Contacts of the helix formed by residues 438 - 451 (chain A) in PDB entry 4JJ7
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 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436A GLY 3.6 1.6 + - - -
437A ASP* 1.3 77.5 - - - +
439A ILE* 1.3 65.7 + - - +
440A LEU* 3.0 32.9 + - - +
441A THR* 2.8 29.3 + - - -
442A ILE* 3.0 20.4 + - - +
473A LYS* 3.5 40.8 - - + +
474A LEU 3.2 16.9 + - - +
475A VAL* 3.9 1.8 - - - -
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Residues in contact with ILE 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A PHE* 4.8 10.1 - - + -
400A LEU* 3.5 34.8 - - + -
425A LEU* 5.2 0.4 - - + -
429A LEU* 3.5 31.9 - - + -
438A ASP* 1.3 73.9 - - - +
440A LEU* 1.3 63.5 + - + +
442A ILE* 3.3 9.1 + - + -
443A LEU* 2.8 39.7 + - + +
470A LEU* 4.2 9.0 - - + -
474A LEU* 2.8 42.9 + - + +
476A PHE* 4.3 14.6 - - + -
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Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LEU* 4.0 22.7 - - + -
438A ASP* 3.0 12.6 + - - +
439A ILE* 1.3 84.6 - - + +
441A THR* 1.3 59.8 + - - +
443A LEU* 3.4 6.9 + - + +
444A THR* 2.9 33.2 + - - -
466A PRO* 5.2 4.0 - - + -
468A PHE* 3.6 54.3 - - + -
470A LEU* 4.4 9.4 - - + -
472A LYS 6.1 0.2 - - - +
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Residues in contact with THR 441 (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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432A ARG* 4.2 20.2 - - - +
437A ASP* 4.5 10.8 - - + +
438A ASP* 2.8 32.6 + - - -
440A LEU* 1.3 79.8 - - - +
442A ILE* 1.3 63.0 + - - +
444A THR* 3.2 9.3 + - - -
445A GLU* 3.1 19.9 + - - +
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Residues in contact with ILE 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A LEU* 5.1 2.0 - - + -
428A SER* 3.1 29.6 - - - +
429A LEU* 4.1 22.7 - - + +
432A ARG* 3.8 30.3 - - + +
433A CYS* 3.8 27.6 - - - +
437A ASP* 3.7 24.7 - - + +
438A ASP 3.0 11.5 + - - +
439A ILE* 3.7 12.1 - - + +
441A THR* 1.3 76.3 - - - +
443A LEU* 1.3 57.6 + - - +
445A GLU* 3.1 7.8 + - - +
446A VAL* 2.9 29.2 + - + +
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Residues in contact with LEU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A PHE* 4.2 7.9 - - + -
400A LEU* 4.0 37.5 - - + -
402A GLY* 5.0 2.9 - - - -
421A TYR* 3.9 19.3 - - + +
425A LEU* 3.8 28.3 - - + -
439A ILE* 2.8 31.5 + - + +
440A LEU* 4.0 7.4 - - + +
441A THR 3.3 0.2 - - - -
442A ILE* 1.3 72.5 - - - +
444A THR* 1.3 57.1 + - - +
446A VAL* 3.3 11.5 + - + +
447A ASN* 2.9 32.6 + - - +
466A PRO* 3.8 26.5 - - + -
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Residues in contact with THR 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A LEU 2.9 18.7 + - - -
441A THR* 3.4 12.8 - - - -
443A LEU* 1.3 73.0 - - - +
445A GLU* 1.3 60.0 + - - +
447A ASN* 3.1 14.4 + - + +
448A TYR* 2.9 26.6 + - + +
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Residues in contact with GLU 445 (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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428A SER* 2.8 29.5 + - - +
431A GLU* 5.5 1.4 - - - +
432A ARG* 2.4 49.8 + - - +
441A THR 3.1 10.8 + - - +
442A ILE 3.1 10.1 + - - +
444A THR* 1.3 73.9 - - - +
446A VAL* 1.3 59.5 + - - +
448A TYR* 3.1 9.8 + - + +
449A GLU* 2.8 42.5 + - + +
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Residues in contact with VAL 446 (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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421A TYR* 3.8 35.2 - - + -
424A SER* 3.7 20.2 - - - +
425A LEU* 3.7 32.5 - - + +
428A SER* 3.9 13.9 - - - -
442A ILE 2.9 19.3 + - - +
443A LEU* 3.6 14.1 - - + +
444A THR 3.3 0.2 - - - -
445A GLU* 1.3 74.4 - - - +
447A ASN* 1.3 64.3 + - - +
449A GLU 3.3 0.2 + - - -
450A VAL* 2.9 30.5 + - + +
464A PRO* 4.7 2.5 - - + -
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Residues in contact with ASN 447 (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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443A LEU 2.9 18.5 + - - +
444A THR* 3.1 15.1 + - + +
446A VAL* 1.3 77.2 - - - +
448A TYR* 1.3 59.6 + - - +
450A VAL* 4.4 0.2 - - - +
451A SER* 2.7 34.1 + - - -
463A MET* 3.7 20.8 - - + +
464A PRO* 3.3 34.4 + - - +
465A GLN 4.1 0.7 + - - -
466A PRO* 3.8 21.2 - - - +
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Residues in contact with TYR 448 (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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374A ASP* 2.7 36.8 + - - +
444A THR* 2.9 13.6 + - + +
445A GLU* 3.1 12.1 + - + +
447A ASN* 1.3 78.4 - - - +
449A GLU* 1.3 82.1 + - + +
451A SER* 3.4 11.2 + - - -
452A ASN* 3.3 41.9 + - - +
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Residues in contact with GLU 449 (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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424A SER* 3.7 19.3 - - - +
427A GLN* 5.7 2.7 - - - +
428A SER* 6.5 0.2 - - - -
445A GLU* 2.8 37.9 + - + +
446A VAL* 5.0 0.2 - - - -
448A TYR* 1.3 88.8 - - + +
450A VAL* 1.3 66.3 + - - +
452A ASN* 3.1 21.7 + - - +
453A LYS* 3.7 11.9 - - - +
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Residues in contact with VAL 450 (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 TRP* 3.9 23.8 - - + +
421A TYR* 4.3 4.0 - - - -
424A SER* 3.8 26.0 - - - -
446A VAL* 2.9 28.6 + - + +
449A GLU* 1.3 74.7 - - - +
451A SER* 1.3 61.2 + - - +
453A LYS* 3.1 26.8 + - + +
462A GLN* 3.5 38.3 + - + +
464A PRO* 3.7 22.0 - - + -
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Residues in contact with SER 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ASN 2.7 24.3 + - - -
448A TYR* 3.5 8.5 - - - -
449A GLU 3.2 0.2 - - - -
450A VAL* 1.3 77.1 - - - +
452A ASN* 1.3 61.7 + - - +
453A LYS 3.4 0.2 - - - -
461A LYS* 2.8 26.2 + - - +
462A GLN 4.0 8.1 + - - -
463A MET* 3.4 27.0 - - - +
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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