Contacts of the helix formed by residues 3786 - 3800 (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 GLY3786 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3785B THR* 1.3 75.1 - - - +
3787B ALA* 1.3 64.2 + - - -
3788B MET* 3.2 3.8 - - - -
3789B VAL* 3.2 23.4 + - - +
3790B SER* 3.5 10.6 + - - -
3875B PHE* 5.2 4.3 - - - -
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Residues in contact with ALA3787 (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 GLU* 5.5 6.7 - - - +
3719B MET* 6.1 0.9 - - - -
3786B GLY* 1.3 73.4 - - - -
3788B MET* 1.3 60.1 + - - +
3790B SER* 2.9 18.8 + - - +
3791B SER* 2.9 19.6 + - - -
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Residues in contact with MET3788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3712B LEU* 4.6 8.7 - - + -
3713B ASP* 3.4 27.1 - - + +
3714B GLU 3.9 21.5 - - - +
3715B ASP* 4.0 9.6 - - - +
3718B TYR* 3.7 37.2 - - + -
3719B MET* 5.7 5.8 - - + +
3777B MET* 3.7 28.0 - - + +
3786B GLY* 3.2 1.4 - - - -
3787B ALA* 1.3 75.4 - - - +
3789B VAL* 1.3 70.3 + - + +
3791B SER* 3.3 9.3 + - - -
3792B THR* 3.2 23.5 + - + +
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Residues in contact with VAL3789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3777B MET* 6.5 0.7 - - + -
3778B ILE* 4.8 10.1 - - + -
3781B CYS* 4.4 17.0 - - + -
3784B GLU* 3.4 24.5 - - + +
3786B GLY* 3.2 22.3 + - - +
3788B MET* 1.3 84.2 - - + +
3790B SER* 1.3 60.1 + - - +
3792B THR* 3.0 17.7 + - - -
3793B LEU* 3.4 18.0 + - + +
3830B LEU* 4.3 25.4 - - + -
3875B PHE* 4.4 12.8 - - + -
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Residues in contact with SER3790 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3786B GLY 3.5 6.4 + - - -
3787B ALA* 2.9 20.1 + - - +
3788B MET 3.3 0.2 - - - -
3789B VAL* 1.3 77.9 - - - +
3791B SER* 1.3 63.5 + - - +
3793B LEU* 3.7 5.2 + - - +
3794B LYS* 3.1 22.3 + - - +
3874B GLU 5.1 9.2 - - - -
3875B PHE* 4.3 23.5 - - - -
3878B ASP* 6.0 0.7 - - - +
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Residues in contact with SER3791 (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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3718B TYR* 6.5 0.2 - - - -
3719B MET* 4.0 20.0 - - - +
3722B ALA* 4.3 24.6 - - - +
3787B ALA 2.9 16.5 + - - -
3788B MET* 3.3 11.6 + - - -
3789B VAL 3.3 0.8 - - - -
3790B SER* 1.3 78.3 + - - +
3792B THR* 1.3 66.0 + - - +
3794B LYS* 3.3 15.8 + - - +
3795B LEU* 3.3 13.5 + - - +
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Residues in contact with THR3792 (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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3718B TYR* 3.4 42.2 - - + +
3722B ALA* 5.8 1.8 - - + -
3774B VAL* 4.7 17.1 - - + +
3777B MET* 3.7 19.8 - - + +
3778B ILE* 4.0 16.5 - - - +
3788B MET* 3.2 11.7 + - + +
3789B VAL* 3.0 19.6 + - - -
3791B SER* 1.3 77.0 - - - +
3793B LEU* 1.3 57.7 + - - +
3795B LEU* 3.4 6.4 + - - +
3796B GLY* 3.1 22.9 + - - -
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Residues in contact with LEU3793 (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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3778B ILE* 3.8 25.8 - - + -
3789B VAL* 3.4 22.8 + - + +
3790B SER* 4.1 5.4 - - - +
3791B SER 3.3 0.4 - - - -
3792B THR* 1.3 74.9 + - - +
3794B LYS* 1.3 64.2 + - - +
3796B GLY* 4.0 1.7 - - - +
3797B ILE* 3.3 29.6 + - - +
3830B LEU* 4.9 4.9 - - + -
3875B PHE* 4.7 18.4 - - + +
3878B ASP* 4.9 15.1 - - + +
3879B LEU* 4.7 29.4 - - + +
3882B PHE* 4.6 27.8 - - + -
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Residues in contact with LYS3794 (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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3723B ASP* 6.2 2.9 - - - -
3726B ALA* 4.2 11.5 - - + +
3790B SER 3.1 15.2 + - - +
3791B SER* 3.5 12.3 - - - +
3792B THR 3.2 0.4 - - - -
3793B LEU* 1.3 77.3 - - - +
3795B LEU* 1.3 59.4 + - - +
3797B ILE* 3.3 32.4 - - + +
3798B SER* 3.7 8.8 + - - -
3877B GLN* 5.6 9.4 - - - +
3878B ASP* 5.5 4.5 - - + +
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Residues in contact with LEU3795 (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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3722B ALA* 3.5 31.0 - - + +
3725B MET* 3.8 35.2 - - + -
3726B ALA* 3.8 17.7 - - + +
3765B LEU* 5.1 3.4 - - + -
3770B ALA* 5.3 6.3 - - + +
3774B VAL* 3.9 23.3 - - + -
3791B SER 3.3 9.7 + - - +
3792B THR* 3.4 8.3 + - - +
3794B LYS* 1.3 78.3 - - - +
3796B GLY* 1.3 64.3 + - - +
3798B SER* 3.4 10.4 + - - -
3799B ILE* 3.5 25.2 - - + +
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Residues in contact with GLY3796 (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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3774B VAL* 4.9 11.7 - - - -
3792B THR 3.1 14.8 + - - -
3793B LEU* 3.5 2.6 + - - -
3794B LYS 3.4 0.6 - - - -
3795B LEU* 1.3 80.7 - - - +
3797B ILE* 1.3 59.9 + - - +
3798B SER 3.3 0.7 + - - -
3799B ILE* 3.4 12.6 + - - +
3800B LEU* 3.5 22.2 - - - +
3882B PHE* 3.9 21.1 - - - -
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Residues in contact with ILE3797 (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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3793B LEU 3.3 14.1 + - - +
3794B LYS* 3.3 34.3 - - + +
3796B GLY* 1.3 75.7 - - - +
3798B SER* 1.3 61.5 + - - +
3799B ILE 3.3 0.2 - - - -
3800B LEU* 3.8 3.8 + - - +
3801B ASN* 3.3 25.8 + - - +
3877B GLN* 5.6 5.4 - - - +
3878B ASP* 4.1 18.2 - - + +
3881B ARG* 4.5 16.8 - - + -
3882B PHE* 3.8 38.4 - - + +
3885B LEU* 4.5 7.6 - - + +
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Residues in contact with SER3798 (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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3726B ALA* 3.2 30.6 + - - -
3729B CYS* 3.2 28.4 - - - +
3730B HIS* 3.8 12.5 + - - +
3758B LEU* 5.8 2.4 - - - +
3794B LYS 3.7 10.5 + - - -
3795B LEU 3.4 11.2 + - - -
3796B GLY 3.2 1.2 - - - -
3797B ILE* 1.3 83.4 - - - +
3799B ILE* 1.3 61.5 + - - +
3801B ASN* 3.9 14.4 - - - +
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Residues in contact with ILE3799 (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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3726B ALA* 6.5 0.2 - - - -
3729B CYS* 3.9 16.8 - - + -
3758B LEU* 5.4 2.4 - - - +
3762B GLN* 3.9 28.9 - - + +
3765B LEU* 3.7 36.8 - - + -
3766B HIS* 5.6 4.0 - - + +
3770B ALA* 6.1 1.3 - - + -
3771B ALA* 6.1 1.1 - - + -
3774B VAL* 6.3 0.7 - - + -
3795B LEU* 3.5 24.2 - - + +
3796B GLY* 3.4 8.0 + - - +
3797B ILE 3.3 0.6 - - - -
3798B SER* 1.3 82.9 - - - +
3800B LEU* 1.3 61.2 + - + +
3801B ASN 3.2 4.3 + - - -
3802B GLY 4.6 2.1 + - - -
3804B ASN* 3.7 11.4 + - - +
3807B VAL* 3.9 30.5 - - + -
3811B MET* 6.3 0.2 - - + -
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Residues in contact with LEU3800 (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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3796B GLY* 3.5 20.5 + - - +
3797B ILE* 3.8 2.4 + - - +
3799B ILE* 1.3 80.1 - - + +
3801B ASN* 1.3 63.8 + - - +
3802B GLY 3.3 3.1 - - - -
3803B GLY* 3.1 15.8 + - - -
3804B ASN* 4.2 13.9 - - - +
3807B VAL* 3.7 26.2 - - + -
3808B GLN* 5.0 8.7 - - + -
3811B MET* 4.2 19.5 - - + -
3882B PHE* 4.7 9.0 - - + +
3885B LEU* 3.1 46.8 - - + +
3886B LEU* 3.9 24.9 - - + +
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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