Contacts of the helix formed by residues 491 - 506 (chain D) in PDB entry 2JBG
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 SER 491 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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448D ASN* 3.5 23.3 - - - +
489D PHE* 3.1 2.6 - - - +
490D LYS* 1.3 83.9 - - - +
492D PHE* 1.3 66.0 + - - +
493D ASP* 3.9 10.0 + - - +
494D ASP* 2.9 32.6 + - - +
495D PHE 3.0 4.5 + - - -
556D TYR* 3.1 16.6 + - - -
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Residues in contact with PHE 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448D ASN 3.8 10.1 - - - +
491D SER* 1.3 70.5 - - - +
493D ASP* 1.3 55.4 + - - +
495D PHE* 2.7 27.4 + + + +
496D ARG* 2.7 59.0 + - - +
543D LEU* 3.6 43.5 - - + -
545D HIS* 3.2 41.1 - + + -
555D VAL 3.7 11.0 - - - +
556D TYR* 3.4 12.3 + + + -
561D ILE* 3.7 14.6 - - + -
1578D SO4 5.8 0.4 - - - -
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Residues in contact with ASP 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491D SER* 3.2 10.4 + - - +
492D PHE* 1.3 78.0 - - - +
494D ASP* 1.3 56.7 + - - +
496D ARG* 2.7 37.5 + - - +
497D LYS* 3.0 52.8 + - - +
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Residues in contact with ASP 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488D GLU 4.4 0.9 - - - +
489D PHE* 3.1 31.5 - - - -
490D LYS* 3.8 9.7 + - + +
491D SER* 2.9 29.7 + - - +
493D ASP* 1.3 78.4 - - - +
495D PHE* 1.3 62.6 + - - +
497D LYS* 3.4 10.2 + - - +
498D LYS* 3.1 24.6 + - - +
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Residues in contact with PHE 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453D ALA* 4.0 16.2 - - + -
476D VAL* 5.6 1.3 - - + -
484D LEU* 3.6 26.9 - - + -
489D PHE* 3.8 32.9 - + + -
491D SER 3.0 4.6 + - - -
492D PHE* 2.7 28.3 + + - +
494D ASP* 1.3 77.2 - - - +
496D ARG* 1.3 54.0 + - - +
498D LYS* 3.3 1.6 + - - +
499D PHE* 2.7 51.7 + + + +
543D LEU* 4.4 8.3 - - + -
556D TYR* 3.9 29.6 - + + -
558D MET* 3.9 21.1 - - + -
561D ILE* 3.9 22.2 - - + -
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Residues in contact with ARG 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492D PHE* 2.7 35.9 + - + +
493D ASP* 2.7 49.7 + - - +
495D PHE* 1.3 73.8 - - - +
497D LYS* 1.3 65.1 + - + +
499D PHE* 3.2 6.5 + - - +
500D TRP* 3.1 49.9 + - + +
524D GLY 4.9 3.4 - - - +
526D ALA* 5.6 5.2 - - - +
541D PHE 6.0 1.6 - - - -
542D GLU* 6.3 0.9 - - - +
543D LEU* 4.0 26.5 + - + +
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Residues in contact with LYS 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ALA 5.9 2.9 - - - -
493D ASP* 3.0 36.3 + - - +
494D ASP* 3.8 10.5 - - - +
495D PHE 3.3 0.2 - - - -
496D ARG* 1.3 77.5 - - + +
498D LYS* 1.3 64.6 + - - +
500D TRP 3.4 0.3 + - - -
501D GLU* 3.0 34.2 + - - +
523D VAL 5.2 4.3 - - - +
524D GLY* 3.3 30.6 - - - +
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Residues in contact with LYS 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483D LYS 4.4 1.0 + - - -
484D LEU* 3.6 15.0 - - + +
487D LYS* 3.8 32.0 - - - +
489D PHE* 3.7 21.5 - - + -
494D ASP* 3.1 16.5 + - - +
495D PHE 3.6 3.6 - - - +
497D LYS* 1.3 78.7 - - - +
499D PHE* 1.3 62.6 + - - +
501D GLU* 3.2 15.4 + - + +
502D GLU* 3.0 48.8 + - - +
505D LYS* 5.4 0.4 - - - +
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Residues in contact with PHE 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D TRP* 3.8 26.0 - + - -
476D VAL* 4.1 22.2 - - + -
477D PRO* 4.4 2.5 - - + -
480D ILE* 3.8 25.1 - - + -
484D LEU* 4.0 17.4 - - + +
495D PHE* 2.7 39.4 + + + +
496D ARG* 3.3 7.4 - - - +
497D LYS 3.2 0.2 - - - -
498D LYS* 1.3 71.8 - - - +
500D TRP* 1.3 111.3 + + - +
502D GLU* 3.1 6.9 + - - +
503D VAL* 3.1 26.7 + - + +
543D LEU* 4.2 14.8 - - + -
561D ILE* 6.2 0.4 - - + -
563D VAL* 4.0 8.3 - - + -
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Residues in contact with TRP 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D TRP* 4.1 19.3 - + - -
465D LEU* 4.6 2.9 - - + -
496D ARG* 3.1 42.9 + - + +
497D LYS 4.0 3.1 - - - +
499D PHE* 1.3 107.5 - + - +
501D GLU* 1.3 65.2 + - - +
503D VAL* 3.3 5.8 + - + +
504D SER 3.2 17.0 + - - -
513D PHE* 5.0 0.2 - + - -
521D MET* 3.2 35.6 - - - +
524D GLY 4.2 4.7 - - - -
525D LYS 4.0 11.9 - - - +
526D ALA* 3.4 32.2 - - + +
527D PRO* 3.4 35.0 - - + -
541D PHE* 4.3 12.1 + - + -
543D LEU* 4.4 10.0 - - + +
563D VAL* 4.0 22.0 - - + -
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Residues in contact with GLU 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA* 4.7 7.8 - - - +
497D LYS* 3.0 27.2 + - - +
498D LYS* 3.2 19.3 + - + +
500D TRP* 1.3 76.3 - - - +
502D GLU* 1.3 61.9 + - - +
504D SER* 2.6 21.5 + - - +
505D LYS* 3.3 17.7 + - - +
521D MET 3.3 6.5 - - - +
522D LYS* 3.5 13.3 - - + +
523D VAL* 3.6 6.9 - - - +
524D GLY* 3.5 27.9 + - - +
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Residues in contact with GLU 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480D ILE* 3.9 23.0 - - + +
483D LYS* 3.5 32.8 - - + +
484D LEU* 3.8 21.5 - - + -
498D LYS* 3.0 39.5 + - + +
499D PHE 3.1 9.4 + - - +
501D GLU* 1.3 77.4 - - - +
503D VAL* 1.3 62.8 + - - +
505D LYS* 3.0 43.7 + - - +
506D ASP* 3.2 10.0 + - - +
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Residues in contact with VAL 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D TRP* 4.1 24.9 - - + -
480D ILE* 3.8 20.0 - - + -
499D PHE* 3.1 29.3 + - + +
500D TRP* 3.4 21.1 - - + +
502D GLU* 1.3 75.2 - - - +
504D SER* 1.3 61.6 + - - +
506D ASP* 3.1 22.0 + - - +
509D LEU* 4.1 13.6 - - + +
510D SER 3.9 3.8 + - - -
513D PHE* 4.4 2.9 - - + -
521D MET* 3.5 28.9 - - + -
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Residues in contact with SER 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLU* 5.0 11.3 - - - +
500D TRP 3.2 6.3 + - - -
501D GLU 2.6 21.7 + - - -
503D VAL* 1.3 78.9 - - - +
505D LYS* 1.3 59.5 + - - +
506D ASP 3.5 0.2 - - - -
510D SER* 3.7 14.2 - - - -
518D ASN* 4.1 19.3 + - - +
521D MET* 3.9 7.9 - - - -
522D LYS* 3.6 46.0 - - - +
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Residues in contact with LYS 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLU* 4.8 4.2 + - - +
70A LYS* 5.9 0.7 + - - -
73A LYS* 4.6 18.1 - - - +
498D LYS* 5.4 0.4 - - - +
501D GLU* 3.6 16.4 - - - +
502D GLU* 3.0 42.5 + - - +
504D SER* 1.3 82.8 + - - +
506D ASP* 1.3 57.7 + - - +
507D PRO* 3.1 15.6 - - - +
522D LYS* 4.2 20.9 - - - +
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Residues in contact with ASP 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479D ARG* 3.1 52.5 + - - +
480D ILE* 4.3 5.3 - - + +
502D GLU 3.2 8.8 + - - +
503D VAL 3.1 9.3 + - - +
505D LYS* 1.3 75.0 - - - +
507D PRO* 1.3 65.5 - - - +
508D GLU* 3.1 18.0 + - - +
509D LEU* 3.0 15.7 + - + +
510D SER* 2.8 30.2 + - - -
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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