Contacts of the helix formed by residues 510 - 528 (chain m) in PDB entry 6QX2
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 510 (chain m).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24l ASP* 4.2 4.6 - - - +
435m GLU* 4.3 2.3 - - - +
508m ASP* 3.1 17.1 - - - +
509m ALA* 1.3 78.9 - - - +
511m VAL* 1.3 65.7 + - + +
512m ASP* 3.4 9.6 + - - +
513m GLY* 2.7 34.3 + - - -
514m ALA* 3.4 18.0 + - - +
517m ARG* 5.4 1.0 + - - -
580m TYR 5.7 2.0 - - - +
581m LYS 3.4 21.7 - - - +
582m GLY* 5.1 0.2 - - - -
8o C 6.1 0.5 - - - +
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Residues in contact with VAL 511 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24l ASP* 4.1 20.4 - - - +
25l TYR* 3.5 20.8 - - + +
28l SER* 3.4 37.7 - - - +
29l VAL* 5.9 0.4 - - + -
33l ARG* 4.0 11.4 - - - +
81l HIS* 5.4 5.6 - - + -
510m ASP* 1.3 79.0 - - + +
512m ASP* 1.3 78.1 + - - +
513m GLY 3.2 0.2 - - - -
514m ALA* 3.2 6.3 + - - +
515m HIS 3.1 20.4 + - - -
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Residues in contact with ASP 512 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25l TYR* 3.8 2.8 - - - -
33l ARG* 2.6 38.9 + - - -
81l HIS* 4.5 3.5 + - - -
435m GLU* 4.4 3.6 - - - +
460m LYS* 2.9 27.2 + - - -
510m ASP* 3.4 8.4 + - - +
511m VAL* 1.3 81.0 - - - +
513m GLY* 1.3 59.4 + - - +
515m HIS* 3.6 6.9 + - - +
516m ILE* 3.2 33.7 + - - +
7o A 3.7 2.4 - - - +
8o C 3.5 39.8 + - - +
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Residues in contact with GLY 513 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435m GLU* 3.3 20.6 + - - -
507m THR* 3.3 18.4 + - - +
508m ASP 3.6 12.6 - - - -
510m ASP* 2.7 16.9 + - - -
512m ASP* 1.3 73.8 - - - +
514m ALA* 1.3 57.4 + - - +
516m ILE* 3.2 2.3 + - - -
517m ARG* 2.9 26.7 + - - +
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Residues in contact with ALA 514 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21l SER* 3.4 24.0 - - - +
24l ASP* 3.8 18.8 - - + +
25l TYR 4.6 0.9 - - - +
510m ASP 3.4 6.8 + - - +
511m VAL 3.2 10.8 + - - +
513m GLY* 1.3 72.9 - - - +
515m HIS* 1.3 56.2 + - - +
517m ARG* 3.3 31.1 + - - +
518m THR* 3.0 33.8 + - - +
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Residues in contact with HIS 515 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22l PHE* 4.4 6.0 - + - -
25l TYR* 3.3 62.7 - + + +
460m LYS* 3.3 20.4 + - + +
511m VAL 3.1 6.0 + - - +
512m ASP 3.8 7.6 - - - +
513m GLY 3.2 0.2 - - - -
514m ALA* 1.3 75.7 - - - +
516m ILE* 1.3 56.7 + - - +
518m THR* 2.7 31.4 + - - -
519m LEU* 3.0 31.5 + - + +
2015n A 3.2 27.7 + - - -
2016n C 3.2 23.6 + - - -
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Residues in contact with ILE 516 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435m GLU* 3.6 38.8 - - + +
457m LEU* 4.8 5.4 - - + -
459m GLY* 4.1 27.4 - - - +
460m LYS* 4.0 26.0 - - + +
461m ILE* 4.7 9.4 - - + +
507m THR* 4.0 15.0 - - + -
512m ASP 3.2 16.0 + - - +
513m GLY 3.2 3.8 + - - +
515m HIS* 1.3 73.8 - - - +
517m ARG* 1.3 57.2 + - - +
519m LEU* 3.7 7.7 - - + +
520m LEU* 3.1 42.3 + - + +
8o C 4.9 4.9 - - + -
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Residues in contact with ARG 517 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17l GLU* 2.5 27.3 + - - +
21l SER* 3.0 18.6 + - - +
24l ASP* 5.5 0.8 + - - -
505m ILE* 4.1 16.3 - - + +
507m THR* 2.9 34.4 + - - +
508m ASP 4.4 6.1 + - - -
510m ASP 5.4 0.6 + - - -
513m GLY 2.9 10.6 + - - +
514m ALA* 3.3 33.9 - - - +
516m ILE* 1.3 75.3 - - - +
518m THR* 1.3 57.3 + - - +
519m LEU 3.3 0.3 + - - -
520m LEU* 3.4 2.6 + - - +
521m LEU* 3.0 44.1 + - + +
539m ILE* 4.0 26.7 - - + +
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Residues in contact with THR 518 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18l MET* 3.7 27.2 - - + +
21l SER* 3.5 8.7 - - - -
22l PHE* 3.3 42.0 - - + +
514m ALA 3.0 20.1 + - - +
515m HIS* 2.7 26.2 + - - -
517m ARG* 1.3 75.5 - - - +
519m LEU* 1.3 52.3 + - - +
521m LEU* 3.7 0.8 + - - -
522m THR* 2.6 37.2 + - - -
622m MET* 3.7 15.1 - - - +
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Residues in contact with LEU 519 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460m LYS* 4.1 12.1 - - + -
461m ILE* 3.6 43.6 - - + +
462m LEU 4.6 2.8 - - - +
463m ASN* 3.7 36.5 - - + +
464m VAL* 5.2 1.2 + - - +
515m HIS* 3.0 48.5 + - + +
516m ILE* 3.7 8.3 - - - +
517m ARG 3.2 0.4 - - - -
518m THR* 1.3 74.3 + - - +
520m LEU* 1.3 64.8 + - - +
522m THR* 3.5 5.0 + - - -
523m PHE* 3.2 16.1 + - - +
622m MET* 3.7 15.5 - - + -
2015n A 4.1 11.7 - - - +
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Residues in contact with LEU 520 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433m LEU* 4.5 12.1 - - + +
457m LEU* 3.9 26.0 - - + -
461m ILE* 3.9 17.3 - - + -
481m MET* 3.6 32.5 - - + -
505m ILE* 4.0 37.0 - - + -
507m THR* 4.8 2.9 - - + -
516m ILE* 3.1 28.6 + - + +
517m ARG 3.8 3.4 - - - +
519m LEU* 1.3 74.3 - - - +
521m LEU* 1.3 54.1 + - - +
523m PHE* 3.0 6.3 + - + +
524m PHE* 2.9 42.0 + - + -
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Residues in contact with LEU 521 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14l ILE* 4.7 10.1 - - + -
17l GLU* 3.5 33.9 - - + -
18l MET* 3.7 26.5 - - + +
21l SER* 6.2 0.4 - - - -
505m ILE* 3.9 21.8 - - + -
517m ARG* 3.0 25.3 + - + +
518m THR* 4.9 0.4 - - - -
520m LEU* 1.3 74.4 - - - +
522m THR* 1.3 57.3 + - - +
524m PHE* 3.5 7.2 + - + +
525m TYR* 2.9 31.9 + - - +
532m ILE* 4.6 1.7 - - + +
537m VAL* 4.3 7.6 - - + -
539m ILE* 4.3 5.6 - - + -
606m VAL* 4.3 26.0 - - + -
618m PHE* 3.7 6.0 - - + -
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Residues in contact with THR 522 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18l MET* 3.5 0.2 - - - +
463m ASN* 4.2 4.7 - - - +
464m VAL* 3.9 11.4 - - + +
465m GLU* 3.9 33.7 - - + +
518m THR 2.6 23.6 + - - -
519m LEU* 3.6 7.9 - - - -
520m LEU 3.2 0.2 - - - -
521m LEU* 1.3 75.8 - - - +
523m PHE* 1.3 61.7 + - - +
525m TYR* 4.0 0.7 - - - +
526m ARG* 3.2 26.2 + - + +
618m PHE* 3.2 20.9 - - + -
622m MET* 3.2 26.7 - - + +
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Residues in contact with PHE 523 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461m ILE* 4.4 9.9 - - + -
464m VAL* 3.6 21.9 - - + +
472m ILE* 5.2 0.2 - - + -
478m ILE* 3.7 40.6 - - + -
481m MET* 3.6 30.5 - - + -
482m ILE* 4.0 19.3 - - + -
519m LEU 3.2 12.4 + - - +
520m LEU 3.0 8.4 + - - +
522m THR* 1.3 72.2 - - - +
524m PHE* 1.3 82.7 + + - +
526m ARG 3.4 0.9 + - - -
527m PHE* 3.0 56.8 + + + +
528m MET* 4.0 16.8 - - + -
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Residues in contact with PHE 524 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433m LEU* 3.7 22.9 - - + -
481m MET* 4.5 5.6 - - - -
485m PHE* 3.4 25.6 - + - -
503m ILE* 3.8 15.5 - - + -
505m ILE* 3.8 32.8 - - + -
520m LEU* 2.9 25.7 + - + +
521m LEU* 3.9 7.0 - - - +
523m PHE* 1.3 91.3 - + - +
525m TYR* 1.3 57.6 + - - +
528m MET* 2.9 54.0 + - + +
529m ARG* 3.7 0.2 - - - -
531m LEU* 5.3 2.9 - - + -
532m ILE* 3.8 18.2 - - + -
537m VAL* 4.2 18.6 - - + -
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Residues in contact with TYR 525 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14l ILE* 4.1 11.4 - - + -
521m LEU 2.9 18.5 + - - +
522m THR 4.1 2.7 - - - +
524m PHE* 1.3 76.9 - - - +
526m ARG* 1.3 74.6 + - - +
529m ARG* 3.4 64.9 + - + +
532m ILE* 3.6 11.2 - - + +
608m LEU* 3.8 18.2 - - + -
611m ALA* 3.1 21.0 + - - -
614m ALA* 3.4 19.2 - - + +
615m ASP* 3.0 23.3 + - - -
618m PHE* 3.6 38.6 - + + -
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Residues in contact with ARG 526 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464m VAL* 4.5 6.1 - - + -
465m GLU* 2.9 41.1 + - - +
490m GLY* 5.6 2.4 - - - -
522m THR* 3.2 21.8 + - + +
525m TYR* 1.3 92.4 - - + +
527m PHE* 1.3 82.1 + - + +
528m MET 3.9 0.2 - - - -
529m ARG* 3.9 8.6 - - - +
615m ASP* 3.1 49.3 + - - +
618m PHE* 3.8 10.7 - - + +
619m GLU* 4.4 1.8 - - - +
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Residues in contact with PHE 527 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464m VAL* 4.1 18.2 - - + -
469m LEU* 3.9 24.7 - - + -
472m ILE* 3.7 33.0 - - + -
482m ILE* 6.0 0.4 - - + -
489m ILE* 3.6 36.2 - - + -
490m GLY* 3.1 30.3 + - - +
493m PHE* 4.5 2.1 - - - +
523m PHE* 3.0 39.1 + + + +
526m ARG* 1.3 99.9 - - + +
528m MET* 1.3 64.0 + - + +
529m ARG 3.9 1.6 - - - -
530m PRO* 5.6 0.4 - - - +
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Residues in contact with MET 528 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482m ILE* 3.9 21.3 - - + -
485m PHE* 3.7 30.1 - - + -
487m THR* 3.9 12.6 - - - +
488m GLY 3.9 1.8 - - - +
489m ILE* 3.8 21.8 - - + -
493m PHE* 3.9 14.6 - - + -
523m PHE* 4.0 10.1 - - + -
524m PHE* 2.9 29.5 + - + +
527m PHE* 1.3 85.7 - - + +
529m ARG* 1.3 63.9 + - - +
530m PRO* 3.3 9.2 - - - -
531m LEU* 3.1 45.0 - - + +
532m ILE* 3.8 2.8 + - - +
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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