Contacts of the helix formed by residues 373 - 393 (chain A) in PDB entry 4ZSL
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 THR 373 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL* 4.8 3.4 - - - -
371A ALA 4.4 0.6 + - - +
372A LEU* 1.3 77.7 - - - +
374A ARG* 1.3 64.3 + - - +
375A GLU* 3.7 7.4 + - - +
376A ARG* 3.2 34.6 + - + +
377A ILE* 3.0 22.5 + - - +
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Residues in contact with ARG 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 3.5 17.8 - - - +
91A ASP* 2.8 45.6 + - - +
92A VAL* 3.9 1.6 - - - +
93A VAL* 3.5 34.3 - - + +
96A ALA* 5.2 2.8 - - + +
373A THR* 1.3 71.7 - - - +
375A GLU* 1.3 63.3 + - - +
377A ILE* 3.2 10.2 + - - +
378A LYS* 3.0 23.0 + - - +
405A GOL 3.5 45.7 + - - +
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Residues in contact with GLU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TYR* 2.7 40.7 + - - -
373A THR* 3.2 7.6 + - - +
374A ARG* 1.3 76.6 - - - +
376A ARG* 1.3 57.9 + - + +
378A LYS* 3.2 14.2 + - - +
379A GLU* 2.9 42.1 + - - +
405A GOL 3.2 32.6 + - - +
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Residues in contact with ARG 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ALA 5.5 0.7 - - - -
372A LEU* 4.0 33.8 - - + +
373A THR* 3.2 31.2 + - - +
375A GLU* 1.3 76.7 - - + +
377A ILE* 1.3 55.7 - - - +
379A GLU* 3.4 21.2 + - - +
380A ALA* 3.1 26.0 + - - +
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Residues in contact with ILE 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A VAL* 4.0 17.0 - - + +
96A ALA* 3.4 40.2 - - + +
97A LYS* 3.7 29.8 - - + +
100A LEU* 4.3 11.4 - - + -
372A LEU* 3.5 33.9 - - + +
373A THR 3.0 22.5 + - - +
374A ARG* 3.2 8.3 + - - +
376A ARG* 1.3 72.1 - - - +
378A LYS* 1.3 60.3 + - - +
380A ALA* 3.1 7.3 + - - +
381A ILE* 2.8 34.7 + - + +
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Residues in contact with LYS 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 3.6 46.9 - - + -
127A TYR* 2.9 53.9 + - + +
128A GLY* 3.9 10.1 + - - -
130A PHE* 2.9 31.6 + - - -
131A LYS* 5.6 0.8 - - - +
374A ARG 3.0 12.9 + - - +
375A GLU* 3.3 23.7 + - - +
377A ILE* 1.3 76.0 - - - +
379A GLU* 1.4 55.7 + - - +
381A ILE* 3.3 1.9 + - - +
382A VAL* 2.9 36.4 + - + +
405A GOL 4.4 4.8 + - - +
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Residues in contact with GLU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TYR* 3.3 19.4 + - + +
375A GLU* 2.9 30.9 + - - +
376A ARG* 3.4 24.7 + - - +
377A ILE 3.2 0.2 - - - -
378A LYS* 1.4 75.1 - - - +
380A ALA* 1.4 56.0 + - - +
382A VAL* 3.6 5.2 + - - +
383A ALA* 2.9 28.6 + - - +
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Residues in contact with ALA 380 (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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100A LEU* 3.8 27.8 - - + -
372A LEU* 5.1 5.6 - - + -
376A ARG 3.1 13.5 + - - +
377A ILE* 3.1 8.0 + - - +
379A GLU* 1.4 74.6 - - - +
381A ILE* 1.4 58.0 + - - +
383A ALA* 3.3 7.9 + - - +
384A GLU* 3.0 32.7 + - - +
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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
----------------------------------------------------------
89A ALA 5.1 0.4 - - - +
90A PHE* 3.8 32.5 - - + -
96A ALA* 3.5 26.0 - - - +
99A THR* 4.0 15.7 - - + -
100A LEU* 3.9 25.6 - - + +
103A LEU* 3.8 18.2 - - + -
133A VAL* 4.4 9.6 - - + -
377A ILE* 2.8 27.9 + - + +
378A LYS 3.8 3.1 - - - +
380A ALA* 1.4 67.3 - - - +
382A VAL* 1.3 66.4 + - - +
384A GLU* 3.0 8.1 + - - +
385A ILE* 3.0 34.5 + - + +
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Residues in contact with VAL 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 5.0 0.7 - - + -
123A PRO* 5.1 12.1 - - + -
127A TYR* 3.8 32.5 - - + -
130A PHE* 3.9 31.9 - - + -
378A LYS* 2.9 23.5 + - + +
379A GLU* 3.8 4.9 - - - +
381A ILE* 1.3 75.3 - - - +
383A ALA* 1.4 61.3 + - - +
385A ILE* 3.2 10.5 + - + +
386A GLU* 3.1 42.7 + - + +
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Residues in contact with ALA 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A GLU 2.9 18.8 + - - +
380A ALA* 3.6 9.4 - - - +
381A ILE 3.3 0.2 - - - -
382A VAL* 1.4 74.8 - - - +
384A GLU* 1.4 59.9 + - - +
386A GLU* 3.4 16.1 + - - +
387A ASP* 2.9 30.9 + - - +
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Residues in contact with GLU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 3.8 17.5 - - + +
103A LEU* 4.5 17.9 - - + -
104A LYS* 3.3 41.0 + - + +
107A LYS* 2.7 55.8 + - + +
120A ILE* 5.0 1.3 - - - -
380A ALA 3.0 18.4 + - - +
381A ILE* 3.0 10.7 + - - +
383A ALA* 1.4 74.8 - - - +
385A ILE* 1.3 58.7 + - - +
387A ASP* 4.4 3.0 - - - +
388A PHE* 3.0 16.6 + - - +
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Residues in contact with ILE 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 4.9 3.6 - - + -
120A ILE* 3.7 31.6 - - + -
121A LEU 4.0 15.7 - - - +
122A ARG* 4.2 11.7 - - + -
123A PRO* 4.7 6.7 - - + -
130A PHE* 3.9 33.9 - - + -
133A VAL* 4.4 5.2 - - + -
381A ILE* 3.0 31.1 + - + +
382A VAL* 3.2 10.1 + - + +
384A GLU* 1.3 74.2 - - - +
386A GLU* 1.3 64.8 + - + +
388A PHE* 3.4 6.8 - - - +
389A HIS* 3.1 45.1 + - + +
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Residues in contact with GLU 386 (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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122A ARG* 6.4 0.2 - - - -
382A VAL* 3.1 34.3 + - + +
383A ALA* 3.6 16.7 - - - +
385A ILE* 1.3 76.0 - - + +
387A ASP* 1.4 55.4 + - - +
389A HIS* 3.2 7.0 + - - +
390A ALA* 2.9 30.7 + - - +
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Residues in contact with ASP 387 (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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107A LYS* 2.8 28.4 + - - +
383A ALA 2.9 16.8 + - - +
384A GLU* 4.4 2.9 - - - +
385A ILE 3.4 0.2 - - - -
386A GLU* 1.4 71.0 - - - +
388A PHE* 1.4 58.2 + - - +
390A ALA* 3.3 7.0 + - - +
391A ARG* 2.8 72.6 + - - +
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Residues in contact with PHE 388 (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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107A LYS* 3.6 25.2 - - + +
117A ILE* 3.7 23.6 - - + -
118A LYS 3.8 7.6 - - - -
119A ASP* 3.6 42.6 - - - -
120A ILE* 3.9 24.2 - - + -
384A GLU 3.0 14.3 + - - +
385A ILE 3.4 9.2 - - - +
386A GLU 3.3 0.2 - - - -
387A ASP* 1.4 77.0 - - - +
389A HIS* 1.3 75.5 + + - +
391A ARG* 3.6 4.8 + - - +
392A ARG* 3.4 46.9 + - + +
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Residues in contact with HIS 389 (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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119A ASP* 3.1 26.9 - - - -
120A ILE 2.6 23.6 + - - -
122A ARG* 3.1 60.6 + - + +
385A ILE* 3.1 25.9 + - + +
386A GLU* 3.2 9.8 + - - +
388A PHE* 1.3 83.6 - + - +
390A ALA* 1.3 62.3 + - - +
391A ARG 3.4 0.2 - - - -
392A ARG* 3.6 19.9 + - - +
393A GLU* 3.2 22.5 + - - +
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Residues in contact with ALA 390 (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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386A GLU 2.9 17.8 + - - +
387A ASP* 3.7 9.4 - - - +
389A HIS* 1.3 75.2 - - - +
391A ARG* 1.4 63.5 + - + +
393A GLU 3.3 21.3 - - - -
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Residues in contact with ARG 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS* 5.5 2.7 - - - +
387A ASP* 2.8 57.6 + - - +
388A PHE* 4.0 6.1 - - - +
390A ALA* 1.4 75.3 - - + +
392A ARG* 1.4 61.4 + - + +
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Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LYS 3.2 23.8 + - - -
119A ASP* 3.4 28.0 + - - +
122A ARG* 5.3 2.2 - - - +
388A PHE* 3.4 33.6 + - + +
389A HIS* 3.8 22.2 + - - +
390A ALA 3.3 0.4 - - - -
391A ARG* 1.4 78.7 - - + +
393A GLU* 1.4 61.1 + - + +
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Residues in contact with GLU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A HIS 3.2 12.2 + - - +
390A ALA* 3.3 21.9 + - - -
392A ARG* 1.4 80.5 - - + +
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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
------------------------------------------------------------
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