Contacts of the helix formed by residues 3399 - 3427 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3398B GLU* 1.3 77.3 - - - +
3400B SER* 1.3 59.4 + - - +
3402B LEU* 3.9 5.3 - - - +
3403B CYS* 3.0 31.7 + - - +
3452B PHE* 6.4 1.8 - - + -
3455B GLU* 3.7 37.1 - - + +
3456B GLU* 5.2 1.1 - - - +
3459B PHE* 4.6 2.9 - - + +
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Residues in contact with SER3400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3398B GLU 3.3 5.2 - - - +
3399B PHE* 1.3 79.6 - - - +
3401B VAL* 1.3 57.5 + - - +
3404B ARG* 3.1 29.6 + - - +
3459B PHE* 3.7 40.9 - - - -
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Residues in contact with VAL3401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3398B GLU* 3.6 13.1 + - - +
3399B PHE 3.4 0.2 - - - -
3400B SER* 1.3 79.4 - - - +
3402B LEU* 1.3 61.4 + - - +
3404B ARG* 4.0 5.3 - - - +
3405B ASP* 3.1 24.8 + - - +
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Residues in contact with LEU3402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3398B GLU 3.1 19.7 + - - +
3399B PHE* 3.9 6.5 - - - +
3401B VAL* 1.3 75.8 - - - +
3403B CYS* 1.3 58.7 + - - +
3405B ASP* 3.5 4.3 + - - +
3406B LEU* 3.0 28.4 + - - +
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Residues in contact with CYS3403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3399B PHE 3.0 19.2 + - - +
3402B LEU* 1.3 74.5 - - - +
3404B ARG* 1.3 65.5 + - - +
3406B LEU* 3.4 7.6 + - - +
3407B TYR* 3.3 20.4 + - - +
3456B GLU* 4.3 16.6 - - + +
3459B PHE* 3.6 32.8 - - + -
3460B VAL* 5.4 3.1 - - + +
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Residues in contact with ARG3404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3400B SER 3.1 20.1 + - - +
3401B VAL* 4.0 6.1 - - - +
3403B CYS* 1.3 77.9 - - - +
3405B ASP* 1.3 61.7 + - - +
3407B TYR* 3.4 14.7 + - - +
3408B ALA* 3.5 10.9 + - - +
3459B PHE* 4.6 10.5 - - + -
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Residues in contact with ASP3405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3401B VAL 3.1 18.5 + - - +
3402B LEU* 4.0 4.7 - - - +
3404B ARG* 1.3 74.6 - - - +
3406B LEU* 1.3 59.1 + - - +
3408B ALA* 3.4 7.7 + - - +
3409B LEU* 3.0 28.2 + - - +
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Residues in contact with LEU3406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3402B LEU 3.0 18.4 + - - +
3403B CYS* 3.7 9.4 - - - +
3404B ARG 3.2 0.4 - - - -
3405B ASP* 1.3 78.3 - - - +
3407B TYR* 1.3 57.5 + - - +
3409B LEU* 3.4 5.9 + - - +
3410B TYR* 2.9 30.4 + - - +
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Residues in contact with TYR3407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3403B CYS 3.3 10.1 + - - +
3404B ARG* 3.7 10.3 - - - +
3405B ASP 3.3 0.6 - - - -
3406B LEU* 1.3 80.5 - - - +
3408B ALA* 1.3 61.4 + - - +
3410B TYR* 3.4 5.9 + - - +
3411B PRO* 3.1 23.4 - - - +
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Residues in contact with ALA3408 (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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3404B ARG 3.5 7.8 + - - +
3405B ASP* 3.4 10.0 + - - +
3406B LEU 3.3 0.4 - - - -
3407B TYR* 1.3 77.0 - - - +
3409B LEU* 1.3 62.3 + - - +
3411B PRO* 3.5 7.0 - - - +
3412B LEU* 3.1 23.2 + - - +
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Residues in contact with LEU3409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3405B ASP 3.0 17.0 + - - +
3406B LEU* 3.9 6.7 - - - +
3408B ALA* 1.3 74.5 - - - +
3410B TYR* 1.3 60.8 + - - +
3412B LEU* 4.0 5.1 - - - +
3413B LEU* 3.0 30.8 + - - +
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Residues in contact with TYR3410 (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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3406B LEU 2.9 17.7 + - - +
3407B TYR* 3.8 7.4 - - - +
3408B ALA 3.3 0.2 - - - -
3409B LEU* 1.3 77.9 - - - +
3411B PRO* 1.3 55.6 - - - +
3413B LEU* 3.5 4.2 + - - +
3414B ILE* 3.0 30.5 + - - +
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Residues in contact with PRO3411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3407B TYR 3.1 17.5 - - - +
3408B ALA* 3.8 6.5 - - - +
3410B TYR* 1.3 78.1 - - - +
3412B LEU* 1.3 61.9 + - - +
3414B ILE* 3.4 5.2 + - + +
3415B ARG* 3.1 23.6 + - - +
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Residues in contact with LEU3412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3408B ALA 3.1 17.3 + - - +
3409B LEU* 4.0 6.1 - - - +
3410B TYR 3.4 0.2 - - - -
3411B PRO* 1.3 77.8 - - - +
3413B LEU* 1.3 57.5 + - - +
3415B ARG* 3.5 4.6 + - - +
3416B TYR* 3.0 29.7 + - - +
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Residues in contact with LEU3413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3409B LEU 3.0 19.0 + - - +
3410B TYR* 4.0 4.9 - - - +
3412B LEU* 1.3 74.3 - - - +
3414B ILE* 1.3 60.3 + - - +
3416B TYR* 3.8 5.6 - - - +
3417B VAL* 3.0 29.3 + - - +
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Residues in contact with ILE3414 (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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3410B TYR 3.0 17.7 + - - +
3411B PRO* 3.8 7.2 - - + +
3413B LEU* 1.3 77.4 - - - +
3415B ARG* 1.3 62.2 + - - +
3417B VAL* 3.3 17.5 + - - +
3418B ASP* 3.9 4.9 + - - +
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Residues in contact with ARG3415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3411B PRO 3.1 17.6 + - - +
3412B LEU* 4.0 4.9 - - - +
3414B ILE* 1.3 76.2 - - - +
3416B TYR* 1.3 62.6 + - - +
3417B VAL 3.4 0.3 + - - -
3418B ASP* 3.5 17.7 + - - +
3419B ASN* 4.5 1.9 + - - +
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Residues in contact with TYR3416 (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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3412B LEU 3.0 18.1 + - - +
3413B LEU* 3.9 6.7 - - - +
3414B ILE 3.3 0.2 - - - -
3415B ARG* 1.3 73.7 - - - +
3417B VAL* 1.3 59.2 + - - +
3418B ASP 3.2 1.5 + - - -
3419B ASN* 3.3 6.5 + - - +
3420B ASN* 2.9 29.5 + - + +
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Residues in contact with VAL3417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3413B LEU 3.0 17.5 + - - +
3414B ILE* 3.6 10.5 - - - +
3415B ARG 3.2 1.0 - - - -
3416B TYR* 1.3 74.4 - - - +
3418B ASP* 1.3 64.0 + - - +
3419B ASN 3.2 0.4 + - - -
3420B ASN* 3.6 15.1 + - - +
3421B ARG* 3.8 12.6 + - - +
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Residues in contact with ASP3418 (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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3414B ILE 3.9 4.4 + - - +
3415B ARG* 3.5 13.8 + - - +
3416B TYR 3.2 0.8 - - - -
3417B VAL* 1.3 81.1 - - - +
3419B ASN* 1.3 57.5 + - + +
3421B ARG* 4.7 6.6 + - - +
3422B ALA* 5.2 2.3 + - - +
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Residues in contact with ASN3419 (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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3415B ARG 4.5 1.7 + - - +
3416B TYR* 3.3 7.1 + - - +
3417B VAL 3.2 0.2 - - - -
3418B ASP* 1.3 76.8 - - + +
3420B ASN* 1.3 64.3 + - - +
3421B ARG 3.2 2.7 - - - -
3422B ALA* 3.6 8.2 + - - +
3423B HIS* 3.2 23.1 + - - +
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Residues in contact with ASN3420 (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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3416B TYR* 2.9 19.3 + - + +
3417B VAL* 3.6 11.3 + - - +
3419B ASN* 1.3 77.4 - - - +
3421B ARG* 1.3 60.2 + - - +
3423B HIS* 3.8 5.8 - - - -
3424B TRP* 2.9 32.7 + - - +
3429B ASN* 4.4 8.4 + - - +
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Residues in contact with ARG3421 (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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3417B VAL 3.8 11.5 + - - +
3418B ASP 4.9 4.5 - - - +
3419B ASN 3.2 1.0 - - - -
3420B ASN* 1.3 79.7 - - - +
3422B ALA* 1.3 61.1 + - - +
3424B TRP* 4.2 3.0 - - - +
3425B LEU* 3.4 20.8 + - - +
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Residues in contact with ALA3422 (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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3418B ASP 5.2 1.9 + - - +
3419B ASN* 3.6 10.3 + - - +
3420B ASN 3.4 0.4 - - - -
3421B ARG* 1.3 76.9 - - - +
3423B HIS* 1.3 63.4 + - - +
3425B LEU* 3.6 15.4 + - - +
3426B THR* 3.9 10.9 + - - +
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Residues in contact with HIS3423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3419B ASN 3.2 18.5 + - - +
3420B ASN* 4.0 5.4 - - - +
3422B ALA* 1.3 75.9 - - - +
3424B TRP* 1.3 60.5 - - - +
3426B THR* 2.9 20.6 + - - -
3427B GLU 2.9 15.0 - - - +
3429B ASN* 4.2 18.2 - - - +
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Residues in contact with TRP3424 (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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3420B ASN 2.9 19.6 + - - +
3421B ARG* 4.2 3.8 - - - +
3423B HIS* 1.3 74.3 - - - +
3425B LEU* 1.3 65.9 + - - +
3426B THR 3.3 0.2 - - - -
3427B GLU* 3.4 20.5 + - - +
3428B PRO* 4.1 8.0 - - + +
3429B ASN* 3.9 12.7 - - - +
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Residues in contact with LEU3425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3421B ARG 3.4 12.9 + - - +
3422B ALA* 3.7 13.0 - - - +
3423B HIS 3.2 0.8 - - - -
3424B TRP* 1.3 80.3 - - - +
3426B THR* 1.3 64.7 + - + +
1215H ALA* 6.3 3.6 - - + -
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Residues in contact with THR3426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3422B ALA 3.9 8.2 + - - +
3423B HIS* 2.9 19.6 + - - -
3424B TRP 4.3 0.2 - - - -
3425B LEU* 1.3 81.4 - - + +
3427B GLU* 1.3 60.7 + - - +
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Residues in contact with GLU3427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3423B HIS 2.9 16.3 - - - +
3424B TRP* 3.4 8.8 - - - -
3425B LEU 3.5 0.4 - - - -
3426B THR* 1.3 85.9 + - - +
3428B PRO* 1.3 78.1 - - + +
3429B ASN* 3.7 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) + - + + + + + -
------------------------------------------------------------
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