Contacts of the helix formed by residues 364 - 377 (chain A) in PDB entry 1ZDT
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 ASP 364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A TYR* 3.9 7.2 - - - -
362A GLN 4.2 5.5 - - - +
363A LEU* 1.3 75.8 - - - +
365A ARG* 1.3 52.0 + - - +
366A GLN* 3.1 14.2 + - - +
367A GLU* 3.0 34.7 + - - +
368A PHE* 2.8 33.5 + - - +
404A TYR* 2.5 29.9 + - - -
408A HIS* 5.5 0.9 - - - +
415A LYS* 5.3 0.7 + - - -
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Residues in contact with ARG 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU* 3.7 20.7 - - + +
234A GLU* 3.1 33.8 + - - +
236A ASP* 3.4 32.9 + - - +
312A TYR* 3.4 40.0 + - - +
316A GLN* 4.0 12.9 - - - +
364A ASP* 1.3 73.3 - - - +
366A GLN* 1.3 71.0 + - - +
368A PHE* 3.5 9.9 - - + +
369A VAL* 3.1 27.8 + - + +
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Residues in contact with GLN 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A VAL* 4.5 9.2 - - + +
227A ILE* 3.7 28.0 - - + +
231A LEU* 4.1 22.1 - - + +
364A ASP* 3.1 21.2 + - - +
365A ARG* 1.3 82.5 + - - +
367A GLU* 1.3 65.6 + - - +
369A VAL* 3.6 6.2 - - - +
370A CYS* 3.4 21.3 + - - +
404A TYR* 3.5 34.9 + - + +
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Residues in contact with GLU 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ILE* 5.5 0.4 - - - -
363A LEU* 3.5 16.8 - - + +
364A ASP* 3.0 32.1 + - - +
366A GLN* 1.3 75.2 - - - +
368A PHE* 1.3 66.7 + - - +
370A CYS* 3.2 7.3 + - - +
371A LEU* 2.9 35.3 + - + +
401A LEU* 4.2 14.6 - - + -
404A TYR* 3.4 29.3 - - + -
405A THR* 3.9 7.3 - - + +
408A HIS* 5.5 0.5 - - - +
409A TYR* 5.3 1.6 - - - +
415A LYS* 2.9 43.3 + - - +
419A LEU* 4.2 4.0 - - + -
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Residues in contact with PHE 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A GLU* 3.6 23.1 - - - -
308A PHE* 3.6 28.0 - + - -
309A ASP* 5.1 13.5 - - - -
312A TYR* 3.3 61.0 - + + -
363A LEU* 4.1 3.6 - - + +
364A ASP 2.8 15.9 + - - +
365A ARG* 3.5 16.6 - - - +
366A GLN 3.2 0.2 - - - -
367A GLU* 1.3 79.5 - - - +
369A VAL* 1.3 71.4 + - + +
371A LEU* 3.2 2.3 + - - +
372A LYS* 3.1 49.1 + - + +
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Residues in contact with VAL 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ILE* 4.2 8.5 - - + +
230A LEU* 3.5 42.1 - - + +
231A LEU* 4.2 20.2 - - + -
234A GLU* 3.3 33.2 - - + +
279A TRP* 6.2 0.9 - - + +
365A ARG* 3.1 16.4 + - + +
366A GLN 3.6 11.2 - - - +
368A PHE* 1.3 87.4 - - + +
370A CYS* 1.3 63.4 + - - +
372A LYS* 3.7 11.1 - - - +
373A PHE* 3.2 16.6 + - - +
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Residues in contact with CYS 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LEU* 5.2 3.4 - - - -
227A ILE* 3.9 23.1 - - + -
230A LEU* 4.2 8.5 - - - -
366A GLN 3.4 10.9 + - - +
367A GLU 3.2 8.8 + - - +
369A VAL* 1.3 80.0 - - - +
371A LEU* 1.3 59.5 + - - +
373A PHE* 3.3 4.2 + - - +
374A ILE* 3.0 33.3 + - - +
397A ALA* 3.4 28.9 - - - -
400A ALA* 4.2 3.4 - - - -
401A LEU* 3.9 27.8 - - + -
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Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A PHE* 3.7 18.6 - - + -
358A LEU* 5.7 1.8 - - + -
363A LEU* 4.1 18.2 - - + -
367A GLU* 2.9 26.6 + - + +
368A PHE 3.2 4.7 + - - +
370A CYS* 1.3 78.3 - - - +
372A LYS* 1.3 57.2 + - - +
374A ILE* 3.2 7.4 + - + +
375A ILE* 3.0 33.2 + - - +
401A LEU* 3.5 33.0 - - + -
419A LEU* 4.1 25.6 - - + +
423A LEU* 3.9 32.1 - - + +
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Residues in contact with LYS 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A GLU* 3.3 35.2 + - - -
235A PRO* 5.9 0.4 - - - +
276A ILE* 5.8 5.7 - - - +
279A TRP* 3.5 54.8 - - + +
305A LEU* 3.7 15.1 - - + +
308A PHE* 3.9 14.3 - - + -
309A ASP* 5.7 2.4 + - - -
368A PHE* 3.1 40.2 + - + +
369A VAL* 3.7 12.6 - - - +
370A CYS 3.3 0.2 - - - -
371A LEU* 1.3 74.3 - - - +
373A PHE* 1.3 66.1 + - - +
375A ILE* 3.5 7.7 + - - -
376A LEU* 3.1 17.0 + - - +
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Residues in contact with PHE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LEU* 4.2 16.4 - - + -
230A LEU* 3.7 28.3 - - + -
279A TRP* 4.2 2.9 - - + -
283A CYS* 4.3 11.7 - - + -
284A MET* 3.5 36.3 - - - -
285A VAL* 4.3 6.7 - - + -
369A VAL 3.2 14.1 + - - +
370A CYS 3.6 7.6 - - - +
372A LYS* 1.3 75.6 - - - +
374A ILE* 1.3 64.2 + - - +
376A LEU* 3.3 8.5 + - + +
377A PHE* 3.1 49.0 + + + -
393A ALA* 3.9 30.1 - - + -
397A ALA* 3.6 18.6 - - + -
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Residues in contact with ILE 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A CYS* 3.0 25.3 + - - +
371A LEU* 3.2 12.8 + - + +
373A PHE* 1.3 78.7 - - - +
375A ILE* 1.3 56.2 + - - +
377A PHE* 3.3 5.3 + - - -
378A SER* 2.9 30.4 + - - -
394A GLN 5.7 0.2 - - - +
397A ALA* 3.7 34.5 - - + +
398A ASN* 3.7 23.8 - - - +
401A LEU* 4.1 22.4 - - + -
420A LEU* 5.2 3.6 - - + -
423A LEU* 3.9 19.3 - - + -
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Residues in contact with ILE 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A ASN* 5.1 0.2 + - - -
301A CYS* 3.6 14.2 - - + +
304A GLU* 3.7 27.1 - - + -
305A LEU* 3.8 15.7 - - + +
308A PHE* 3.7 38.4 - - + -
371A LEU 3.0 21.5 + - - +
372A LYS* 3.7 6.7 - - - +
374A ILE* 1.3 73.6 - - - +
376A LEU* 1.3 66.9 + - - +
378A SER* 2.6 29.3 + - - +
423A LEU* 4.2 26.2 - - + -
426A VAL* 4.7 8.3 - - + -
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Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A TRP* 3.8 23.3 - - + -
280A ALA* 4.1 11.4 - - + -
283A CYS* 4.2 13.9 - - + -
286A PHE* 3.9 31.6 - - + -
297A LEU* 3.7 21.4 - - + +
298A LEU* 4.0 22.9 - - + -
300A ASN* 5.6 0.7 + - - -
301A CYS* 3.8 16.9 - - - +
305A LEU* 4.4 4.7 - - + +
372A LYS 3.1 11.1 + - - +
373A PHE* 3.4 10.8 - - + +
375A ILE* 1.3 81.6 - - - +
377A PHE* 1.3 78.2 + - + +
378A SER 3.7 1.0 + - - -
379A LEU* 5.4 0.3 - - - +
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Residues in contact with PHE 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A MET 4.4 1.3 - - - -
285A VAL* 3.6 29.4 - - + -
286A PHE* 3.7 21.5 - + + -
289A LEU* 4.1 2.2 - - + -
297A LEU* 4.0 21.1 - - + -
373A PHE* 3.1 54.3 + + + +
374A ILE* 3.4 4.5 - - - +
376A LEU* 1.3 91.4 - - + +
378A SER* 1.3 55.3 + - - +
379A LEU* 3.0 6.7 + - - -
390A VAL* 3.8 30.6 - - + +
393A ALA* 4.1 9.9 - - + -
394A GLN* 2.9 42.9 + - + +
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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