Contacts of the helix formed by residues 460 - 480 (chain H) in PDB entry 6X34
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 GLN 460 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458H GLU 5.0 3.0 + - - +
459H LEU* 1.3 94.1 - - - +
461H HIS* 1.3 61.0 + - - +
462H GLU* 3.5 2.5 - - + +
463H GLU* 3.9 16.5 - - + +
464H LYS* 2.8 27.9 + - - +
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Residues in contact with HIS 461 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459H LEU 3.8 1.0 + - - -
460H GLN* 1.3 73.7 - - - +
462H GLU* 1.3 66.1 + - + +
464H LYS* 3.3 5.0 + - - +
465H GLN* 2.9 63.4 + - + +
3702H SER 5.3 2.0 - - - -
3703H ARG* 3.4 69.5 + - + +
3706H LEU* 4.5 5.7 + - + -
3707H THR* 5.9 2.2 - - + -
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Residues in contact with GLU 462 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460H GLN* 4.5 2.5 - - + +
461H HIS* 1.3 85.9 - - + +
463H GLU* 1.3 58.3 + - - +
465H GLN* 3.3 6.4 + - - +
466H SER* 2.9 30.0 + - - -
3702H SER* 6.1 1.2 - - - -
3706H LEU* 5.3 15.2 - - + +
3776H GLN* 4.1 18.3 + - - -
3814H TYR* 5.1 6.0 + - - -
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Residues in contact with GLU 463 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459H LEU* 3.7 27.6 - - + -
460H GLN* 3.5 15.8 + - + +
461H HIS 3.3 0.4 - - - -
462H GLU* 1.3 78.8 - - - +
464H LYS* 1.3 57.5 + - - +
466H SER* 2.7 20.5 + - - -
467H LYS* 2.9 26.8 + - - +
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Residues in contact with LYS 464 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455H PRO* 4.5 7.3 - - + +
456H SER 4.9 6.3 - - - +
459H LEU* 4.0 19.9 - - + +
460H GLN 2.8 22.5 + - - +
461H HIS* 3.7 5.6 - - - +
463H GLU* 1.3 72.5 - - - +
465H GLN* 1.3 59.7 + - + +
467H LYS* 3.3 5.0 + - - +
468H LEU* 2.9 38.1 + - + +
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Residues in contact with GLN 465 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461H HIS* 2.9 48.5 + - + +
462H GLU* 3.7 7.0 - - - +
464H LYS* 1.3 77.7 - - + +
466H SER* 1.3 57.8 + - - +
468H LEU* 3.3 18.7 + - - +
469H ARG* 2.9 28.8 + - - +
3706H LEU* 3.5 26.0 + - + +
3707H THR* 3.1 26.1 + - - +
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Residues in contact with SER 466 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462H GLU 2.9 15.6 + - - -
463H GLU* 2.7 25.5 + - - -
465H GLN* 1.3 75.5 - - - +
467H LYS* 1.3 63.1 + - - +
469H ARG* 3.3 6.6 + - - +
470H SER* 2.9 29.5 + - - -
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Residues in contact with LYS 467 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455H PRO* 3.9 22.8 - - + +
459H LEU* 4.3 17.2 - - + +
463H GLU* 2.9 27.0 + - - +
464H LYS 3.7 4.3 - - - +
466H SER* 1.3 83.4 + - - +
468H LEU* 1.3 56.1 + - - +
470H SER* 3.3 8.6 + - - +
471H LEU* 2.9 29.7 + - - +
474H ARG* 4.2 8.1 + - - +
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Residues in contact with LEU 468 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454H PRO* 6.2 0.2 - - + -
455H PRO* 3.8 27.8 - - + -
464H LYS* 2.9 26.1 + - + +
465H GLN* 3.7 21.1 - - - +
467H LYS* 1.3 75.7 - - - +
469H ARG* 1.3 58.6 + - - +
471H LEU* 3.3 7.0 + - + +
472H ARG* 2.9 59.8 + - + +
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Residues in contact with ARG 469 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465H GLN 2.9 16.7 + - - +
466H SER* 3.7 8.1 - - - +
467H LYS 3.3 0.2 - - - -
468H LEU* 1.3 76.6 - - - +
470H SER* 1.3 57.1 + - - +
472H ARG* 3.3 6.8 + - - +
473H ASN* 2.9 40.9 + - - +
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Residues in contact with SER 470 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466H SER 2.9 17.8 + - - -
467H LYS* 3.7 10.4 - - - +
469H ARG* 1.3 75.3 - - - +
471H LEU* 1.3 58.0 + - - +
473H ASN* 3.3 8.4 + - - +
474H ARG* 2.9 51.3 + - - +
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Residues in contact with LEU 471 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452H PHE* 4.4 27.1 - - + -
453H GLU 4.7 5.2 - - - +
454H PRO* 4.6 23.6 - - + -
455H PRO* 4.7 2.2 - - + -
467H LYS 2.9 16.9 + - - +
468H LEU* 3.6 14.1 - - + +
469H ARG 3.3 0.2 - - - -
470H SER* 1.3 78.3 - - - +
472H ARG* 1.3 78.7 + - - +
474H ARG* 3.3 21.7 + - - +
475H GLN* 2.9 58.4 + - + +
531H ARG 5.5 0.7 - - - +
532H GLY* 5.7 0.4 - - - -
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Residues in contact with ARG 472 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468H LEU* 2.9 42.7 + - + +
469H ARG* 3.3 7.2 + - - +
471H LEU* 1.3 107.6 - - - +
473H ASN* 1.3 61.8 + - - +
475H GLN* 3.3 10.5 + - - +
476H SER* 2.9 29.5 + - - -
532H GLY* 2.8 43.8 + - - -
533H ASN* 4.7 6.2 + - - +
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Residues in contact with ASN 473 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469H ARG* 2.9 22.0 + - - +
470H SER* 3.7 7.6 - - - +
471H LEU 3.3 0.2 - - - -
472H ARG* 1.3 79.9 - - - +
474H ARG* 1.3 56.5 + - + +
476H SER* 2.6 21.7 + - - -
477H LEU* 2.9 28.9 + - + +
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Residues in contact with ARG 474 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400H ALA* 5.9 7.2 - - + -
451H TYR* 3.3 62.0 + - + +
452H PHE* 3.6 18.9 - - + -
453H GLU 4.9 7.7 + - - +
467H LYS* 4.2 8.7 + - - +
470H SER* 2.9 33.4 + - - +
471H LEU* 3.5 37.9 - - - +
472H ARG 3.3 0.2 - - - -
473H ASN* 1.3 76.3 - - + +
475H GLN* 1.3 58.3 + - - +
477H LEU* 3.4 6.3 + - - +
478H PHE* 2.9 29.3 + - - +
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Residues in contact with GLN 475 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452H PHE* 5.0 3.6 - - + +
471H LEU* 2.9 47.3 + - + +
472H ARG* 3.7 12.5 - - - +
474H ARG* 1.3 76.8 - - - +
476H SER* 1.3 57.7 + - - +
478H PHE* 3.1 8.9 + - - +
479H GLN* 2.9 28.4 + - - +
528H SER 3.9 10.3 + - - -
529H LEU* 4.1 17.5 + - + +
531H ARG 2.7 26.4 + - - -
532H GLY* 3.5 4.6 - - - -
533H ASN* 3.1 41.9 + - + +
536H ASN* 4.7 5.6 + - - +
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Residues in contact with SER 476 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472H ARG 2.9 15.0 + - - -
473H ASN* 2.6 27.2 + - - -
475H GLN* 1.3 77.1 - - - +
477H LEU* 1.3 63.5 + - - +
479H GLN* 3.3 8.2 + - - +
480H GLU* 3.3 22.0 + - - +
533H ASN* 4.0 8.7 - - - +
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Residues in contact with LEU 477 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221H ARG* 6.0 3.6 - - - +
254H THR 4.1 21.5 - - - +
255H HIS* 5.1 0.9 - - - +
256H ALA* 4.3 31.6 - - + +
394H GLN* 6.0 0.4 - - - +
397H GLU* 4.8 20.0 - - + +
400H ALA* 4.7 21.5 - - + -
401H ALA 6.1 0.4 - - - +
404H ILE* 4.8 10.2 - - + +
473H ASN* 2.9 36.1 + - + +
474H ARG* 3.9 5.8 - - - +
476H SER* 1.3 79.9 + - - +
478H PHE* 1.3 62.6 + - - +
480H GLU* 3.6 17.5 + - - +
481H GLU* 4.5 0.5 + - - +
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Residues in contact with PHE 478 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403H MET* 6.0 2.9 - - + -
404H ILE* 4.4 19.5 - - + -
407H THR* 5.0 5.8 - - + -
448H LEU* 6.2 2.5 - - + -
452H PHE* 3.5 36.3 - + - -
474H ARG 2.9 16.1 + - - +
475H GLN* 3.1 11.9 + - - +
477H LEU* 1.3 77.7 - - - +
479H GLN* 1.3 62.1 + - - +
480H GLU 3.4 0.3 + - - -
481H GLU* 3.8 7.8 + - - +
483H MET* 3.5 54.3 - - + +
484H LEU* 4.3 6.9 - - + +
525H ILE* 5.5 9.0 - - + -
529H LEU* 3.5 35.0 - - + -
536H ASN* 6.1 1.6 - - - +
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Residues in contact with GLN 479 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475H GLN 2.9 15.0 + - - +
476H SER* 3.3 8.3 + - - +
478H PHE* 1.3 72.3 - - - +
480H GLU* 1.3 62.1 + - - +
481H GLU 3.0 10.9 + - - -
482H GLY* 3.5 10.8 + - - -
484H LEU* 3.6 23.1 - - + +
533H ASN* 5.4 0.9 - - - +
535H ALA* 5.3 7.8 - - + +
536H ASN* 3.4 25.5 - - - +
539H LEU* 3.6 24.8 - - + +
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Residues in contact with GLU 480 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255H HIS* 3.7 32.0 - - + +
256H ALA* 4.2 11.4 + - - +
257H ARG* 5.4 4.5 + - - +
476H SER 3.3 15.3 + - - +
477H LEU* 3.6 9.4 + - - +
478H PHE 3.3 2.4 - - - -
479H GLN* 1.3 79.4 + - - +
481H GLU* 1.3 55.7 + - - +
482H GLY 3.8 0.4 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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