Contacts of the helix formed by residues 419 - 430 (chain A) in PDB entry 4ZZH
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 PRO 419 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A ILE* 6.4 1.3 - - + -
361A GLN 4.3 11.7 - - - +
362A CYS* 3.5 23.3 - - - +
364A GLY* 4.8 4.0 - - - +
410A GLU 5.9 0.7 - - - +
412A VAL* 3.6 18.4 - - + -
417A ASN 3.5 2.2 - - - +
418A LEU* 1.3 87.0 - - + +
420A GLU* 1.3 62.2 + - - +
421A GLN* 3.0 13.5 + - + +
422A PHE* 3.2 23.4 + - + +
423A HIS* 4.2 4.3 + - - -
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Residues in contact with GLU 420 (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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418A LEU 3.5 3.3 + - - -
419A PRO* 1.3 72.1 - - - +
421A GLN* 1.3 62.2 + - - +
422A PHE 3.2 0.5 + - - -
423A HIS* 3.6 10.7 + - + +
424A ARG* 3.3 48.9 + - + +
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Residues in contact with GLN 421 (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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341A ARG* 5.7 2.4 - - - +
359A ILE 4.0 8.2 + - - -
360A ILE* 3.3 28.6 - - + +
419A PRO* 3.0 9.0 - - + +
420A GLU* 1.3 79.5 - - - +
422A PHE* 1.3 62.0 + - - +
424A ARG* 3.6 24.2 + - - +
425A ALA* 3.2 23.2 + - + +
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Residues in contact with PHE 422 (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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343A TYR* 3.8 25.8 - + - -
360A ILE* 4.1 14.5 - - + +
362A CYS* 4.0 17.3 - - + -
418A LEU* 5.0 5.6 - - + -
419A PRO* 3.2 19.2 + - + +
420A GLU 3.1 0.4 - - - -
421A GLN* 1.3 77.0 - - - +
423A HIS* 1.3 108.1 + + - +
425A ALA* 3.1 5.5 + - - +
426A MET* 3.1 51.7 + - + +
447A PRO* 3.5 43.3 - - + -
451A ILE* 4.4 4.5 - - + -
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Residues in contact with HIS 423 (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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417A ASN* 5.3 4.0 - - - -
418A LEU* 4.4 26.2 + - + +
419A PRO 4.3 7.0 + - - -
420A GLU* 3.6 10.1 + - + +
422A PHE* 1.3 108.4 - + - +
424A ARG* 1.3 63.7 + - - +
425A ALA 3.2 0.5 + - - -
426A MET* 3.4 5.2 + - + +
427A LYS* 3.2 23.6 + - - +
447A PRO* 5.8 0.6 - - - +
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Residues in contact with ARG 424 (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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420A GLU* 3.3 55.9 + - + +
421A GLN* 3.6 24.8 + - - +
422A PHE 3.3 0.6 - - - -
423A HIS* 1.3 79.1 - - - +
425A ALA* 1.3 62.3 + - - +
427A LYS* 3.8 7.2 + - - +
428A TYR* 3.7 15.8 + - - +
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Residues in contact with ALA 425 (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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341A ARG* 4.4 10.1 - - - +
343A TYR* 3.4 15.7 - - + +
360A ILE* 4.1 18.6 - - + -
421A GLN* 3.2 19.8 + - + +
422A PHE 3.1 5.5 + - - +
423A HIS 3.1 0.4 - - - -
424A ARG* 1.3 77.0 - - - +
426A MET* 1.3 59.4 + - - +
428A TYR* 3.2 6.2 + - - +
429A ASP* 2.8 36.0 + - - +
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Residues in contact with MET 426 (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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257A ILE* 6.0 1.8 - - - -
343A TYR* 3.7 23.8 - - - +
422A PHE* 3.1 40.3 + - + +
423A HIS* 3.4 8.9 + - + +
425A ALA* 1.3 73.4 - - - +
427A LYS* 1.3 66.0 + - - +
429A ASP* 4.3 4.0 - - - +
430A LYS* 2.9 38.1 + - + +
447A PRO 5.7 0.2 - - - +
450A LEU 5.2 0.9 - - - +
451A ILE* 4.0 32.1 - - + -
454A SER* 3.6 26.0 - - - +
455A ILE* 5.8 1.8 - - + -
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Residues in contact with LYS 427 (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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423A HIS 3.2 14.0 + - - +
424A ARG* 3.9 9.0 - - - +
426A MET* 1.3 78.6 - - - +
428A TYR* 1.3 60.3 + - - +
430A LYS* 4.0 17.2 - - - +
431A ASP* 3.8 16.9 - - - +
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Residues in contact with TYR 428 (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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255A LYS* 4.7 5.4 + - - -
340A LEU* 4.5 7.2 - - + -
341A ARG* 4.1 10.5 - - - -
358A ARG* 5.8 1.6 - - - -
424A ARG 3.7 8.6 + - - +
425A ALA* 3.2 8.6 + - - +
426A MET 3.1 0.2 - - - -
427A LYS* 1.3 81.2 - - - +
429A ASP* 1.3 85.7 + - - +
430A LYS 3.3 1.1 + - - -
431A ASP* 3.4 13.0 + - - +
432A GLU* 3.6 45.9 + - + +
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Residues in contact with ASP 429 (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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257A ILE* 4.0 15.5 - - + -
340A LEU* 3.6 21.9 - - + +
341A ARG* 2.8 44.2 + - - +
343A TYR* 2.7 25.1 + - - +
425A ALA 2.8 18.6 + - - +
426A MET* 3.1 3.6 + - - +
428A TYR* 1.3 80.7 - - - +
430A LYS* 1.3 66.0 + - - +
432A GLU* 3.0 2.5 + - - -
433A VAL* 3.0 29.1 + - - +
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Residues in contact with LYS 430 (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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257A ILE* 5.3 0.2 - - - -
426A MET* 2.9 25.8 + - + +
427A LYS* 4.0 19.3 - - - +
429A ASP* 1.3 78.8 - - - +
431A ASP* 1.3 84.6 + - - +
432A GLU 3.3 2.5 + - - -
433A VAL* 3.9 6.9 - - - +
454A SER* 4.2 18.4 + - - +
455A ILE* 4.2 23.6 - - + -
456A PRO* 3.2 28.2 - - + +
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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