Contacts of the helix formed by residues 433 - 446 (chain A) in PDB entry 5JG8
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 LYS 433 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A LEU* 1.3 83.3 - - + +
434A SER* 1.3 73.3 + - - +
435A TRP 3.4 1.3 - - - +
436A SER* 3.4 3.9 + - - -
437A TRP* 3.0 60.1 + - - +
601A ALA* 4.6 4.9 - - - +
602A ASP* 3.1 34.1 - - - +
705A NAG 3.9 23.2 + - - +
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Residues in contact with SER 434 (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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171A PHE 5.2 1.4 + - - -
172A SER 3.8 4.0 + - - -
173A SER* 3.5 16.5 + - - -
174A TRP* 3.5 34.1 - - - -
432A LEU* 4.8 0.8 - - - +
433A LYS* 1.3 78.7 - - - +
435A TRP* 1.3 63.8 + - - +
437A TRP* 3.3 0.9 + - - -
438A ASN* 2.4 34.2 + - - -
705A NAG 3.0 26.7 + - - -
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Residues in contact with TRP 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A TRP* 3.6 31.4 - + + -
380A LEU* 4.5 4.5 - - + -
382A MET* 4.2 17.7 - - + -
384A PHE* 3.6 27.7 + - - +
385A CYS* 3.2 42.1 - - + +
398A ASP* 4.9 2.0 + - - -
399A PRO* 4.3 10.5 - - + +
402A GLN* 4.0 26.5 - - + +
403A LEU* 3.3 34.2 - - + +
428A PRO* 5.2 2.0 - - + -
431A CYS* 4.7 3.4 - - + -
432A LEU* 5.0 10.6 - - + +
433A LYS 3.4 0.8 - - - +
434A SER* 1.3 79.6 - - - +
436A SER* 1.3 65.9 + - - +
438A ASN* 3.2 2.1 + - - +
439A TYR* 2.9 54.2 + + + -
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Residues in contact with SER 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A PRO* 4.9 2.2 - - - +
429A GLY 3.6 10.5 + - - +
431A CYS* 4.2 15.9 - - - +
433A LYS 3.4 9.7 + - - -
434A SER 3.3 0.4 - - - -
435A TRP* 1.3 82.2 - - - +
437A TRP* 1.3 58.6 + - - +
439A TYR* 3.1 6.1 + - - +
440A TYR* 2.9 29.1 + - - +
599A ALA 3.8 2.3 + - - +
600A ARG* 3.2 10.0 - - - -
601A ALA* 2.7 42.4 + - - -
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Residues in contact with TRP 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A LYS* 3.0 54.8 + - + +
434A SER 3.8 3.1 - - - +
436A SER* 1.3 76.9 - - - +
438A ASN* 1.3 59.6 + - - +
440A TYR* 3.5 1.9 + - - +
441A ARG* 2.9 28.6 + - - +
469A GLU* 4.2 10.1 - - + +
600A ARG* 3.4 54.4 - - + +
601A ALA 3.3 20.5 + - - -
602A ASP* 4.6 0.4 - - - +
603A SER* 3.3 19.7 - - - -
705A NAG 4.1 38.1 - - - +
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Residues in contact with ASN 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A TRP* 3.2 32.5 + - - -
175A ASN* 3.3 6.8 + - - +
176A ILE* 3.0 37.4 + - + +
403A LEU* 3.8 15.9 - - + -
434A SER* 2.4 35.1 + - - +
435A TRP 3.7 3.4 - - - +
437A TRP* 1.3 73.6 - - - +
439A TYR* 1.3 64.2 + - - +
441A ARG* 3.3 13.4 + - - +
442A ILE* 2.9 32.6 + - + +
705A NAG 4.6 4.9 + - - -
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Residues in contact with TYR 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LEU* 3.8 21.3 - - + -
382A MET* 5.6 0.9 - - + -
403A LEU* 4.2 8.0 - - + +
406A LEU* 3.9 13.2 - - + -
422A ILE* 3.2 29.3 - - + +
428A PRO* 3.6 30.1 - - + -
435A TRP* 2.9 42.2 + + + +
436A SER* 3.5 9.0 - - - +
438A ASN* 1.3 75.0 - - - +
440A TYR* 1.3 66.4 + - - +
442A ILE* 2.8 19.5 + - + +
443A VAL* 2.9 33.6 + - + +
453A GLN* 2.9 28.7 + - - -
455A PHE* 3.8 8.5 - + - -
466A PHE* 4.0 6.1 - + - -
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Residues in contact with TYR 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A SER 2.9 13.9 + - - +
437A TRP 3.6 5.4 - - - +
439A TYR* 1.3 76.0 - - - +
441A ARG* 1.3 62.3 + - - +
443A VAL* 3.1 10.5 - - + +
444A ALA* 2.9 26.7 + - + +
465A VAL 4.0 0.7 + - - -
466A PHE* 3.5 17.4 - + + -
467A TYR* 2.6 63.5 + - + +
468A ASP 5.0 4.5 - - - -
469A GLU* 4.8 7.6 - - + -
472A LEU* 5.5 2.0 - - + -
599A ALA* 3.6 30.0 + - + -
600A ARG* 3.3 52.7 - - + +
606A LEU* 4.0 13.3 - - + +
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Residues in contact with ARG 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASN* 4.5 11.2 - - - +
176A ILE* 3.7 27.3 - - - +
177A SER* 3.8 12.3 - - - +
178A LEU* 3.4 47.5 - - + +
437A TRP 2.9 16.0 + - - +
438A ASN* 3.5 18.2 + - - +
440A TYR* 1.3 76.2 - - - +
442A ILE* 1.3 57.1 + - - +
444A ALA* 3.7 2.5 - - - +
445A ARG* 3.0 27.7 + - - +
469A GLU* 3.2 37.4 + - - +
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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
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176A ILE* 4.3 10.3 - - + -
178A LEU* 4.0 17.0 - - + -
403A LEU* 3.9 29.2 - - + +
406A LEU* 4.7 6.5 - - + -
407A VAL* 3.6 23.1 - - + -
410A LEU* 3.2 33.9 - - + -
438A ASN 2.9 22.7 - - - +
439A TYR* 2.8 15.4 + - + +
441A ARG* 1.3 69.2 - - - +
443A VAL* 1.3 68.4 + - + +
445A ARG* 3.0 4.0 + - - -
446A TYR* 2.8 39.9 + - + +
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Residues in contact with VAL 443 (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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410A LEU* 5.9 0.9 - - + -
422A ILE* 5.4 0.7 - - + -
439A TYR* 2.9 48.6 + - + +
440A TYR* 3.1 12.1 - - + +
442A ILE* 1.3 73.6 - - + +
444A ALA* 1.3 67.7 + - + +
446A TYR* 3.1 5.5 + - - +
447A GLU* 3.0 27.2 + - - +
450A LEU* 4.3 14.2 - - + +
453A GLN* 4.1 18.4 - - - +
466A PHE* 3.3 32.1 - - + -
476A LEU* 4.0 12.3 - - + +
477A ALA* 5.5 0.4 - - + +
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Residues in contact with ALA 444 (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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183A LYS* 3.2 14.0 + - - +
440A TYR* 2.9 14.9 + - + +
441A ARG 3.7 4.5 - - - +
443A VAL* 1.3 82.9 - - + +
445A ARG* 1.3 62.7 + - - +
447A GLU* 2.9 19.3 - - - +
467A TYR 4.2 6.3 - - - +
468A ASP* 4.8 0.4 - - - -
469A GLU* 4.3 21.5 - - + +
476A LEU* 3.5 28.0 - - + -
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Residues in contact with ARG 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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178A LEU* 3.8 24.4 - - + +
179A PRO* 5.4 4.8 + - - +
181A VAL* 3.3 24.9 + - - +
182A PRO 3.8 1.6 + - - -
183A LYS* 3.5 45.1 - - - +
184A PRO* 3.6 10.9 - - - +
411A GLN* 3.6 13.5 + - - -
414A GLU* 2.7 34.7 + - - -
441A ARG 3.0 18.8 + - - +
442A ILE 3.0 4.0 + - - +
444A ALA* 1.3 77.9 - - - +
446A TYR* 1.3 86.2 + - + +
447A GLU 3.4 2.4 + - - -
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Residues in contact with TYR 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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178A LEU* 4.7 4.5 - - + -
179A PRO* 3.4 18.2 - - - +
407A VAL* 3.7 11.9 - - + +
410A LEU* 3.9 31.4 - - + -
411A GLN* 3.0 54.3 + - - +
414A GLU* 4.1 10.8 - - + -
442A ILE* 2.8 44.1 + - + +
443A VAL* 3.4 4.9 - - - +
445A ARG* 1.3 100.3 - - + +
447A GLU* 1.3 64.1 + - - +
448A ASN 3.4 2.0 - - - -
449A THR* 2.8 25.2 + - - -
450A LEU* 3.0 14.5 + - + +
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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
------------------------------------------------------------
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