Contacts of the helix formed by residues 3704 - 3721 (chain B) 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 THR3704 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3522B GLN* 2.8 49.2 + - + +
3570B ASP* 4.0 7.6 + - - +
3571B ASP* 4.9 1.2 + - - -
3572B LEU* 4.1 20.9 - - + -
3702B THR* 4.3 2.9 + - - +
3703B VAL* 1.3 79.7 - - - +
3705B ARG* 1.3 65.0 + - - +
3706B SER* 4.1 4.7 + - - -
3707B SER* 3.2 23.1 + - - -
3708B LEU* 3.0 25.1 + - - +
3813B PHE* 3.8 7.9 - - - -
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Residues in contact with ARG3705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3522B GLN* 6.0 0.2 - - - +
3523B GLN* 4.6 19.3 - - - +
3704B THR* 1.3 75.5 - - - +
3706B SER* 1.3 60.8 + - - +
3709B GLN* 3.0 44.3 + - - +
3809B SER* 3.4 19.4 + - - +
3810B SER* 6.5 0.4 - - - -
3813B PHE* 3.8 34.4 - - + +
4350B GLU* 4.8 18.0 + - - +
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Residues in contact with SER3706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3570B ASP* 5.7 2.7 - - - -
3571B ASP* 5.7 5.2 - - - -
3704B THR* 3.4 4.5 + - - -
3705B ARG* 1.3 76.6 - - - +
3707B SER* 1.3 60.8 + - - +
3709B GLN* 3.2 15.1 + - - +
3710B SER* 2.9 33.7 + - - -
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Residues in contact with SER3707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3568B PRO* 5.1 4.7 - - - +
3570B ASP* 3.5 36.2 + - - +
3703B VAL* 5.1 5.2 - - - +
3704B THR* 3.2 26.5 + - - -
3706B SER* 1.3 78.2 - - - +
3708B LEU* 1.3 59.5 + - - +
3710B SER* 3.2 10.5 + - - -
3711B GLN* 2.9 33.5 + - - +
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Residues in contact with LEU3708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3703B VAL* 4.1 8.9 - - + +
3704B THR 3.0 14.6 + - - +
3705B ARG 3.7 4.0 - - - +
3707B SER* 1.3 81.2 - - - +
3709B GLN* 1.3 57.4 + - - +
3711B GLN* 3.2 13.0 + - + +
3712B CYS* 2.9 47.7 + - - -
3808B CYS 4.2 1.1 - - - +
3809B SER* 3.0 38.6 - - - +
3812B TYR* 3.4 31.4 - - + -
3813B PHE* 4.5 2.0 - - + -
3829B LEU* 4.1 21.8 - - + -
3832B PHE* 4.1 11.4 - - + -
3833B LEU* 5.6 2.0 - - + -
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Residues in contact with GLN3709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3705B ARG* 3.0 36.2 + - - +
3706B SER* 3.4 12.0 - - - +
3708B LEU* 1.3 77.1 - - - +
3710B SER* 1.3 57.1 + - - +
3712B CYS 3.2 0.7 + - - -
3713B LEU* 2.9 30.1 + - - +
3802B LEU* 4.1 17.5 - - + +
3805B SER* 3.3 21.7 + - - +
3806B THR* 3.6 48.7 + - - +
3809B SER* 4.0 5.5 - - - -
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Residues in contact with SER3710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3569B ALA* 5.7 9.2 - - - +
3706B SER* 2.9 16.6 + - - -
3707B SER* 3.2 11.2 + - - -
3709B GLN* 1.3 77.8 - - - +
3711B GLN* 1.3 64.3 + - - +
3713B LEU* 3.9 6.8 - - - +
3714B ASN* 3.2 32.6 + - - +
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Residues in contact with GLN3711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3568B PRO* 5.5 7.8 - - - +
3595B GLN* 4.6 19.2 + - - +
3707B SER* 2.9 16.8 + - - +
3708B LEU* 3.3 18.6 - - + +
3710B SER* 1.3 77.8 - - - +
3712B CYS* 1.3 63.6 + - - +
3714B ASN* 3.7 9.4 + - - +
3715B GLU* 3.4 28.8 + - - +
3829B LEU* 5.7 5.3 - - + +
3833B LEU* 4.6 24.3 - - + +
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Residues in contact with CYS3712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3708B LEU* 2.9 38.0 + - - +
3709B GLN* 3.2 1.1 + - - +
3711B GLN* 1.3 77.1 - - - +
3713B LEU* 1.3 65.3 + - - +
3715B GLU* 3.1 9.3 + - - +
3716B VAL* 2.9 26.1 + - + +
3805B SER* 3.6 21.1 - - - +
3808B CYS* 3.9 23.3 - - + -
3832B PHE* 4.2 7.2 - - - -
3833B LEU* 5.4 4.5 - - - -
3836B TYR* 3.9 19.9 - - + -
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Residues in contact with LEU3713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3709B GLN 2.9 13.3 + - - +
3710B SER* 3.9 7.6 - - - +
3712B CYS* 1.3 74.3 - - - +
3714B ASN* 1.3 63.3 + - - +
3716B VAL* 3.2 5.1 + - - +
3717B LEU* 2.9 42.7 + - + +
3728B ARG* 6.0 3.1 - - - -
3794B VAL* 5.7 6.1 - - + -
3797B VAL* 4.3 17.5 - - + +
3798B SER* 4.6 12.8 - - - +
3801B TYR* 3.8 33.4 - - + -
3802B LEU* 4.3 19.3 - - + +
3805B SER* 3.0 20.9 + - - +
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Residues in contact with ASN3714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3710B SER* 3.2 20.9 + - - +
3711B GLN* 3.8 10.1 + - - +
3712B CYS 3.2 0.2 - - - -
3713B LEU* 1.3 80.9 - - - +
3715B GLU* 1.3 60.9 + - + +
3717B LEU* 3.2 5.5 + - - +
3718B LYS* 2.9 37.2 + - - +
3725B ASP* 3.6 12.7 - - - +
3728B ARG* 2.8 31.2 + - - +
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Residues in contact with GLU3715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3711B GLN* 3.4 17.5 + - - +
3712B CYS* 3.1 10.1 + - - +
3714B ASN* 1.3 81.8 - - + +
3716B VAL* 1.3 62.4 + - - +
3718B LYS* 3.2 13.2 + - + +
3719B ALA* 3.0 18.2 + - - +
3833B LEU* 3.5 24.2 - - - +
3836B TYR* 3.2 26.9 - - + +
3837B HIS* 3.2 32.0 + - - -
3840B LEU* 3.7 16.6 - - + +
3841B TYR* 4.9 7.0 + - - +
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Residues in contact with VAL3716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3712B CYS* 2.9 20.2 + - + +
3713B LEU* 3.2 11.4 + - - +
3715B GLU* 1.3 76.1 - - - +
3717B LEU* 1.3 52.5 + - + +
3719B ALA* 3.2 3.9 + - - +
3720B GLU* 2.6 44.0 + - + +
3801B TYR* 3.4 44.0 - - + +
3804B LEU* 3.4 32.8 - - + -
3805B SER* 4.9 2.5 - - - +
3836B TYR* 4.8 7.4 - - + -
3840B LEU* 4.1 19.5 - - + -
3856B LEU* 4.7 1.1 - - + -
3859B ILE* 6.1 0.2 - - + -
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Residues in contact with LEU3717 (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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3713B LEU* 2.9 31.3 + - + +
3714B ASN 3.4 6.3 - - - +
3716B VAL* 1.3 79.1 - - + +
3718B LYS* 1.3 57.3 + - - +
3720B GLU* 4.5 1.1 - - - -
3721B ARG* 2.6 42.8 + - + +
3724B VAL* 5.5 2.9 - - + -
3725B ASP* 3.5 36.1 - - + +
3728B ARG* 3.8 20.2 - - - +
3797B VAL* 3.4 41.7 - - + -
3801B TYR* 3.9 23.6 - - + -
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Residues in contact with LYS3718 (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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3714B ASN* 2.9 16.8 + - - +
3715B GLU* 3.2 15.0 + - + +
3717B LEU* 1.3 75.2 - - - +
3719B ALA* 1.3 61.1 + - - +
3722B PRO* 3.4 30.5 - - - +
3725B ASP* 3.1 28.5 - - + +
3726B GLU* 5.9 6.5 - - + -
3841B TYR* 4.5 16.5 - - - +
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Residues in contact with ALA3719 (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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3715B GLU 3.0 11.4 + - - +
3716B VAL 3.4 7.4 - - - +
3718B LYS* 1.3 79.5 - - - +
3720B GLU* 1.3 64.6 + - + +
3722B PRO* 4.4 3.3 - - - +
3840B LEU* 3.6 44.4 - - + +
3841B TYR* 4.4 14.9 - - + -
3855B ARG* 3.9 19.4 + - - +
3859B ILE* 5.2 2.5 - - + -
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Residues in contact with GLU3720 (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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3716B VAL* 2.6 28.1 + - + +
3717B LEU* 4.5 0.4 - - - -
3719B ALA* 1.3 77.1 - - + +
3721B ARG* 1.3 66.6 + - + +
3722B PRO* 3.1 11.6 - - - +
3801B TYR* 3.3 35.7 + - + +
3852B HIS* 4.0 21.6 + - - +
3855B ARG* 3.5 28.6 + - - +
3856B LEU* 3.1 40.2 + - - +
3859B ILE* 3.6 19.8 - - + +
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Residues in contact with ARG3721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3717B LEU* 2.6 20.1 + - + +
3720B GLU* 1.3 73.4 - - + +
3722B PRO* 1.4 56.7 - - - +
3723B ASP 3.3 2.0 - - - -
3724B VAL* 2.8 57.3 + - + +
3725B ASP 3.1 9.1 + - - +
3796B THR* 6.4 0.2 - - - +
3797B VAL* 5.9 7.0 - - + +
3800B GLN* 5.0 14.8 - - - +
3801B TYR* 3.5 28.0 + - + +
3852B HIS* 3.1 57.5 + - - +
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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) + - + + + + + -
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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