Contacts of the helix formed by residues 361 - 374 (chain B) in PDB entry 1Z6T
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 361 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352B ARG* 3.7 42.8 - - + +
354B ARG* 5.1 4.5 + - - -
356B SER* 3.6 35.9 + - - -
359B TYR* 3.6 39.2 + + + +
360B ASP* 1.3 72.1 + - - +
362B GLU* 1.3 68.7 + - - +
363B ALA 3.2 2.5 - - - -
364B LEU* 2.9 11.9 + - + -
365B ASP* 2.7 43.2 + - - +
440B LEU* 4.2 11.0 - - + +
443B ASP* 2.7 36.6 + - + -
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Residues in contact with GLU 362 (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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318B LYS* 2.9 24.5 + - - +
348B LYS* 4.0 24.2 + - + +
360B ASP* 3.4 21.4 + - - +
361B TYR* 1.3 78.8 - - - +
363B ALA* 1.3 61.2 + - - +
365B ASP* 3.8 5.1 - - - +
366B GLU* 3.2 23.7 + - - +
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Residues in contact with ALA 363 (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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316B GLU 3.6 24.2 - - - +
317B CYS 4.2 9.0 - - - +
318B LYS* 4.6 10.1 - - + +
323B VAL* 3.9 17.5 - - + +
345B LEU* 4.6 4.5 - - + +
348B LYS* 4.3 10.3 - - - +
360B ASP* 4.7 2.7 + - - +
361B TYR 2.9 1.0 + - - -
362B GLU* 1.3 76.9 - - - +
364B LEU* 1.3 62.6 + - - +
366B GLU* 3.3 4.2 + - - +
367B ALA* 2.9 31.5 + - - +
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Residues in contact with LEU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B LEU* 3.9 22.0 - - + -
323B VAL* 3.7 19.5 - - + +
326B LEU* 3.7 24.5 - - + -
359B TYR* 4.1 16.8 + - + +
360B ASP 5.2 1.0 + - - -
361B TYR* 2.9 14.4 + - + +
363B ALA* 1.3 79.1 - - - +
365B ASP* 1.3 59.4 + - - +
367B ALA* 3.7 1.0 - - - +
368B MET* 2.8 40.1 + - + +
440B LEU* 3.2 51.6 - - + +
441B GLN* 5.1 1.1 - - + -
444B PHE* 5.5 0.7 - - + -
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Residues in contact with ASP 365 (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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350B PHE* 3.5 25.5 - - + -
352B ARG* 2.9 54.2 + - - +
361B TYR* 2.7 33.2 + - - +
362B GLU* 3.8 5.7 - - - +
364B LEU* 1.3 74.2 - - - +
366B GLU* 1.3 59.1 - - - +
369B SER* 2.9 25.1 + - - -
444B PHE* 3.2 27.0 - - - +
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Residues in contact with GLU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B GLN* 3.8 21.0 - - - +
345B LEU* 4.6 9.0 - - + -
347B ASN 4.2 0.5 - - - +
348B LYS* 3.7 21.5 - - + +
349B GLN* 3.1 30.5 + - - +
350B PHE* 3.0 31.5 + - - +
362B GLU 3.2 16.4 + - - +
363B ALA* 3.8 3.6 - - - +
365B ASP* 1.3 75.7 - - - +
367B ALA* 1.3 60.3 + - - +
369B SER* 3.2 8.3 + - - -
370B ILE* 2.9 47.1 + - + +
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Residues in contact with ALA 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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323B VAL* 3.8 21.1 - - + -
326B LEU* 4.0 18.9 - - + +
327B ILE* 3.9 23.6 - - + -
330B LEU* 4.7 2.1 - - - +
345B LEU* 4.6 2.3 - - + +
363B ALA 2.9 17.8 + - - +
364B LEU 3.7 3.4 - - - +
366B GLU* 1.3 76.5 - - - +
368B MET* 1.3 62.1 + - - +
370B ILE* 3.6 3.3 + - - +
371B SER* 3.0 26.9 + - - -
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Residues in contact with MET 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LEU* 3.8 14.4 - - + -
364B LEU* 2.8 34.5 + - + +
365B ASP 3.7 4.3 - - - +
367B ALA* 1.3 72.4 - - - +
369B SER* 1.3 57.6 + - - +
371B SER* 3.3 2.1 + - - -
372B VAL* 2.8 37.1 + - + +
383B TYR* 3.5 30.5 - - + +
423B LEU* 3.5 22.0 - - + -
441B GLN* 3.7 34.5 - - + +
444B PHE* 3.7 39.7 - - + -
445B LEU* 4.9 0.7 - - + -
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Residues in contact with SER 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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350B PHE* 4.1 18.0 - - - +
365B ASP 2.9 18.4 + - - -
366B GLU* 3.4 15.0 + - - -
368B MET* 1.3 77.5 - - - +
370B ILE* 1.3 57.5 + - - +
372B VAL* 3.9 3.1 - - - +
373B GLU* 3.0 30.9 + - - +
444B PHE* 3.6 16.9 - - - -
448B LYS* 6.0 2.4 - - - +
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Residues in contact with ILE 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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327B ILE* 4.8 4.0 - - + -
330B LEU* 3.5 22.0 - - + -
341B TYR* 3.7 16.6 - - + +
344B GLN* 3.6 57.9 - - + +
345B LEU* 4.2 14.8 - - + +
366B GLU* 2.9 36.3 + - + +
367B ALA* 4.0 5.2 - - - +
369B SER* 1.3 71.6 - - - +
371B SER* 1.3 63.4 + - - +
373B GLU* 3.3 6.9 + - - +
374B MET* 3.1 25.8 + - + +
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Residues in contact with SER 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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326B LEU* 4.5 8.3 + - - +
330B LEU* 3.9 26.3 - - - +
367B ALA 3.0 20.4 + - - -
368B MET* 3.7 3.6 - - - -
370B ILE* 1.3 74.2 - - - +
372B VAL* 1.3 67.0 + - - +
374B MET* 3.2 13.0 + - - +
375B LEU* 3.4 14.4 + - - +
421B LYS* 4.4 14.0 + - - +
423B LEU* 3.7 28.1 - - - +
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Residues in contact with VAL 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B MET* 2.8 26.9 + - + +
369B SER* 3.9 5.4 - - - +
371B SER* 1.3 72.0 - - - +
373B GLU* 1.3 64.2 + - - +
375B LEU* 3.1 32.6 + - + +
380B LYS* 3.7 12.4 - - + +
383B TYR* 3.6 35.2 - - + -
384B THR* 5.8 2.7 - - - +
423B LEU* 4.4 7.9 - - + -
444B PHE* 4.3 12.8 - - + -
445B LEU* 5.2 0.9 - - + -
448B LYS* 4.1 26.7 - - + +
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Residues in contact with GLU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B GLN* 6.1 2.7 - - - +
369B SER 3.0 20.1 + - - +
370B ILE* 3.5 8.7 - - - +
371B SER 3.2 0.2 - - - -
372B VAL* 1.3 77.3 - - - +
374B MET* 1.3 75.5 + - + +
375B LEU 3.3 0.7 - - - +
377B GLU* 4.9 0.3 - - - +
380B LYS* 3.2 37.6 + - - +
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Residues in contact with MET 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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330B LEU* 3.8 11.9 - - + -
334B PHE* 3.6 31.7 - - + -
337B ARG* 3.5 26.5 - - - +
340B TYR* 4.0 21.5 - - + +
341B TYR* 3.6 24.0 - - + +
344B GLN* 5.4 2.9 - - - +
370B ILE* 3.1 16.5 + - + +
371B SER 3.2 6.4 + - - +
373B GLU* 1.3 95.5 - - + +
375B LEU* 1.3 63.7 + - - +
376B ARG* 3.5 2.4 + - - -
421B LYS* 4.1 4.6 + - - +
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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