Contacts of the helix formed by residues 510 - 528 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B ASP* 3.1 26.3 - - - +
509B ALA* 1.3 79.0 - - - +
511B VAL* 1.3 65.1 + - + +
512B ASP* 3.4 8.8 + - - +
513B GLY* 2.7 34.3 + - - -
514B ALA* 3.4 18.4 + - - +
517B ARG* 5.3 1.2 + - - -
581B LYS* 5.9 7.6 - - + +
582B GLY* 5.3 2.6 + - - -
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Residues in contact with VAL 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 3.9 15.9 - - + +
25A TYR* 3.4 15.9 - - + +
28A SER* 3.1 42.0 - - - +
33A ARG* 3.7 21.1 - - - +
81A HIS* 6.1 1.1 - - + -
510B ASP* 1.3 76.4 - - + +
512B ASP* 1.3 65.8 + - + +
513B GLY 3.2 0.4 - - - -
514B ALA* 3.2 9.8 + - - +
515B HIS 3.1 21.0 + - - -
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Residues in contact with ASP 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 4.3 9.0 - - + -
33A ARG* 4.8 7.6 - - - +
81A HIS* 6.6 0.2 - - + -
460B LYS* 4.1 9.7 - - - +
510B ASP* 3.4 8.5 + - - +
511B VAL* 1.3 81.6 - - + +
513B GLY* 1.3 64.7 + - - +
515B HIS* 3.6 3.3 + - - +
516B ILE* 3.2 31.6 + - + +
8E C 3.9 34.8 - - - -
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Residues in contact with GLY 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B THR* 3.3 25.3 + - - +
508B ASP* 3.6 18.6 - - - -
510B ASP* 2.7 18.2 + - - -
512B ASP* 1.3 74.0 - - - +
514B ALA* 1.3 57.9 + - - +
516B ILE* 3.2 4.9 + - - -
517B ARG* 2.9 26.5 + - - +
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Residues in contact with ALA 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER* 3.2 28.5 - - - +
24A ASP* 4.4 10.8 - - + +
510B ASP 3.4 11.7 + - - +
511B VAL 3.2 12.0 + - - +
513B GLY* 1.3 72.7 - - - +
515B HIS* 1.3 56.6 + - - +
517B ARG* 3.3 30.8 + - - +
518B THR* 3.0 31.5 + - - +
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Residues in contact with HIS 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 4.5 4.5 - + - -
25A TYR* 3.0 68.1 + + + +
460B LYS* 3.3 15.8 + - + +
511B VAL 3.1 5.9 + - - -
512B ASP 3.8 7.4 - - - +
513B GLY 3.2 0.4 - - - -
514B ALA* 1.3 76.2 - - - +
516B ILE* 1.3 56.9 + - - +
518B THR* 2.7 32.3 + - - -
519B LEU* 3.0 26.5 + - + +
2015F A 3.0 45.2 + - - -
2016F C 3.1 12.9 + - - -
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Residues in contact with ILE 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B GLU* 4.4 24.5 - - + -
457B LEU* 4.8 9.0 - - + -
459B GLY* 4.2 26.7 - - - +
460B LYS* 4.0 24.7 - - + +
461B ILE* 5.2 6.1 - - + -
507B THR* 4.0 16.4 - - + -
512B ASP 3.2 20.5 + - - +
513B GLY* 3.2 5.1 + - - +
515B HIS* 1.3 74.2 - - - +
517B ARG* 1.3 56.6 + - - +
519B LEU* 3.4 8.8 + - - +
520B LEU* 3.1 41.6 + - + +
8E C 4.8 9.4 - - + +
9E G 4.9 0.2 - - - +
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Residues in contact with ARG 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU* 2.5 26.1 + - - +
21A SER* 2.9 19.8 + - - +
505B ILE* 4.1 20.8 - - + +
507B THR* 2.9 30.4 + - - +
508B ASP 4.3 6.9 + - - -
510B ASP 5.3 0.8 + - - -
513B GLY 2.9 14.3 + - - +
514B ALA* 3.3 28.8 - - - +
516B ILE* 1.3 75.0 - - - +
518B THR* 1.3 56.6 + - - +
519B LEU 3.3 0.2 + - - -
520B LEU* 3.4 2.4 + - - +
521B LEU* 3.0 47.0 + - + +
539B ILE* 3.9 27.4 - - + +
540B ALA 6.0 0.2 + - - -
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Residues in contact with THR 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET* 3.7 29.2 - - + +
21A SER* 3.6 9.0 - - - -
22A PHE* 3.5 40.9 - - + +
514B ALA 3.0 20.3 + - - +
515B HIS* 2.7 26.9 + - - -
517B ARG* 1.3 74.5 - - - +
519B LEU* 1.3 51.7 + - - +
521B LEU* 3.9 0.6 - - - +
522B THR* 2.6 37.1 + - - -
622B MET* 3.7 14.8 - - - +
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Residues in contact with LEU 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B LYS* 4.1 12.8 - - + -
461B ILE* 3.5 39.9 - - + +
462B LEU 4.5 4.7 - - - +
463B ASN* 3.7 36.5 - - + -
464B VAL* 5.2 1.2 + - - +
515B HIS* 3.0 52.2 + - + +
516B ILE* 3.7 6.7 - - - +
517B ARG 3.2 0.2 - - - -
518B THR* 1.3 75.5 + - - +
520B LEU* 1.3 63.2 + - - +
522B THR* 3.5 4.6 + - - -
523B PHE* 3.2 20.1 + - - +
622B MET* 3.7 15.7 - - + -
2015F A 4.2 6.3 - - - +
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Residues in contact with LEU 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LEU* 4.5 11.9 - - + +
457B LEU* 3.9 26.5 - - + -
461B ILE* 3.9 9.2 - - + -
481B MET* 3.6 37.9 - - + -
505B ILE* 4.0 36.3 - - + -
507B THR* 4.8 2.2 - - + -
516B ILE* 3.1 29.3 + - + +
517B ARG 3.4 3.8 + - - +
519B LEU* 1.3 74.7 - - - +
521B LEU* 1.3 53.7 + - - +
522B THR 3.2 0.2 - - - -
523B PHE* 3.0 8.6 + - + +
524B PHE* 2.9 42.7 + - + -
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Residues in contact with LEU 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 4.7 9.0 - - + -
17A GLU* 3.8 30.5 - - + -
18A MET* 3.7 30.5 - - + -
21A SER* 6.3 0.2 - - - -
505B ILE* 3.9 20.6 - - + -
517B ARG* 3.0 28.9 + - + +
518B THR* 3.9 0.7 - - + +
520B LEU* 1.3 74.1 - - - +
522B THR* 1.3 56.1 + - - +
524B PHE* 3.8 6.9 - - + +
525B TYR* 2.9 33.1 + - - +
532B ILE* 4.6 1.7 - - + +
537B VAL* 4.2 16.6 - - + -
539B ILE* 4.5 2.5 - - + -
606B VAL* 4.3 17.7 - - + -
618B PHE* 3.7 6.1 - - + -
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Residues in contact with THR 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET* 3.7 0.2 - - - +
463B ASN* 4.2 4.7 - - - +
464B VAL* 3.9 11.7 - - + +
465B GLU* 3.9 33.9 - - + +
518B THR 2.6 23.3 + - - -
519B LEU* 3.6 8.3 - - - -
520B LEU 3.2 0.2 - - - -
521B LEU* 1.3 75.9 - - - +
523B PHE* 1.3 60.8 + - - +
525B TYR* 3.6 0.9 + - - +
526B ARG* 3.2 26.4 + - + +
618B PHE* 3.2 21.2 - - + -
622B MET* 3.2 26.8 - - + +
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Residues in contact with PHE 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B ILE* 6.1 1.8 - - + -
462B LEU 5.6 0.9 - - - +
464B VAL* 3.6 23.9 - - + +
472B ILE* 5.2 0.2 - - + -
478B ILE* 3.7 43.3 - - + -
481B MET* 3.6 31.9 - - + -
482B ILE* 4.0 9.9 - - + -
489B ILE* 4.6 0.2 - - + -
519B LEU 3.2 12.6 + - - +
520B LEU* 3.0 10.4 + - - +
522B THR* 1.3 73.4 - - - +
524B PHE* 1.3 81.8 + + - +
526B ARG 3.4 1.0 + - - -
527B PHE* 3.0 56.4 + + + +
528B MET* 4.0 26.7 - - + -
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Residues in contact with PHE 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B LEU* 3.7 22.4 - - + -
481B MET* 4.5 5.2 - - - -
485B PHE* 3.4 25.1 - + - -
503B ILE* 3.8 15.9 - - + -
505B ILE* 3.8 32.3 - - + -
520B LEU* 2.9 28.9 + - + +
521B LEU* 3.9 6.5 - - - +
523B PHE* 1.3 87.9 - + - +
525B TYR* 1.3 57.4 + - - +
528B MET* 2.9 52.5 + - - +
529B ARG* 3.7 0.2 - - - -
531B LEU* 4.6 6.5 - - + -
532B ILE* 3.8 17.7 - - + -
537B VAL* 4.2 17.3 - - + -
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Residues in contact with TYR 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE* 4.3 10.8 - - + -
521B LEU 2.9 19.0 + - - +
522B THR 4.1 2.5 - - - +
523B PHE 3.3 0.2 - - - -
524B PHE* 1.3 76.3 - - - +
526B ARG* 1.3 79.9 + - + +
529B ARG* 3.4 42.7 + - + +
532B ILE* 3.6 13.6 - - + +
608B LEU* 3.8 21.8 - - + -
611B ALA* 3.0 20.8 + - - -
614B ALA* 3.4 20.0 - - + +
615B ASP* 3.0 31.0 + - - -
618B PHE* 3.6 37.7 - + + -
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Residues in contact with ARG 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B VAL* 4.4 6.7 - - + -
465B GLU* 2.9 41.0 + - - +
490B GLY* 5.6 2.4 - - - -
522B THR* 3.2 21.1 + - + +
525B TYR* 1.3 91.8 - - + +
527B PHE* 1.3 81.3 + - + +
529B ARG* 5.1 1.3 - - - -
615B ASP* 3.1 49.8 + - - +
618B PHE* 3.8 10.9 - - + +
619B GLU* 4.1 3.0 + - - +
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Residues in contact with PHE 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B VAL* 4.1 18.4 - - + -
469B LEU* 3.9 24.2 - - + -
472B ILE* 3.7 33.4 - - + -
478B ILE* 6.2 0.2 - - + -
482B ILE* 6.0 0.2 - - + -
489B ILE* 3.6 35.6 - - + -
490B GLY* 3.1 30.7 + - - +
493B PHE* 4.6 2.3 - - - +
523B PHE* 3.0 37.1 + + + +
526B ARG* 1.3 99.0 - - + +
528B MET* 1.3 64.8 + - + +
529B ARG 3.9 1.3 - - - -
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Residues in contact with MET 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B ILE* 3.9 21.1 - - + -
485B PHE* 3.7 36.6 - - + -
487B THR* 3.9 15.7 - - - +
488B GLY 3.9 2.0 - - - +
489B ILE* 3.8 22.2 - - + -
493B PHE* 3.9 20.4 - - + -
523B PHE* 4.0 9.2 - - + -
524B PHE* 2.9 29.8 + - + +
527B PHE* 1.3 87.0 - - + +
529B ARG* 1.3 63.5 + - - +
530B PRO* 3.3 8.5 - - - -
531B LEU* 3.1 28.9 - - + +
532B 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