Contacts of the helix formed by residues 373 - 386 (chain A) in PDB entry 2Z1Z
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 SER 373 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A GLN* 1.3 76.0 - - - +
374A SER* 1.3 59.8 + - - +
375A TRP* 3.5 9.4 + - - +
376A ASP* 3.1 41.0 + - - +
377A VAL* 3.0 26.7 + - - +
400A GLU* 3.4 15.1 + - - -
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Residues in contact with SER 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLN 3.6 0.8 + - - -
373A SER* 1.3 70.1 + - - +
375A TRP* 1.3 59.6 + - - +
377A VAL* 3.8 7.4 - - - +
378A PHE* 2.9 30.7 + - - +
391A PRO* 3.4 6.1 - - - +
392A GLY 3.5 6.4 + - - -
393A SER* 2.9 35.5 + - - -
400A GLU* 2.6 17.8 + - - -
401A GLY* 3.8 9.9 - - - -
402A PHE 3.2 27.8 - - - -
403A VAL* 4.4 2.4 - - - +
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Residues in contact with TRP 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.9 15.0 - - + -
41A GLU* 4.1 17.5 - - + -
42A ILE* 3.4 30.3 - - + -
45A ARG* 3.6 42.8 + - - +
373A SER* 3.2 8.1 + - - +
374A SER* 1.3 81.2 + - - +
376A ASP* 1.3 57.7 + - - +
378A PHE* 3.5 14.5 - + - +
379A ALA* 3.1 27.0 + - - +
391A PRO* 3.5 20.5 - - + +
393A SER* 3.4 27.3 + - - -
394A GLY* 4.4 5.3 - - - +
400A GLU* 5.6 1.3 - - - -
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Residues in contact with ASP 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLN* 5.7 1.8 - - + -
373A SER* 3.1 33.9 + - - +
375A TRP* 1.3 74.1 - - - +
377A VAL* 1.3 69.2 + - + +
379A ALA* 3.2 7.3 + - - +
380A GLU* 2.9 23.7 + - - +
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Residues in contact with VAL 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A PHE* 3.9 30.5 - - + -
372A GLN* 3.6 32.5 - - + +
373A SER 3.0 16.1 + - - +
374A SER* 3.4 6.7 + - - +
376A ASP* 1.3 75.1 - - + +
378A PHE* 1.3 62.9 + - - +
380A GLU* 3.1 10.8 + - - +
381A ILE* 2.9 45.6 + - + +
403A VAL* 3.9 15.7 - - + -
425A TYR* 4.0 4.7 - - - +
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Residues in contact with PHE 378 (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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42A ILE* 4.1 20.0 - - + -
45A ARG* 3.8 45.1 - - + -
46A ARG* 5.9 0.2 - - + -
374A SER 2.9 18.6 + - - +
375A TRP* 3.5 18.2 - + - +
377A VAL* 1.3 75.4 - - - +
379A ALA* 1.3 62.6 + - - +
381A ILE* 4.0 2.4 - - - +
382A LEU* 3.0 46.0 + - + +
387A VAL 4.9 0.5 - - - +
388A VAL* 3.9 14.6 - - + -
389A THR* 3.2 47.9 + - - +
391A PRO* 3.9 20.6 - - + -
403A VAL* 5.0 1.2 - - + +
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Residues in contact with ALA 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ARG* 4.2 24.0 - - - +
375A TRP 3.1 18.4 + - - +
376A ASP* 3.2 6.5 + - - +
378A PHE* 1.3 81.3 - - - +
380A GLU* 1.3 55.7 + - - +
382A LEU* 3.5 5.0 + - - +
383A GLU* 3.0 31.7 + - - +
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Residues in contact with GLU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLN* 5.2 4.9 - - - +
376A ASP 2.9 16.1 + - - +
377A VAL* 3.5 12.6 - - - +
379A ALA* 1.3 70.7 - - - +
381A ILE* 1.3 60.1 + - - +
383A GLU* 4.0 2.2 - - - +
384A LYS* 2.9 71.9 + - + +
424A LEU* 4.8 7.0 - - + +
425A TYR* 3.7 24.9 + - - -
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Residues in contact with ILE 381 (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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349A PHE* 5.8 2.9 - - + -
369A PHE* 4.5 5.6 - - + -
377A VAL* 2.9 39.7 + - + +
378A PHE 4.0 2.5 - - - +
380A GLU* 1.3 72.6 - - - +
382A LEU* 1.3 60.2 + - - +
385A THR* 2.6 53.7 + - + +
386A HIS 3.5 0.2 + - - -
387A VAL* 3.6 14.1 - - + +
389A THR* 4.1 25.4 - - + +
403A VAL* 4.5 8.3 - - + -
421A PHE* 3.7 24.7 - - + -
424A LEU* 4.4 8.3 - - + -
425A TYR* 3.3 26.5 - - + +
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Residues in contact with LEU 382 (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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45A ARG* 3.8 20.2 - - + +
46A ARG* 4.3 11.2 - - + -
49A HIS* 3.3 47.7 - - + +
58A VAL* 4.9 3.4 - - + -
378A PHE* 3.0 42.0 + - + +
379A ALA* 3.9 4.5 - - - +
381A ILE* 1.3 76.5 - - - +
383A GLU* 1.3 56.6 + - - +
386A HIS* 2.8 34.1 + - - -
387A VAL 3.6 23.5 + - - +
388A VAL* 4.4 13.7 - - + +
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Residues in contact with GLU 383 (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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49A HIS* 3.7 10.5 + - - -
52A LYS* 3.0 26.4 + - - +
53A TYR* 2.4 41.0 + - - -
379A ALA 3.0 19.2 + - - +
380A GLU* 4.0 3.4 - - - +
382A LEU* 1.3 74.1 - - - +
384A LYS* 1.3 70.9 + - + +
386A HIS* 3.4 18.9 + - - -
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Residues in contact with LYS 384 (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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380A GLU* 2.9 56.4 + - + +
383A GLU* 1.3 83.3 - - + +
385A THR* 1.4 69.6 + - + +
386A HIS* 4.1 8.9 - - - -
424A LEU* 3.7 23.3 - - + -
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Residues in contact with THR 385 (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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381A ILE* 2.6 36.4 + - + +
384A LYS* 1.4 76.7 - - + +
386A HIS* 1.3 69.2 + - - +
387A VAL* 3.4 9.9 + - - +
420A ARG* 2.9 58.7 + - + +
421A PHE* 4.4 3.5 - - + +
424A LEU* 3.5 44.0 - - + -
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Residues in contact with HIS 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A HIS* 2.7 39.2 + + - +
53A TYR* 4.3 9.4 - + - +
56A ALA* 3.6 23.1 - - + +
57A GLN 3.7 16.2 + - - +
58A VAL* 3.3 9.7 - - + +
59A ILE 2.7 32.6 + - - +
382A LEU* 2.8 26.7 + - - -
383A GLU 3.4 16.0 + - - -
384A LYS 4.1 9.4 - - - -
385A THR* 1.3 73.4 + - - +
387A VAL* 1.3 54.1 + - - +
388A VAL 4.1 0.2 - - - -
420A ARG* 3.5 4.7 + - - -
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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