Contacts of the helix formed by residues 361 - 374 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352C ARG* 3.6 35.0 - - + +
354C ARG* 5.1 3.6 + - - -
356C SER* 3.6 33.8 + - - -
359C TYR* 3.6 37.8 + + + +
360C ASP* 1.3 72.7 + - - +
362C GLU* 1.3 68.4 + - - +
363C ALA 3.2 2.5 - - - -
364C LEU* 2.9 11.8 + - + -
365C ASP* 2.7 43.9 + - - +
440C LEU* 4.1 12.5 - - + +
443C ASP* 2.5 46.1 + - + -
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Residues in contact with GLU 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C LYS* 2.8 25.3 + - - +
348C LYS* 3.8 23.4 + - + +
360C ASP* 3.4 22.4 + - - +
361C TYR* 1.3 79.0 - - - +
363C ALA* 1.3 60.9 + - - +
365C ASP* 3.7 5.6 + - - +
366C GLU* 3.2 23.2 + - - +
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Residues in contact with ALA 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C GLU 3.5 24.0 - - - +
317C CYS 4.2 9.2 - - - +
318C LYS* 4.4 9.2 - - + +
323C VAL* 3.9 17.5 - - + +
345C LEU* 4.7 5.4 - - + +
348C LYS* 4.3 10.8 - - - +
360C ASP* 4.8 3.1 + - - +
361C TYR 3.0 1.0 + - - -
362C GLU* 1.3 75.6 - - - +
364C LEU* 1.3 68.3 + - - +
366C GLU* 3.3 4.1 + - - +
367C ALA* 2.9 26.2 + - - +
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Residues in contact with LEU 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C SER* 5.7 0.2 - - - +
322C LEU* 3.9 20.0 - - + -
323C VAL* 3.5 21.9 - - + +
326C LEU* 3.8 23.8 - - + -
359C TYR* 4.2 17.0 - - + +
360C ASP 5.2 0.8 + - - -
361C TYR* 2.9 16.4 + - + +
363C ALA* 1.3 79.9 - - - +
365C ASP* 1.3 58.4 + - - +
367C ALA* 3.7 1.0 - - - +
368C MET* 2.8 39.6 + - + +
440C LEU* 3.2 51.1 - - + +
441C GLN* 5.1 0.9 - - + -
444C PHE* 5.4 0.4 - - + -
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Residues in contact with ASP 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C PHE* 3.5 25.1 - - + -
352C ARG* 2.9 53.9 + - - +
361C TYR* 2.7 34.7 + - - +
362C GLU* 3.7 5.6 - - - +
364C LEU* 1.3 72.7 - - - +
366C GLU* 1.3 58.3 + - - +
369C SER* 2.9 25.5 + - - -
444C PHE* 3.1 26.6 - - - +
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Residues in contact with GLU 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344C GLN* 3.7 22.1 - - - +
345C LEU* 4.6 7.4 - - + -
347C ASN 4.2 0.7 - - - +
348C LYS* 3.8 20.2 - - + +
349C GLN* 3.2 29.8 + - - +
350C PHE* 3.1 31.1 + - - +
362C GLU 3.2 15.7 + - - +
363C ALA* 3.8 4.0 - - - +
365C ASP* 1.3 76.3 - - - +
367C ALA* 1.3 61.1 + - - +
369C SER* 3.2 8.1 + - - -
370C ILE* 2.9 47.4 + - + +
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Residues in contact with ALA 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C VAL* 3.7 22.0 - - + -
326C LEU* 4.1 18.2 - - + +
327C ILE* 3.8 24.0 - - + -
330C LEU* 4.7 2.1 - - - +
345C LEU* 4.5 2.6 - - + +
363C ALA 2.9 18.0 + - - +
364C LEU 3.7 2.9 - - - +
366C GLU* 1.3 74.0 - - - +
368C MET* 1.3 64.9 + - - +
370C ILE* 3.5 3.8 + - - +
371C SER* 3.0 26.7 + - - -
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Residues in contact with MET 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C LEU* 3.9 9.2 - - + -
364C LEU* 2.8 36.1 + - + +
365C ASP 3.5 4.7 - - - +
367C ALA* 1.3 75.2 - - - +
369C SER* 1.3 57.6 + - - +
371C SER* 3.3 2.7 + - - -
372C VAL* 2.8 37.2 + - + +
383C TYR* 3.4 32.1 - - + +
423C LEU* 3.6 21.8 - - + -
441C GLN* 3.7 33.9 - - + +
444C PHE* 3.6 41.3 - - + -
445C LEU* 4.8 0.4 - - + -
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Residues in contact with SER 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C PHE* 4.1 18.3 - - - +
365C ASP 2.9 18.6 + - - -
366C GLU* 3.4 14.6 + - - -
368C MET* 1.3 78.4 - - - +
370C ILE* 1.3 57.3 + - - +
372C VAL* 3.9 3.0 - - - +
373C GLU* 3.0 30.5 + - - +
444C PHE* 3.6 16.3 - - - -
448C LYS* 5.9 2.7 - - - +
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Residues in contact with ILE 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C ILE* 5.0 3.8 - - + -
330C LEU* 3.5 21.5 - - + -
341C TYR* 3.7 16.2 - - + +
344C GLN* 3.5 61.7 - - + +
345C LEU* 4.2 14.8 - - + +
366C GLU* 2.9 35.6 + - + +
367C ALA* 4.0 4.5 - - - +
369C SER* 1.3 75.9 - - - +
371C SER* 1.3 64.1 + - - +
373C GLU* 3.3 7.1 + - + +
374C MET* 3.2 25.5 + - + +
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Residues in contact with SER 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326C LEU* 4.5 9.0 + - - +
329C ALA* 6.0 0.2 - - - +
330C LEU* 3.9 25.1 - - - +
367C ALA 3.0 19.9 + - - -
368C MET 3.7 3.4 - - - -
370C ILE* 1.3 77.3 - - - +
372C VAL* 1.3 62.1 + - - +
374C MET* 3.2 13.2 + - - +
375C LEU* 3.4 15.5 + - - +
421C LYS* 4.5 13.5 + - - +
423C LEU* 3.7 28.4 - - - +
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Residues in contact with VAL 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368C MET* 2.8 27.0 + - + +
369C SER* 4.0 4.7 - - - +
371C SER* 1.3 71.8 - - - +
373C GLU* 1.3 62.5 + - - +
375C LEU* 3.2 29.9 + - + +
380C LYS* 3.7 11.8 - - + +
383C TYR* 3.6 38.8 - - + -
384C THR* 6.0 1.6 - - - +
423C LEU* 4.2 9.0 - - + -
444C PHE* 4.3 10.3 - - + -
445C LEU* 5.2 0.9 - - + -
448C LYS* 4.0 29.8 - - + +
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Residues in contact with GLU 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C GLN* 5.8 5.4 - - - +
369C SER 3.0 19.7 + - - +
370C ILE* 3.4 9.4 - - - +
371C SER 3.3 0.2 - - - -
372C VAL* 1.3 78.7 - - - +
374C MET* 1.3 75.6 + - + +
375C LEU 4.1 0.5 - - - +
377C GLU* 4.8 0.2 - - - +
380C LYS* 3.0 33.8 + - - +
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Residues in contact with MET 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C LEU* 3.7 9.0 - - + -
334C PHE* 3.6 34.1 - - + -
337C ARG* 3.4 29.2 - - - +
340C TYR* 4.3 14.4 - - + +
341C TYR* 3.5 24.5 - - + +
344C GLN* 5.5 2.2 - - - +
370C ILE* 3.2 17.5 + - + +
371C SER 3.2 6.7 + - - +
373C GLU* 1.3 101.2 - - + +
375C LEU* 1.3 65.8 + - - +
376C ARG* 3.4 2.6 + - - -
421C LYS* 4.4 5.0 + - - +
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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