Contacts of the strand formed by residues 386 - 392 (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 TYR 386 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376B GLU* 3.2 44.2 + - + +
379B LEU* 3.7 25.1 - - + -
380B LYS* 3.5 34.2 - - + -
384B ILE 3.4 15.9 - - - +
385B ASP* 1.3 80.9 + - - +
387B LYS* 1.3 58.9 + - - +
388B ILE* 3.7 30.6 + - + +
412B LEU* 4.0 8.3 - - + -
413B ILE 3.2 15.9 - - - +
415B SER* 3.5 7.6 + - - -
421B LEU* 4.0 15.0 - - + -
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Residues in contact with LYS 387 (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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386B TYR* 1.3 75.4 - - - +
388B ILE* 1.3 63.3 + - - +
411B ILE 3.8 0.3 - - - +
412B LEU* 3.7 3.3 - - - -
413B ILE* 2.8 56.5 + - + +
414B ASP 4.3 0.7 - - - -
415B SER* 3.5 37.6 + - - +
418B GLU* 3.0 27.6 + - - -
471B ALA 3.9 13.0 - - - +
472B TYR 4.5 7.7 + - - -
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Residues in contact with ILE 388 (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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225B GLU* 5.5 2.5 - - - +
376B GLU* 3.5 26.0 - - - +
386B TYR* 3.7 24.9 - - + +
387B LYS* 1.3 76.5 - - - +
389B GLY* 1.3 64.9 + - - +
390B LYS* 4.4 6.5 + - + -
410B LYS* 3.9 29.8 - - + -
411B ILE 3.8 2.7 - - - -
412B LEU* 4.1 4.7 - - + -
470B ALA 4.2 4.3 - - - +
471B ALA* 4.1 9.1 - - - +
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Residues in contact with GLY 389 (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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388B ILE* 1.3 74.9 - - - +
390B LYS* 1.3 61.1 + - - -
409B VAL 3.5 0.9 - - - +
410B LYS* 3.2 5.2 - - - +
411B ILE 2.9 34.9 + - - +
467B ALA* 3.5 22.0 - - - +
470B ALA* 4.0 2.2 - - - -
471B ALA* 3.5 17.8 - - - +
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Residues in contact with LYS 390 (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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225B GLU* 2.9 39.3 + - - +
388B ILE* 4.3 6.0 + - + -
389B GLY* 1.3 74.7 - - - +
391B PHE* 1.3 65.9 + - - +
392B PRO* 4.3 6.1 - - + +
408B PHE* 4.1 29.4 - - + -
409B VAL 3.2 9.6 - - - +
410B LYS* 4.4 8.7 - - + -
467B ALA* 4.2 2.8 + - - -
470B ALA* 4.1 13.6 - - - +
478B CYS* 4.3 8.7 - - - -
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Residues in contact with PHE 391 (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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390B LYS* 1.3 75.5 - - - +
392B PRO* 1.3 86.4 - - + +
395B ALA* 3.6 30.3 - - + -
396B ASN* 3.9 13.2 - - - -
408B PHE* 3.6 1.7 - - - -
409B VAL* 2.9 32.2 + - - +
463B ALA* 3.5 42.4 - - + +
466B GLU* 3.5 28.5 - - + -
467B ALA* 3.7 11.7 - - + +
475B ALA* 4.4 0.2 - - + -
477B HIS* 3.8 29.6 - - + -
478B CYS* 3.8 18.4 - - + -
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Residues in contact with PRO 392 (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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390B LYS* 4.3 7.6 - - + +
391B PHE* 1.3 116.0 - - + +
393B PHE* 1.3 60.7 + - - +
394B ALA* 3.1 14.7 + - + +
395B ALA* 3.4 21.4 + - + +
407B GLY 3.5 11.7 - - - +
408B PHE* 3.9 6.3 - - + -
478B CYS* 5.0 8.7 - - + -
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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