Contacts of the helix formed by residues 3399 - 3427 (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 PHE3399 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3398H GLU* 1.3 78.7 - - + +
3400H SER* 1.3 60.1 + - - +
3402H LEU* 3.9 5.3 - - - +
3403H CYS* 3.0 31.5 + - - +
3452H PHE* 6.4 1.6 - - + -
3455H GLU* 3.7 37.2 - - + +
3456H GLU* 5.2 1.6 - - - +
3459H PHE* 4.6 3.5 - - + +
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Residues in contact with SER3400 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3398H GLU 3.3 5.0 - - - +
3399H PHE* 1.3 80.7 - - - +
3401H VAL* 1.3 58.4 + - - +
3404H ARG* 3.1 29.5 + - - +
3459H PHE* 3.7 38.4 - - - -
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Residues in contact with VAL3401 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3398H GLU* 3.6 14.1 + - - +
3400H SER* 1.3 79.2 - - - +
3402H LEU* 1.3 62.7 + - - +
3404H ARG* 4.0 5.1 - - - +
3405H ASP* 3.1 25.1 + - - +
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Residues in contact with LEU3402 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3398H GLU 3.1 19.5 + - - +
3399H PHE* 3.9 6.3 - - - +
3401H VAL* 1.3 76.4 - - - +
3403H CYS* 1.3 61.1 + - - +
3405H ASP* 3.5 4.4 + - - +
3406H LEU* 3.0 27.9 + - - +
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Residues in contact with CYS3403 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3399H PHE 3.0 19.0 + - - +
3402H LEU* 1.3 74.7 - - - +
3404H ARG* 1.3 64.9 + - - +
3406H LEU* 3.4 8.0 + - - +
3407H TYR* 3.3 20.3 + - - +
3456H GLU* 4.3 17.0 - - + +
3459H PHE* 3.6 31.9 - - + -
3460H VAL* 5.4 3.4 - - + +
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Residues in contact with ARG3404 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3400H SER 3.1 19.8 + - - +
3401H VAL* 4.0 6.1 - - - +
3403H CYS* 1.3 76.6 - - - +
3405H ASP* 1.3 62.2 + - - +
3407H TYR* 3.4 14.4 + - - +
3408H ALA* 3.5 11.3 + - - +
3459H PHE* 4.6 9.8 - - + -
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Residues in contact with ASP3405 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3401H VAL 3.1 18.1 + - - +
3402H LEU* 4.0 4.3 - - - +
3404H ARG* 1.3 74.1 - - - +
3406H LEU* 1.3 61.0 + - - +
3408H ALA* 3.4 7.5 + - - +
3409H LEU* 3.0 28.6 + - - +
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Residues in contact with LEU3406 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3402H LEU 3.0 18.8 + - - +
3403H CYS* 3.7 9.4 - - - +
3404H ARG 3.2 0.6 - - - -
3405H ASP* 1.3 78.9 - - - +
3407H TYR* 1.3 56.5 + - - +
3409H LEU* 3.8 6.0 - - - +
3410H TYR* 2.9 30.3 + - - +
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Residues in contact with TYR3407 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3403H CYS 3.3 10.7 + - - +
3404H ARG* 3.7 10.3 - - - +
3405H ASP 3.3 0.8 - - - -
3406H LEU* 1.3 78.8 - - - +
3408H ALA* 1.3 61.6 + - - +
3410H TYR* 3.4 5.9 + - - +
3411H PRO* 3.1 24.1 - - - +
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Residues in contact with ALA3408 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3404H ARG 3.5 8.3 + - - +
3405H ASP* 3.4 10.2 + - - +
3406H LEU 3.3 0.4 - - - -
3407H TYR* 1.3 78.1 - - - +
3409H LEU* 1.3 62.6 + - - +
3411H PRO* 3.5 5.4 - - - +
3412H LEU* 3.1 23.6 + - - +
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Residues in contact with LEU3409 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3405H ASP 3.0 18.1 + - - +
3406H LEU* 3.9 7.0 - - - +
3408H ALA* 1.3 74.5 - - - +
3410H TYR* 1.3 60.8 + - - +
3412H LEU* 3.5 4.9 + - - +
3413H LEU* 3.0 30.7 + - - +
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Residues in contact with TYR3410 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3406H LEU 2.9 19.3 + - - +
3407H TYR* 3.8 7.6 - - - +
3409H LEU* 1.3 77.9 - - - +
3411H PRO* 1.3 57.4 - - - +
3413H LEU* 3.5 4.8 + - - +
3414H ILE* 3.0 29.8 + - - +
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Residues in contact with PRO3411 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3407H TYR 3.1 16.6 - - - +
3408H ALA* 3.8 6.7 - - - +
3409H LEU 3.4 0.2 - - - -
3410H TYR* 1.3 77.5 - - - +
3412H LEU* 1.3 60.8 + - - +
3414H ILE* 3.4 5.8 + - + +
3415H ARG* 3.1 23.9 + - - +
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Residues in contact with LEU3412 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3408H ALA 3.1 17.6 + - - +
3409H LEU* 4.0 5.4 - - - +
3411H PRO* 1.3 75.4 - - - +
3413H LEU* 1.3 59.6 + - - +
3415H ARG* 3.5 5.6 + - - +
3416H TYR* 3.0 28.8 + - - +
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Residues in contact with LEU3413 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3409H LEU 3.0 19.4 + - - +
3410H TYR* 4.0 4.7 - - - +
3412H LEU* 1.3 73.8 - - - +
3414H ILE* 1.3 61.0 + - - +
3416H TYR* 3.8 5.9 - - - +
3417H VAL* 3.0 29.1 + - - +
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Residues in contact with ILE3414 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3410H TYR 3.0 18.4 + - - +
3411H PRO* 3.8 7.0 - - + +
3412H LEU 3.3 0.4 - - - -
3413H LEU* 1.3 77.7 - - - +
3415H ARG* 1.3 60.9 + - - +
3417H VAL* 3.3 17.9 + - - +
3418H ASP* 3.9 5.2 + - - +
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Residues in contact with ARG3415 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3411H PRO 3.1 17.4 + - - +
3412H LEU* 4.0 4.9 - - - +
3414H ILE* 1.3 76.9 - - - +
3416H TYR* 1.3 62.0 + - - +
3417H VAL 3.4 0.7 + - - -
3418H ASP* 3.5 17.4 + - - +
3419H ASN* 4.5 1.9 + - - +
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Residues in contact with TYR3416 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3412H LEU 3.0 18.6 + - - +
3413H LEU* 3.9 6.7 - - - +
3415H ARG* 1.3 73.6 - - - +
3417H VAL* 1.3 59.4 + - - +
3418H ASP 3.2 1.7 + - - -
3419H ASN* 3.3 6.4 + - - +
3420H ASN* 2.9 29.5 + - + +
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Residues in contact with VAL3417 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3413H LEU 3.0 17.7 + - - +
3414H ILE* 3.6 11.0 - - - +
3415H ARG 3.2 0.6 - - - -
3416H TYR* 1.3 75.2 - - - +
3418H ASP* 1.3 64.5 + - - +
3419H ASN 3.2 0.6 + - - -
3420H ASN* 3.6 14.8 + - - +
3421H ARG* 3.8 12.8 + - - +
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Residues in contact with ASP3418 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3414H ILE 3.9 4.6 + - - +
3415H ARG* 3.5 14.8 + - - +
3416H TYR 3.2 0.6 - - - -
3417H VAL* 1.3 80.4 - - - +
3419H ASN* 1.3 57.9 + - + +
3421H ARG* 4.7 6.8 + - - +
3422H ALA* 5.2 2.4 + - - +
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Residues in contact with ASN3419 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3415H ARG 4.5 1.5 + - - +
3416H TYR* 3.3 7.3 + - - +
3418H ASP* 1.3 75.5 - - + +
3420H ASN* 1.3 64.2 + - - +
3421H ARG 3.2 2.5 - - - -
3422H ALA* 3.6 9.0 + - + +
3423H HIS* 3.2 23.0 + - - +
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Residues in contact with ASN3420 (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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3416H TYR* 2.9 19.2 + - + +
3417H VAL* 3.6 10.6 + - - -
3419H ASN* 1.3 76.0 - - - +
3421H ARG* 1.3 60.5 + - - +
3423H HIS* 4.0 6.0 - - - +
3424H TRP* 2.9 32.9 + - - +
3429H ASN* 4.4 7.6 + - - +
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Residues in contact with ARG3421 (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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3417H VAL 3.8 11.5 + - - +
3418H ASP 4.9 4.9 - - - +
3419H ASN 3.2 0.8 - - - -
3420H ASN* 1.3 80.2 - - - +
3422H ALA* 1.3 61.1 + - - +
3424H TRP* 4.2 3.4 - - - +
3425H LEU* 3.4 20.4 + - - +
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Residues in contact with ALA3422 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3418H ASP 5.2 1.9 + - - +
3419H ASN* 3.6 11.5 + - - +
3420H ASN 3.4 0.2 - - - -
3421H ARG* 1.3 76.5 - - - +
3423H HIS* 1.3 64.8 + - - +
3425H LEU* 3.6 16.0 + - - +
3426H THR* 3.9 10.2 + - - +
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Residues in contact with HIS3423 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3419H ASN 3.2 18.6 + - - +
3420H ASN* 4.0 6.1 - - - +
3421H ARG 3.3 0.2 - - - -
3422H ALA* 1.3 75.7 - - - +
3424H TRP* 1.3 60.9 + - - +
3426H THR* 2.9 20.2 + - - -
3427H GLU* 2.9 15.7 - - - +
3429H ASN* 4.2 17.5 - - - +
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Residues in contact with TRP3424 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3420H ASN 2.9 18.8 + - - +
3421H ARG* 4.2 4.0 - - - +
3423H HIS* 1.3 74.0 - - - +
3425H LEU* 1.3 64.1 + - - +
3426H THR 3.3 0.4 + - - -
3427H GLU 3.4 20.2 + - - +
3428H PRO* 4.1 7.8 - - + +
3429H ASN* 3.9 12.3 - - - +
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Residues in contact with LEU3425 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1215F ALA* 6.3 4.0 - - + -
3421H ARG 3.4 12.3 + - - +
3422H ALA* 3.7 13.2 - - - +
3423H HIS 3.2 0.8 - - - -
3424H TRP* 1.3 79.4 - - - +
3426H THR* 1.3 65.3 + - + +
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Residues in contact with THR3426 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3422H ALA 3.9 8.5 + - - +
3423H HIS* 2.9 19.6 + - - -
3425H LEU* 1.3 81.1 - - + +
3427H GLU* 1.3 61.3 + - - +
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Residues in contact with GLU3427 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3423H HIS 2.9 16.3 - - - +
3424H TRP* 3.4 8.5 - - - -
3425H LEU 3.5 0.4 - - - -
3426H THR* 1.3 84.8 + - - +
3428H PRO* 1.3 77.9 - - + +
3429H ASN* 4.3 2.3 + - - +
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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