Contacts of the strand formed by residues 420 - 427 (chain B) in PDB entry 1JEH
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 ILE 420 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411B ILE* 4.0 11.4 - - + -
412B LEU 3.7 5.2 - - - +
413B ILE* 3.8 7.6 - - + -
419B ARG* 1.3 74.6 + - - +
421B LEU* 1.3 62.1 + - - +
422B GLY 3.4 23.3 - - - +
423B ALA* 4.8 3.6 - - + -
437B ALA* 5.8 1.1 - - + -
440B ALA* 3.7 24.7 - - + -
441B LEU* 3.8 34.6 - - + +
445B ALA 3.1 19.3 + - - +
446B SER 3.7 9.9 - - - +
450B VAL* 3.7 12.8 - - + -
464B PHE* 5.5 2.7 - - + -
468B ASN* 3.4 28.3 - - - +
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Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B GLY* 3.6 5.5 - - - -
374B LYS* 3.0 28.0 + - + +
379B LEU* 3.6 41.5 - - + -
384B ILE* 4.0 13.9 - - + -
386B TYR* 4.0 2.0 - - + -
412B LEU 2.8 9.1 + - - +
413B ILE 3.6 6.7 - - - +
414B ASP* 3.5 41.3 - - + +
419B ARG* 3.7 36.6 - - - +
420B ILE* 1.3 73.5 - - - +
422B GLY* 1.3 59.6 + - - +
441B LEU* 4.6 4.4 - - - +
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Residues in contact with GLY 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B VAL 3.4 11.4 - - - -
373B GLY* 4.1 0.4 - - - -
374B LYS 3.4 18.3 + - - -
411B ILE* 3.7 0.3 - - - -
412B LEU* 2.9 31.3 + - - +
420B ILE* 3.4 12.0 - - - +
421B LEU* 1.3 78.2 - - - +
423B ALA* 1.3 60.0 + - - -
424B HIS* 4.2 3.6 - - - -
441B LEU* 5.0 2.0 - - - -
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Residues in contact with ALA 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B TRP* 3.4 4.3 - - - -
372B VAL* 3.0 32.3 + - + +
410B LYS 3.4 6.5 - - - +
411B ILE* 4.5 7.4 - - + +
420B ILE* 4.8 4.3 - - + -
422B GLY* 1.3 75.0 - - - +
424B HIS* 1.3 65.7 + - - +
425B ILE* 4.2 1.8 - - + -
434B ILE* 3.8 7.4 - - + +
437B ALA* 3.7 29.6 - - + -
464B PHE* 4.5 11.7 - - + -
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Residues in contact with HIS 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ASP* 3.5 24.4 - - + +
226B VAL* 3.6 22.4 - - + -
370B ALA 3.9 3.1 - - - -
371B TRP* 3.4 29.7 - + + +
372B VAL 4.6 1.3 - - - -
373B GLY 4.6 1.6 + - - -
374B LYS 3.2 27.8 - - - -
375B THR* 3.4 21.4 + - - -
408B PHE* 4.0 5.0 - - - +
409B VAL* 3.7 1.2 - - - -
410B LYS* 2.8 49.7 + - + +
412B LEU* 3.7 17.5 - - + +
422B GLY* 4.4 0.2 - - - -
423B ALA* 1.3 85.6 + - - +
425B ILE* 1.3 62.5 + - - +
426B ILE 4.1 0.3 + - - -
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Residues in contact with ILE 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B VAL* 5.4 0.6 - - - +
369B VAL* 3.5 3.6 - - - +
370B ALA 2.9 42.6 + - - +
393B PHE* 4.1 11.2 - - + -
408B PHE 3.6 10.5 - - - +
409B VAL* 3.9 12.8 - - + -
423B ALA* 4.9 0.4 - - + -
424B HIS* 1.3 78.8 - - - +
426B ILE* 1.3 62.6 + - - +
430B ALA* 3.5 22.4 - - + +
433B MET* 3.8 37.5 - - + +
434B ILE* 3.8 39.0 - - + +
464B PHE* 4.1 13.7 - - + -
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Residues in contact with ILE 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B VAL* 3.6 41.3 - - + +
229B ALA* 3.7 22.0 - - + -
230B THR* 3.8 6.5 - - - +
233B PHE* 3.7 28.0 - - + -
367B PRO* 4.1 5.8 - - + -
368B GLU 3.5 5.4 - - - +
369B VAL* 4.2 5.8 - - + -
393B PHE* 3.1 5.5 - - - -
406B GLU* 5.8 0.2 - - + -
407B GLY* 3.9 13.0 - - - -
408B PHE* 2.8 58.2 + - + +
424B HIS 4.1 0.6 + - - -
425B ILE* 1.3 77.9 - - - +
427B GLY* 1.3 61.0 + - - +
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Residues in contact with GLY 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B PRO* 3.5 7.8 - - - +
368B GLU 2.9 27.3 + - - +
393B PHE* 3.8 8.7 - - - -
406B GLU 3.3 11.0 - - - -
425B ILE 4.1 0.2 - - - -
426B ILE* 1.3 78.4 - - - +
428B PRO* 1.3 76.5 - - - +
430B ALA* 3.4 7.8 + - - +
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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