Contacts of the helix formed by residues 3399 - 3427 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3398F GLU* 1.3 77.7 - - + +
3400F SER* 1.3 61.9 + - - +
3402F LEU* 3.9 5.7 - - - +
3403F CYS* 3.0 31.0 + - - +
3452F PHE* 6.4 2.0 - - + -
3455F GLU* 3.7 37.5 - - + +
3456F GLU* 5.6 1.2 - - - -
3459F PHE* 4.6 3.3 - - + +
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Residues in contact with SER3400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3398F GLU 3.3 5.0 - - - +
3399F PHE* 1.3 80.1 - - - +
3401F VAL* 1.3 57.5 + - - +
3404F ARG* 3.1 29.3 + - - +
3459F PHE* 3.7 38.8 - - - -
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Residues in contact with VAL3401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3398F GLU* 3.6 13.5 + - - +
3400F SER* 1.3 78.9 - - - +
3402F LEU* 1.3 61.7 + - - +
3404F ARG* 4.0 5.0 - - - +
3405F ASP* 3.1 24.8 + - - +
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Residues in contact with LEU3402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3398F GLU 3.1 19.1 + - - +
3399F PHE* 3.9 6.3 - - - +
3400F SER 3.3 0.2 - - - -
3401F VAL* 1.3 76.5 - - - +
3403F CYS* 1.3 60.0 + - - +
3405F ASP* 3.5 4.2 + - - +
3406F LEU* 3.0 28.6 + - - +
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Residues in contact with CYS3403 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3399F PHE 3.0 19.0 + - - +
3402F LEU* 1.3 74.4 - - - +
3404F ARG* 1.3 63.9 + - - +
3406F LEU* 3.4 7.8 + - - +
3407F TYR* 3.3 21.5 + - - +
3456F GLU* 4.3 17.0 - - + +
3459F PHE* 3.6 32.5 - - + -
3460F VAL* 5.4 3.6 - - + +
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Residues in contact with ARG3404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3400F SER 3.1 18.7 + - - +
3401F VAL* 4.0 6.1 - - - +
3403F CYS* 1.3 77.9 - - - +
3405F ASP* 1.3 60.7 + - - +
3407F TYR* 3.4 15.1 + - - +
3408F ALA* 3.5 10.6 + - - +
3459F PHE* 4.6 9.8 - - + -
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Residues in contact with ASP3405 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3401F VAL 3.1 19.1 + - - +
3402F LEU* 4.0 4.3 - - - +
3404F ARG* 1.3 74.1 - - - +
3406F LEU* 1.3 59.5 + - - +
3408F ALA* 3.4 7.6 + - - +
3409F LEU* 3.0 28.4 + - - +
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Residues in contact with LEU3406 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3402F LEU 3.0 17.9 + - - +
3403F CYS* 3.7 9.2 - - - +
3404F ARG 3.2 0.4 - - - -
3405F ASP* 1.3 77.9 - - - +
3407F TYR* 1.3 56.2 + - - +
3409F LEU* 3.8 6.8 - - - +
3410F TYR* 2.9 30.5 + - - +
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Residues in contact with TYR3407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3403F CYS 3.3 10.1 + - - +
3404F ARG* 3.7 9.9 - - - +
3405F ASP 3.3 0.6 - - - -
3406F LEU* 1.3 79.7 - - - +
3408F ALA* 1.3 61.0 + - - +
3410F TYR* 3.4 6.7 + - - +
3411F PRO* 3.1 23.6 - - - +
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Residues in contact with ALA3408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3404F ARG 3.5 8.7 + - - +
3405F ASP* 3.4 9.5 + - - +
3407F TYR* 1.3 78.2 - - - +
3409F LEU* 1.3 62.2 + - - +
3411F PRO* 3.5 5.7 - - - +
3412F LEU* 3.1 23.4 + - - +
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Residues in contact with LEU3409 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3405F ASP 3.0 16.8 + - - +
3406F LEU* 3.9 6.7 - - - +
3407F TYR 3.3 0.2 - - - -
3408F ALA* 1.3 74.3 - - - +
3410F TYR* 1.3 61.0 + - - +
3412F LEU* 4.0 5.1 - - - +
3413F LEU* 3.0 30.5 + - - +
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Residues in contact with TYR3410 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3406F LEU 2.9 18.4 + - - +
3407F TYR* 3.8 7.2 - - - +
3408F ALA 3.3 0.2 - - - -
3409F LEU* 1.3 77.9 - - - +
3411F PRO* 1.3 57.3 - - - +
3413F LEU* 3.9 4.4 - - - +
3414F ILE* 3.0 29.5 + - - +
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Residues in contact with PRO3411 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3407F TYR 3.1 17.5 - - - +
3408F ALA* 3.8 6.3 - - - +
3409F LEU 3.4 0.2 - - - -
3410F TYR* 1.3 77.9 - - - +
3412F LEU* 1.3 61.2 + - - +
3414F ILE* 3.4 5.6 + - + +
3415F ARG* 3.1 24.3 + - - +
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Residues in contact with LEU3412 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3408F ALA 3.1 17.0 + - - +
3409F LEU* 4.0 5.4 - - - +
3411F PRO* 1.3 75.9 - - - +
3413F LEU* 1.3 59.0 + - - +
3415F ARG* 3.5 5.2 + - - +
3416F TYR* 3.0 29.3 + - - +
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Residues in contact with LEU3413 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3409F LEU 3.0 18.1 + - - +
3410F TYR* 4.0 5.6 - - - +
3412F LEU* 1.3 74.6 - - - +
3414F ILE* 1.3 59.8 + - - +
3416F TYR* 3.5 5.9 + - - +
3417F VAL* 3.0 28.9 + - - +
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Residues in contact with ILE3414 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3410F TYR 3.0 19.0 + - - +
3411F PRO* 3.8 6.7 - - + +
3412F LEU 3.3 0.2 - - - -
3413F LEU* 1.3 78.5 - - - +
3415F ARG* 1.3 61.8 + - - +
3417F VAL* 3.3 17.7 + - - +
3418F ASP* 3.9 5.2 + - - +
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Residues in contact with ARG3415 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3411F PRO 3.1 16.7 + - - +
3412F LEU* 4.0 5.6 - - - +
3413F LEU 3.4 0.2 - - - -
3414F ILE* 1.3 76.5 - - - +
3416F TYR* 1.3 60.4 + - - +
3417F VAL 3.4 0.3 + - - -
3418F ASP* 3.5 18.4 + - - +
3419F ASN* 4.5 2.3 + - - +
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Residues in contact with TYR3416 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3412F LEU 3.0 19.0 + - - +
3413F LEU* 3.9 6.5 - - - +
3415F ARG* 1.3 74.2 - - - +
3417F VAL* 1.3 59.8 + - - +
3418F ASP 3.2 1.5 + - - -
3419F ASN* 3.3 6.1 + - - +
3420F ASN* 2.9 29.5 + - + +
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Residues in contact with VAL3417 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3413F LEU 3.0 17.5 + - - +
3414F ILE* 3.6 11.0 - - - +
3415F ARG 3.2 0.8 - - - -
3416F TYR* 1.3 74.7 - - - +
3418F ASP* 1.3 63.9 + - - +
3419F ASN 3.4 0.3 + - - -
3420F ASN* 3.6 14.6 + - - +
3421F ARG* 3.8 12.8 + - - +
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Residues in contact with ASP3418 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3414F ILE 3.9 4.4 + - - +
3415F ARG* 3.5 13.6 + - - +
3416F TYR 3.2 1.0 - - - -
3417F VAL* 1.3 79.2 - - - +
3419F ASN* 1.3 58.1 + - + +
3421F ARG* 4.7 6.2 + - - +
3422F ALA* 5.2 2.1 + - - +
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Residues in contact with ASN3419 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3415F ARG 4.5 1.5 + - - +
3416F TYR* 3.3 8.4 + - - +
3418F ASP* 1.3 77.1 - - + +
3420F ASN* 1.3 63.5 + - - +
3421F ARG 3.2 2.5 - - - -
3422F ALA* 3.6 8.4 + - - +
3423F HIS* 3.2 22.2 + - - +
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Residues in contact with ASN3420 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3416F TYR* 2.9 19.0 + - + +
3417F VAL* 3.6 11.3 + - - +
3419F ASN* 1.3 76.1 - - - +
3421F ARG* 1.3 60.0 + - - +
3423F HIS* 4.4 6.1 - - - -
3424F TRP* 2.9 32.6 + - - +
3429F ASN* 4.4 8.6 + - - +
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Residues in contact with ARG3421 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3417F VAL 3.8 11.9 + - - +
3418F ASP 4.9 4.7 - - - +
3419F ASN 3.2 0.4 - - - -
3420F ASN* 1.3 80.3 - - - +
3422F ALA* 1.3 60.7 + - - +
3424F TRP* 3.7 3.8 + - - +
3425F LEU* 3.4 21.1 + - - +
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Residues in contact with ALA3422 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3418F ASP 5.2 1.7 + - - +
3419F ASN* 3.6 10.5 + - - +
3420F ASN 3.4 0.4 - - - -
3421F ARG* 1.3 76.3 - - - +
3423F HIS* 1.3 64.7 + - - +
3425F LEU* 3.6 15.9 + - - +
3426F THR* 3.9 10.7 + - - +
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Residues in contact with HIS3423 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3419F ASN 3.2 17.8 + - - +
3420F ASN* 4.0 5.4 - - - +
3422F ALA* 1.3 77.0 - - - +
3424F TRP* 1.3 60.3 + - - +
3426F THR* 2.9 21.2 + - - -
3427F GLU 2.9 14.9 - - - +
3429F ASN* 4.2 17.9 - - - +
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Residues in contact with TRP3424 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3420F ASN 2.9 20.1 + - - +
3421F ARG* 4.2 4.0 - - - +
3423F HIS* 1.3 74.7 - - - +
3425F LEU* 1.3 64.2 + - - +
3426F THR 3.6 0.3 + - - -
3427F GLU* 3.4 19.9 + - - +
3428F PRO* 4.1 7.6 - - + +
3429F ASN* 3.9 12.9 - - - +
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Residues in contact with LEU3425 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1215D ALA* 6.3 3.8 - - + -
3421F ARG 3.4 12.6 + - - +
3422F ALA* 3.7 13.0 - - - +
3423F HIS 3.2 1.0 - - - -
3424F TRP* 1.3 80.9 - - - +
3426F THR* 1.3 63.3 + - + +
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Residues in contact with THR3426 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3422F ALA 3.9 7.7 + - - +
3423F HIS* 2.9 19.6 + - - -
3425F LEU* 1.3 81.0 - - + +
3427F GLU* 1.3 62.2 + - - +
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Residues in contact with GLU3427 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3423F HIS 2.9 16.5 - - - +
3424F TRP* 3.4 8.4 - - - -
3425F LEU 3.5 0.6 - - - -
3426F THR* 1.3 85.7 + - - +
3428F PRO* 1.3 79.5 - - + +
3429F ASN* 3.7 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