Contacts of the helix formed by residues 3570 - 3583 (chain A) in PDB entry 5NUG
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 ASP3570 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3568A PRO* 3.3 5.6 - - - +
3569A ALA* 1.3 84.6 - - - +
3571A ASP* 1.3 65.4 + - - +
3572A LEU* 3.1 28.6 + - - +
3573A CYS* 3.1 34.2 + - - +
3574A THR* 3.2 19.4 + - - -
3702A THR 5.4 2.3 - - - +
3704A THR* 4.0 6.6 + - - +
3706A SER* 5.7 2.2 - - - -
3707A SER* 3.5 41.6 + - - +
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Residues in contact with ASP3571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3522A GLN* 3.7 28.1 + - - +
3549A ARG* 4.8 5.2 + - - -
3550A THR* 4.7 12.0 + - + -
3570A ASP* 1.3 76.1 - - - +
3572A LEU* 1.3 65.0 + - - +
3574A THR* 3.2 8.1 + - - -
3575A GLU* 2.9 44.0 + - + +
3704A THR* 4.9 2.4 + - - -
3706A SER* 5.7 4.5 - - - -
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Residues in contact with LEU3572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3520A PHE 4.8 0.4 - - - +
3521A ASP 4.5 0.4 - - - -
3522A GLN* 4.0 33.9 - - - +
3525A ARG* 4.3 14.6 - - - +
3570A ASP* 3.1 10.2 + - - +
3571A ASP* 1.3 83.8 + - - +
3573A CYS* 1.3 59.2 + - - +
3575A GLU* 3.2 16.5 + - - +
3576A ASN* 2.9 61.5 + - - +
3700A ASN 3.9 9.2 - - - +
3701A PHE* 4.3 2.5 - - + -
3702A THR* 3.6 35.0 - - - +
3704A THR* 4.1 12.1 - - + -
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Residues in contact with CYS3573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3567A LEU* 3.8 18.8 - - + +
3568A PRO* 3.6 31.4 - - - +
3570A ASP* 3.1 34.5 + - - +
3572A LEU* 1.3 80.5 - - - +
3574A THR* 1.3 57.0 + - - +
3576A ASN* 3.2 3.8 + - - +
3577A ALA* 2.9 28.4 + - - +
3701A PHE* 3.9 26.2 - - - -
3702A THR 5.4 4.9 - - - -
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Residues in contact with THR3574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3550A THR* 2.4 32.5 - - + +
3559A ARG* 4.0 25.6 - - + +
3562A TRP* 4.3 3.5 - - + -
3567A LEU* 4.7 6.2 - - - +
3568A PRO 4.7 4.0 + - - -
3569A ALA 4.2 5.9 + - - -
3570A ASP 3.2 12.5 + - - -
3571A ASP* 3.2 11.0 + - - -
3573A CYS* 1.3 78.6 - - - +
3575A GLU* 1.3 55.9 + - - +
3577A ALA* 3.2 7.3 + - - +
3578A ILE* 2.9 43.4 + - + +
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Residues in contact with GLU3575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3513A PHE* 3.3 22.8 - - + -
3514A ILE* 5.5 0.9 - - - +
3522A GLN* 5.6 3.0 + - - -
3525A ARG* 3.3 33.4 + - - +
3549A ARG* 3.2 36.1 + - + +
3550A THR* 4.7 13.0 - - - -
3571A ASP* 2.9 27.2 + - - +
3572A LEU* 3.2 17.9 + - - +
3574A THR* 1.3 75.5 - - - +
3576A ASN* 1.3 57.8 + - - +
3578A ILE* 3.2 13.5 + - - +
3579A MET* 2.9 31.2 + - - +
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Residues in contact with ASN3576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3525A ARG* 2.9 27.7 + - - -
3572A LEU* 2.9 21.2 + - - +
3573A CYS 3.5 2.9 - - - +
3575A GLU* 1.3 76.1 - - - +
3577A ALA* 1.3 55.7 + - - +
3579A MET* 3.2 11.8 + - - +
3580A LEU* 2.9 34.8 + - - +
3699A VAL* 3.4 13.6 - - + +
3700A ASN 3.0 27.3 + - - +
3701A PHE* 3.1 49.5 - - + +
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Residues in contact with ALA3577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3562A TRP* 3.7 23.9 - - + -
3567A LEU* 3.6 26.9 - - + -
3573A CYS 2.9 13.4 + - - +
3574A THR 3.4 9.0 - - - +
3576A ASN* 1.3 75.4 - - - +
3578A ILE* 1.3 57.6 + - - +
3580A LEU* 3.2 13.1 + - - +
3581A LYS* 2.9 28.6 + - - +
3599A PHE* 4.1 9.3 - - + -
3701A PHE* 4.6 1.2 - - - -
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Residues in contact with ILE3578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3514A ILE* 4.2 6.3 - - + -
3550A THR* 3.9 8.3 - - - +
3553A LEU* 3.7 39.5 - - + -
3554A SER* 3.6 19.1 - - - -
3562A TRP* 3.3 28.7 - - + -
3574A THR* 2.9 36.2 + - + +
3575A GLU* 3.2 14.3 + - - +
3577A ALA* 1.3 75.7 - - - +
3579A MET* 1.3 55.2 + - - +
3581A LYS* 3.2 3.7 + - - +
3582A ARG* 2.8 52.7 + - - +
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Residues in contact with MET3579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3513A PHE* 3.2 23.1 - - + +
3514A ILE* 3.2 47.6 - - + +
3517A ALA 3.8 1.6 - - - -
3518A GLY* 3.7 28.5 - - - +
3525A ARG* 3.7 27.4 - - - +
3575A GLU 2.9 8.9 + - - +
3576A ASN* 3.2 13.7 + - - +
3578A ILE* 1.3 80.3 - - - +
3580A LEU* 1.3 54.2 + - - +
3583A PHE* 2.7 39.0 + - - +
3697A THR* 5.2 4.3 - - + +
3698A PHE 4.5 1.1 - - - +
3699A VAL* 4.0 24.2 - - + -
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Residues in contact with LEU3580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3576A ASN 2.9 19.2 + - - +
3577A ALA* 3.5 7.4 - - - +
3579A MET* 1.3 76.7 - - - +
3581A LYS* 1.3 55.9 + - - +
3583A PHE* 2.9 32.1 - - - -
3587A PRO* 3.4 34.9 - - + +
3589A ILE* 3.5 30.7 - - + -
3599A PHE* 4.1 22.9 - - + -
3600A ILE* 4.2 6.1 - - + -
3604A TYR* 5.0 5.1 + - - -
3678A PHE* 3.8 13.7 - - + -
3699A VAL* 4.5 6.7 - - + -
3701A PHE* 3.9 20.2 - - + -
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Residues in contact with LYS3581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3553A LEU 5.5 0.6 + - - -
3555A ASN* 5.7 4.0 - - - +
3558A GLU* 3.2 40.8 + - - +
3562A TRP* 4.2 9.6 - - + -
3577A ALA 2.9 12.8 + - - +
3578A ILE* 3.2 8.7 + - - +
3580A LEU* 1.3 79.6 - - - +
3582A ARG* 1.3 92.1 + - + +
3583A PHE* 3.6 6.4 + - - +
3604A TYR* 5.8 2.7 - - - -
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Residues in contact with ARG3582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3182A HIS* 3.4 18.9 + - + +
3186A LEU* 3.9 12.6 - - - +
3189A GLU* 3.2 33.9 + - - -
3190A LYS* 4.5 4.9 - - - +
3514A ILE* 4.6 17.0 - - + -
3553A LEU* 3.3 54.8 + - - +
3554A SER* 4.6 2.6 - - - +
3562A TRP* 6.2 0.2 - - - -
3578A ILE* 2.8 29.2 + - - +
3579A MET 3.5 1.6 - - - +
3581A LYS* 1.3 108.0 - - + +
3583A PHE* 1.3 67.3 + - - +
3584A ASN* 5.0 0.2 - - - +
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Residues in contact with PHE3583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3182A HIS* 4.6 4.0 - - - -
3514A ILE* 5.4 1.6 - - - -
3579A MET 2.7 19.5 + - - +
3580A LEU 2.9 24.0 - - - +
3581A LYS 4.2 5.8 - - - +
3582A ARG* 1.3 79.1 - - - +
3584A ASN* 1.3 65.2 + - - +
3585A ARG 3.6 14.8 - - - +
3586A TYR* 3.3 32.5 - + - -
3587A PRO* 3.5 33.4 - - + -
3604A TYR* 5.3 3.8 - - - -
3676A VAL* 3.8 31.9 - - + -
3677A ILE 5.3 0.2 - - - -
3678A PHE* 5.2 5.8 - + - -
3697A THR* 4.8 7.2 - - + +
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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