Contacts of the helix formed by residues 444 - 459 (chain J) in PDB entry 5G04
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 TRP 444 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G PRO* 3.4 26.9 - - + -
215J PRO* 6.0 0.9 - - + -
244J ASN 4.3 7.6 + - - -
245J CYS* 4.4 7.9 - - - -
402J PRO* 3.7 34.3 - - + -
403J PHE* 3.6 45.3 - + - -
406J HIS* 4.3 9.6 - + + -
428J ALA* 6.0 0.4 - - + -
432J ILE* 3.2 26.8 - - + +
439J VAL* 4.6 9.9 - - + -
441J VAL* 3.0 38.8 - - + -
442J ASP 3.2 0.6 - - - -
443J LYS* 1.3 78.9 - - + +
445J GLU* 1.3 66.3 + - - +
446J PRO* 3.0 2.7 - - - -
447J LEU* 2.8 38.9 + - + +
448J LEU* 3.2 15.6 + - + +
474J LEU* 3.9 3.8 - - + -
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Residues in contact with GLU 445 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G LYS* 5.8 3.6 - - - +
8G ARG* 3.5 28.3 + - - +
442J ASP* 3.4 13.5 - - - +
443J LYS 3.3 0.4 - - - -
444J TRP* 1.3 78.5 - - - +
446J PRO* 1.4 71.1 - - - +
448J LEU* 3.6 4.8 + - - +
449J ASN* 3.3 16.1 + - - +
471J ALA* 4.2 8.0 - - + +
474J LEU* 3.3 19.2 - - + +
475J ILE* 3.1 52.4 - - + +
478J ASN* 4.8 2.2 + - - -
152P ARG* 5.8 0.5 + - - -
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Residues in contact with PRO 446 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G LYS* 5.6 2.7 - - + -
6G PRO* 3.6 40.2 - - + +
7G THR 4.2 6.5 - - - +
8G ARG* 3.8 29.4 - - + +
443J LYS 2.9 20.0 - - - +
444J TRP 3.2 1.3 - - - -
445J GLU* 1.4 104.4 - - + +
447J LEU* 1.3 57.7 + - - +
449J ASN* 3.4 1.4 + - - +
450J ASN* 2.8 35.2 + - - -
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Residues in contact with LEU 447 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402J PRO* 6.1 0.2 - - + -
406J HIS* 3.6 26.9 - - + +
425J PHE* 3.8 21.0 - - + +
428J ALA* 3.9 11.9 - - + -
429J LEU* 4.2 14.1 - - + +
432J ILE* 3.8 29.6 - - + -
439J VAL* 5.4 0.2 - - + -
444J TRP* 2.8 39.9 + - + +
446J PRO* 1.3 80.2 - - - +
448J LEU* 1.3 64.8 + - + +
450J ASN* 3.2 3.3 + - - +
451J LEU* 2.9 49.3 + - + +
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Residues in contact with LEU 448 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429J LEU* 4.1 28.9 - - + -
439J VAL* 3.6 38.1 - - + -
444J TRP* 3.2 29.9 + - + +
445J GLU 4.1 1.1 - - - +
446J PRO 3.3 0.2 - - - -
447J LEU* 1.3 84.5 - - + +
449J ASN* 1.3 61.2 + - - +
451J LEU* 3.3 9.1 + - + +
452J GLY 3.1 17.8 + - - -
467J TYR* 3.8 18.1 - - + +
470J GLN* 4.1 17.3 - - + +
471J ALA* 3.9 25.4 - - + +
474J LEU* 4.2 13.9 - - + -
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Residues in contact with ASN 449 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ARG* 3.3 58.7 + - - +
9G LEU 3.2 23.2 + - - -
10G GLU* 4.8 0.4 + - - +
445J GLU 3.3 5.4 + - - +
446J PRO 3.5 4.2 + - - +
448J LEU* 1.3 76.5 - - - +
450J ASN* 1.3 72.8 + - - +
452J GLY* 3.1 3.6 + - - -
453J HIS* 3.0 38.4 + - - -
468J HIS* 3.9 16.1 + - + -
471J ALA* 3.9 10.6 - - + +
480J SER 5.9 0.2 - - - -
481J THR* 5.7 1.2 - - + +
484J ALA* 5.0 1.6 - - - +
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Residues in contact with ASN 450 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G THR 3.0 14.3 + - - -
8G ARG* 4.2 0.4 - - - +
9G LEU* 2.9 39.6 + - + +
406J HIS* 2.8 38.8 + - + -
410J VAL* 3.8 7.5 - - - +
425J PHE* 3.9 13.5 - - + -
446J PRO 2.8 20.5 + - - +
447J LEU 3.6 4.0 - - - +
449J ASN* 1.3 80.4 + - - +
451J LEU* 1.3 58.2 - - - +
453J HIS* 3.2 5.9 + - - +
454J VAL* 3.0 33.9 + - - +
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Residues in contact with LEU 451 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422J GLU* 6.3 0.7 - - + -
425J PHE* 3.9 20.2 - - + +
426J LEU* 4.8 11.9 - - + +
429J LEU* 3.7 20.2 - - + -
447J LEU* 2.9 53.5 + - + +
448J LEU* 3.3 10.5 + - - +
450J ASN* 1.3 78.4 - - - +
452J GLY* 1.3 57.9 + - - +
454J VAL* 3.0 28.9 - - + +
455J CYS* 3.1 13.7 + - - -
463J GLU* 5.4 0.2 - - - +
467J TYR* 3.3 48.0 - - + +
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Residues in contact with GLY 452 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448J LEU 3.1 11.8 + - - -
449J ASN 3.1 4.0 + - - -
451J LEU* 1.3 77.9 - - - +
453J HIS* 1.3 61.3 + - - +
455J CYS 3.4 0.7 + - - -
456J ARG* 3.0 18.7 + - - +
464J ALA* 3.4 17.2 - - - +
467J TYR* 4.0 18.3 - - - +
468J HIS* 3.5 21.4 - - - -
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Residues in contact with HIS 453 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G LEU* 3.6 28.8 + - + -
10G GLU* 3.6 15.3 - - - -
11G LEU* 3.6 33.0 - - + +
15G ASP* 4.5 1.8 - - - -
413J PHE* 4.4 16.4 - + + -
449J ASN* 3.0 39.0 + - - +
450J ASN* 3.2 9.8 + - - +
452J GLY* 1.3 75.6 - - - +
454J VAL* 1.3 65.3 + - - +
456J ARG* 3.3 32.8 + - - +
457J LYS* 3.2 25.1 + - - +
468J HIS* 3.8 10.4 + - - -
484J ALA* 4.4 3.4 - - + -
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Residues in contact with VAL 454 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413J PHE* 3.5 26.7 - - + -
418J TRP* 4.8 3.8 - - - +
421J ALA* 4.4 4.3 - - + -
422J GLU* 3.9 33.0 - - + +
425J PHE* 3.3 26.7 - - + -
450J ASN 3.0 14.0 + - - +
451J LEU* 3.0 27.1 - - + +
453J HIS* 1.3 76.5 - - - +
455J CYS* 1.3 54.5 + - - +
457J LYS* 3.1 6.9 + - - +
458J LEU* 2.5 39.5 + - + +
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Residues in contact with CYS 455 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422J GLU* 4.4 9.9 - - - -
451J LEU* 3.1 27.7 + - - +
452J GLY 3.7 4.9 - - - +
454J VAL* 1.3 83.5 - - - +
456J ARG* 1.3 59.9 - - - +
458J LEU* 3.3 9.2 + - - +
459J LYS 3.1 3.8 + - - -
460J LYS* 3.0 35.5 + - + +
463J GLU* 3.6 34.3 - - + -
464J ALA* 3.8 20.2 - - + +
467J TYR* 4.2 8.3 - - - -
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Residues in contact with ARG 456 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G LEU* 3.5 9.7 - - - +
15G ASP* 3.3 25.3 + - - +
18G GLU* 2.8 40.2 + - - +
452J GLY 3.0 13.3 + - - +
453J HIS* 3.3 38.6 + - - +
455J CYS* 1.3 74.4 - - - +
457J LYS* 1.3 75.2 + - - +
459J LYS* 3.2 13.7 + - - +
461J TYR* 4.1 20.4 - - + -
464J ALA* 3.8 5.9 - - + +
468J HIS* 4.8 3.4 - - + -
484J ALA* 4.9 3.0 + - - +
487J TYR* 3.2 39.0 + - - -
488J ILE* 3.3 32.5 - - + +
491J LEU* 4.9 2.8 - - + +
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Residues in contact with LYS 457 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G ASP 4.8 2.0 + - - -
15G ASP* 3.5 36.0 + - - +
18G GLU* 3.4 40.1 + - - +
413J PHE* 4.2 11.9 - - + -
418J TRP* 3.5 57.8 + - + -
453J HIS 3.4 11.9 - - - +
454J VAL 3.1 8.6 + - - +
456J ARG* 1.3 96.3 - - - +
458J LEU* 1.3 61.1 + - - +
459J LYS* 3.3 8.5 + - - +
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Residues in contact with LEU 458 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418J TRP* 4.5 13.9 - - + +
419J LYS* 4.1 28.7 - - + +
422J GLU* 3.4 34.8 - - + +
454J VAL* 2.5 50.5 + - + +
455J CYS* 3.3 11.6 + - - +
457J LYS* 1.3 73.7 - - - +
459J LYS* 1.3 65.8 + - - +
460J LYS* 3.2 34.2 + - + +
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Residues in contact with LYS 459 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G GLU* 3.5 45.8 + - - +
21G ASN* 5.5 5.1 - - - +
22G ILE* 5.2 7.1 - - + +
455J CYS 3.1 3.0 + - - -
456J ARG 3.2 6.8 + - - +
457J LYS 3.1 6.9 - - - +
458J LEU* 1.3 81.2 - - - +
460J LYS* 1.3 59.2 + - - +
461J TYR* 3.0 54.5 + - + +
491J LEU* 4.4 4.4 - - - +
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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