Contacts of the helix formed by residues 366 - 378 (chain B) in PDB entry 1JIH
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 LYS 366 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363B ASP* 3.4 23.5 + - + +
364B PRO 3.2 0.6 - - - -
365B LEU* 1.3 77.5 - - + +
367B THR* 1.3 62.5 + - - +
368B ALA* 3.1 5.2 - - - +
369B ASP* 3.2 32.3 + - + +
370B LEU* 3.4 12.5 + - - +
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Residues in contact with THR 367 (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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343B LYS* 3.3 26.9 - - + +
346B LEU* 3.3 32.7 + - + +
347B ASP* 2.9 30.0 + - - +
350B VAL* 5.5 2.4 - - - +
363B ASP 4.6 1.9 + - - -
364B PRO* 2.9 27.4 + - - +
365B LEU 3.4 3.8 + - - -
366B LYS* 1.3 75.1 - - - +
368B ALA* 1.3 65.0 + - - +
370B LEU* 4.7 1.3 - - - +
371B ALA* 3.1 23.0 + - - +
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Residues in contact with ALA 368 (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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339B ALA* 5.5 1.2 - - - +
343B LYS* 3.5 31.7 - - + +
365B LEU 5.0 1.1 + - - +
366B LYS* 4.9 2.0 - - - -
367B THR* 1.3 79.6 - - - +
369B ASP* 1.3 68.2 + - - +
371B ALA* 3.8 2.4 + - - +
372B GLU* 3.3 23.2 + - - +
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Residues in contact with ASP 369 (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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366B LYS* 3.2 26.2 + - + +
367B THR 3.2 0.4 - - - -
368B ALA* 1.3 83.4 - - - +
370B LEU* 1.3 60.5 + - - +
372B GLU* 3.2 7.0 + - - +
373B LYS* 2.9 29.2 + - - +
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Residues in contact with LEU 370 (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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308B LEU* 5.3 3.8 - - + -
312B LEU* 5.4 9.6 - - + -
315B GLU* 3.2 30.7 - - - +
342B LEU* 5.7 0.4 - - + -
346B LEU* 3.9 27.8 - - + -
362B ILE* 5.3 10.5 - - + -
363B ASP 6.0 0.7 - - - +
366B LYS 3.4 8.9 + - - +
367B THR* 4.1 1.8 - - - +
369B ASP* 1.3 78.7 - - - +
371B ALA* 1.3 64.8 + - - +
373B LYS* 3.4 23.4 + - + +
374B LEU* 3.1 40.8 + - + +
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Residues in contact with ALA 371 (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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339B ALA* 3.8 13.4 - - + +
342B LEU* 4.0 18.1 - - + +
343B LYS* 3.8 31.9 - - + +
346B LEU* 4.6 1.8 - - + +
367B THR 3.1 18.9 + - - +
368B ALA 4.0 3.6 - - - +
370B LEU* 1.3 76.2 - - - +
372B GLU* 1.3 66.8 + - - +
374B LEU* 3.4 1.0 + - - +
375B PHE* 2.9 26.8 + - - +
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Residues in contact with GLU 372 (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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339B ALA* 4.2 15.6 - - + +
368B ALA 3.3 12.9 + - - +
369B ASP* 3.2 10.4 + - - +
371B ALA* 1.3 78.2 - - - +
373B LYS* 1.3 64.2 + - - +
375B PHE* 3.4 1.6 + - - +
376B LYS* 3.0 44.9 + - + +
382B TYR* 5.3 1.1 - - + -
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Residues in contact with LYS 373 (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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307B THR* 3.0 34.7 - - - +
308B LEU* 4.1 16.3 - - + +
312B LEU* 4.8 5.5 - - - +
369B ASP 2.9 15.3 + - - +
370B LEU* 3.6 20.6 - - + +
372B GLU* 1.3 77.3 - - - +
374B LEU* 1.3 59.2 + - + +
376B LYS* 3.9 0.9 - - - +
377B LEU* 2.8 58.0 + - + +
382B TYR* 3.8 39.1 - - + +
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Residues in contact with LEU 374 (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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302B ILE* 4.0 12.8 - - + -
308B LEU* 3.6 34.5 - - + -
315B GLU* 4.0 17.9 - - + +
319B VAL* 5.6 9.2 - - + -
331B ILE* 4.4 16.1 - - + +
342B LEU* 3.9 25.1 - - + -
346B LEU* 6.3 0.2 - - + -
370B LEU* 3.1 40.6 + - + +
373B LYS* 1.3 77.5 - - + +
375B PHE* 1.3 60.9 + - - +
377B LEU* 3.9 4.9 - - + +
378B SER* 2.8 34.8 + - - -
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Residues in contact with PHE 375 (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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331B ILE* 5.3 2.5 - - - -
335B TRP* 3.3 26.0 - - + -
336B PRO 4.2 0.9 - - - -
337B ASP 3.8 8.5 - - - -
338B ASN* 3.5 37.5 - - - -
339B ALA* 3.9 12.3 - - + -
342B LEU* 4.6 6.4 - - + +
371B ALA 2.9 20.4 + - - +
372B GLU* 3.6 6.5 - - - +
374B LEU* 1.3 76.9 - - - +
376B LYS* 1.3 70.0 + - + +
378B SER* 2.6 21.2 + - - -
379B ARG* 3.0 56.8 + - - +
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Residues in contact with LYS 376 (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 GLU* 3.0 32.8 + - + +
373B LYS 3.9 0.2 - - - +
375B PHE* 1.3 84.7 - - + +
377B LEU* 1.3 59.9 + - - +
379B ARG* 2.9 5.4 + - - +
380B GLY 2.8 23.4 + - - -
381B ARG* 2.9 30.3 + - + +
382B TYR* 3.6 32.1 - - + +
383B GLY 5.4 0.7 - - - +
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Residues in contact with LEU 377 (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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269B ASN* 3.9 26.7 - - + +
295B LEU* 3.3 12.0 - - - +
302B ILE* 5.6 0.9 - - + -
305B PHE* 3.5 48.6 - - + -
308B LEU* 4.1 11.9 - - + -
373B LYS* 2.8 55.8 + - + +
374B LEU* 3.9 4.9 - - + +
376B LYS* 1.3 72.6 - - - +
378B SER* 1.3 57.9 + - - +
379B ARG 3.0 0.2 + - - -
380B GLY* 3.0 17.9 + - - +
382B TYR* 3.7 27.6 - - + +
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Residues in contact with SER 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 3.9 2.7 - - - +
302B ILE* 6.0 1.7 - - - +
305B PHE* 4.7 2.7 - - - -
328B ILE* 3.8 28.1 - - - +
331B ILE* 4.1 16.2 - - - +
332B ARG* 2.9 39.7 + - - -
374B LEU 2.8 15.1 + - - -
375B PHE* 2.6 24.3 + - - -
377B LEU* 1.3 76.0 - - - +
379B ARG* 1.3 70.2 + - - +
380B GLY 3.5 0.2 - - - -
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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