Contacts of the helix formed by residues 437 - 452 (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 PRO 437 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413H HIS* 3.8 38.4 - - + +
414H PHE* 6.3 2.0 - - + -
435H ALA 4.3 2.7 - - - +
436H LEU* 1.3 83.3 - - + +
438H LEU* 1.3 63.6 + - - +
439H GLU 3.2 3.6 - - - +
440H GLY* 3.4 10.9 + - - +
441H VAL* 3.2 23.3 + - + +
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Residues in contact with LEU 438 (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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436H LEU* 2.7 29.0 + - + +
437H PRO* 1.3 71.2 - - - +
439H GLU* 1.3 60.6 + - - +
441H VAL* 3.2 10.0 - - - +
442H ILE* 3.2 27.2 - - + +
510H GLU 5.0 4.9 - - - +
511H ALA* 3.9 23.6 - - + -
514H SER* 5.2 6.1 - - - -
518H ILE* 4.4 7.6 - - + -
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Residues in contact with GLU 439 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437H PRO* 3.2 0.6 - - - +
438H LEU* 1.3 78.4 - - - +
440H GLY* 1.3 60.1 + - - +
442H ILE* 3.4 7.0 + - - +
443H LEU* 2.9 30.2 + - - +
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Residues in contact with GLY 440 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H GLY 3.8 8.8 - - - +
44H ASN* 5.0 7.8 + - - -
410H LEU* 6.4 0.4 - - - -
437H PRO* 3.4 14.6 + - - +
439H GLU* 1.3 79.9 - - - +
441H VAL* 1.3 55.3 + - - +
443H LEU* 3.3 7.8 + - - +
444H SER* 2.9 29.9 + - - -
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Residues in contact with VAL 441 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410H LEU* 5.7 9.6 - - + +
411H TYR* 4.9 10.5 - - + -
414H PHE* 4.3 36.6 - - + -
437H PRO* 3.2 16.6 + - + +
438H LEU* 3.2 20.2 - - - +
440H GLY* 1.3 75.0 - - - +
442H ILE* 1.3 67.5 + - + +
444H SER* 2.5 22.6 + - - +
445H LEU* 2.9 36.5 + - + +
518H ILE* 4.8 6.5 - - + -
522H LEU* 5.6 3.6 - - + -
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Residues in contact with ILE 442 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438H LEU 3.2 19.3 - - - +
439H GLU* 3.4 6.7 + - - +
440H GLY 3.3 0.4 - - - -
441H VAL* 1.3 78.3 - - + +
443H LEU* 1.3 59.0 + - - +
445H LEU* 3.3 10.3 + - + +
446H GLN* 2.9 55.2 + - + +
514H SER* 4.3 18.6 - - - +
517H GLU* 4.7 11.9 - - + -
518H ILE* 3.6 34.1 - - + -
521H LEU* 5.0 6.5 - - + +
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Residues in contact with LEU 443 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H GLY 3.4 20.9 - - - +
44H ASN* 4.7 0.4 - - - -
45H ARG* 4.4 20.6 - - + +
439H GLU 2.9 18.0 + - - +
440H GLY* 3.6 6.7 - - - +
442H ILE* 1.3 79.1 - - - +
444H SER* 1.3 56.3 + - - +
446H GLN* 3.3 11.0 + - + +
447H ASP* 2.9 62.7 + - - +
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Residues in contact with SER 444 (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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42H PHE 5.3 0.4 - - - -
43H GLY* 3.6 24.0 - - - +
407H THR* 5.8 7.6 - - - -
410H LEU* 4.8 14.3 - - - +
411H TYR* 5.6 1.3 - - - -
440H GLY 2.9 14.6 + - - -
441H VAL* 2.5 29.3 + - - +
443H LEU* 1.3 76.9 - - - +
445H LEU* 1.3 59.4 + - - +
447H ASP* 3.3 2.5 + - - +
448H LEU* 2.9 31.1 + - - +
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Residues in contact with LEU 445 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407H THR* 5.7 0.2 - - - +
411H TYR* 3.2 40.4 - - + +
441H VAL* 2.9 32.2 + - + +
442H ILE* 3.8 7.4 - - + +
444H SER* 1.3 79.7 + - - +
446H GLN* 1.3 58.4 + - - +
448H LEU* 3.8 4.6 - - + +
449H ILE* 2.9 36.0 + - + +
518H ILE* 4.6 3.4 - - + +
521H LEU* 3.6 32.8 - - + +
522H LEU* 3.5 33.0 - - + +
525H ILE* 4.6 11.4 - - + +
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Residues in contact with GLN 446 (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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442H ILE* 2.9 40.2 + - - +
443H LEU* 3.8 12.4 - - + +
444H SER 3.3 0.2 - - - -
445H LEU* 1.3 77.2 - - - +
447H ASP* 1.3 63.7 + - - +
449H ILE* 4.4 3.8 - - - +
450H GLY* 3.8 13.3 + - - -
521H LEU* 3.8 28.7 - - + +
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Residues in contact with ASP 447 (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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41H GLY 5.0 1.6 - - - +
42H PHE* 4.9 17.5 - - + -
43H GLY 3.8 18.8 + - - +
443H LEU* 2.9 44.0 + - - +
444H SER 3.9 2.9 - - - +
446H GLN* 1.3 80.7 - - - +
448H LEU* 1.3 60.9 + - - +
450H GLY* 3.8 2.1 + - - -
451H TYR* 3.6 17.7 + - - +
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Residues in contact with LEU 448 (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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42H PHE* 6.0 0.7 - - - -
403H MET* 5.3 8.1 - - + -
407H THR* 5.9 6.3 - - - +
411H TYR* 6.0 0.2 - - - +
444H SER 2.9 18.8 + - - +
445H LEU* 3.9 2.9 - - - +
447H ASP* 1.3 77.2 - - - +
449H ILE* 1.3 65.0 + - - +
451H TYR* 3.3 13.4 + - - +
452H PHE* 3.4 28.7 - - + -
478H PHE* 6.2 3.1 - - + -
525H ILE* 4.4 17.7 - - + -
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Residues in contact with ILE 449 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445H LEU* 2.9 17.2 + - + +
446H GLN* 4.4 4.9 - - - +
448H LEU* 1.3 77.0 - - - +
450H GLY* 1.3 62.2 + - - +
452H PHE* 3.0 28.5 + - - +
453H GLU* 4.5 1.9 - - - +
521H LEU* 3.7 30.3 - - + +
524H GLU* 3.8 13.7 - - + -
525H ILE* 3.7 43.1 - - + +
528H SER* 4.6 10.3 - - - +
529H LEU* 6.1 0.4 - - - -
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Residues in contact with GLY 450 (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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446H GLN 3.8 10.2 + - - -
447H ASP 3.8 3.9 + - - -
448H LEU 3.3 0.6 - - - -
449H ILE* 1.3 80.0 - - - +
451H TYR* 1.3 61.6 + - - +
453H GLU* 3.9 15.8 - - - +
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Residues in contact with TYR 451 (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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42H PHE* 4.7 11.7 - + + -
396H GLU* 5.3 4.3 + - - +
399H GLN* 5.8 2.3 - - - +
400H ALA* 5.1 11.4 + - + +
403H MET* 3.6 37.3 - - + -
447H ASP 3.6 12.5 + - - +
448H LEU 3.3 8.6 + - - +
449H ILE 3.2 1.0 - - - -
450H GLY* 1.3 79.8 - - - +
452H PHE* 1.3 86.8 - + - +
453H GLU* 3.5 3.8 + - - +
474H ARG* 3.3 61.3 + - + +
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Residues in contact with PHE 452 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403H MET* 4.6 8.7 - - + -
448H LEU* 3.4 26.7 + - + +
449H ILE* 3.0 15.6 + - - +
451H TYR* 1.3 101.5 - + - +
453H GLU* 1.3 58.0 + - - +
454H PRO* 4.4 2.6 - - - +
471H LEU* 4.4 21.5 - - + -
474H ARG* 3.6 36.1 - - + -
475H GLN* 5.0 2.9 - - + +
478H PHE* 3.5 41.5 - + - -
528H SER* 4.4 18.1 - - - +
529H LEU* 4.3 31.4 - - + -
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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
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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