LEU* 4.8 9.2 - - + -
191s HIS* 3.6 42.4 - - + +
192s ASN* 2.7 42.0 - - + +
195s LEU* 5.7 0.2 - - - -
422s VAL* 2.7 36.9 + - + +
423s HIS* 3.3 14.3 + - + +
425s LEU* 1.3 72.2 - - - +
427s ASN* 1.3 61.0 + - - +
428s ARG* 3.7 6.9 + - - +
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Residues in contact with ASN 427 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192s ASN* 3.9 4.5 + - - -
195s LEU* 5.1 1.0 - - - +
247s LEU* 3.3 42.4 - - - +
248s ALA* 5.7 0.3 - - - +
250s PHE* 4.3 5.0 - - + -
296s HIS* 3.6 9.8 + - - -
358s GLN* 3.3 20.6 - - - +
423s HIS 3.3 12.5 + - - +
424s PHE 3.4 13.9 + - - -
425s LEU 3.8 5.7 - - - +
426s LEU* 1.3 77.9 - - - +
428s ARG* 1.3 60.0 + - - +
429s PRO* 4.5 1.9 - - - +
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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
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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