Contacts of the helix formed by residues 3769 - 3781 (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 GLY3769 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3695B HIS* 3.8 14.1 - - - -
3698B VAL* 3.5 20.7 - - - +
3699B LEU* 5.5 5.9 - - - +
3768B ARG* 1.3 75.2 - - - +
3770B ALA* 1.3 60.1 + - - +
3771B ALA 3.5 2.5 - - - -
3772B GLU* 3.8 16.8 + - - +
3773B MET* 3.6 15.4 + - - +
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Residues in contact with ALA3770 (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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3698B VAL* 4.0 10.0 - - + +
3725B MET* 5.2 6.5 - - - -
3765B LEU* 3.3 42.2 - - + +
3768B ARG* 3.1 5.6 + - + -
3769B GLY* 1.3 75.6 - - - +
3771B ALA* 1.3 65.3 + - - +
3772B GLU 3.2 0.2 - - - -
3773B MET* 3.4 13.6 + - - +
3774B VAL* 3.5 18.9 + - - +
3795B LEU* 5.3 5.9 - - + +
3799B ILE* 6.1 1.6 - - + -
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Residues in contact with ALA3771 (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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3765B LEU 4.6 3.5 + - - +
3766B HIS* 5.4 7.0 - - - +
3768B ARG 4.6 2.3 + - - +
3769B GLY* 3.5 0.4 - - - -
3770B ALA* 1.3 78.8 - - - +
3772B GLU* 1.3 64.4 + - + +
3774B VAL* 3.3 23.7 - - - +
3775B LEU* 3.5 13.2 - - - +
3799B ILE* 6.1 0.7 - - + -
3807B VAL* 3.9 28.0 - - + +
3810B LYS* 4.9 14.8 - - + -
3811B MET* 4.4 9.9 - - + +
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Residues in contact with GLU3772 (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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3769B GLY* 3.8 16.7 + - - +
3770B ALA 3.2 0.6 - - - -
3771B ALA* 1.3 78.1 - - + +
3773B MET* 1.3 64.2 + - - +
3774B VAL 3.3 0.2 - - - -
3775B LEU* 3.5 6.9 + - - +
3776B GLN* 3.3 36.4 + - - +
3810B LYS* 3.1 38.5 + - + +
3813B ASP* 4.7 0.9 - - - +
3814B TYR* 3.2 43.5 - - + +
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Residues in contact with MET3773 (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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3698B VAL* 4.3 16.8 - - - +
3701B PHE* 5.4 9.9 - - + -
3702B SER* 5.7 6.3 - - - +
3718B TYR* 4.4 11.0 + - - +
3769B GLY 3.6 11.6 + - - +
3770B ALA* 3.4 11.1 + - - +
3771B ALA 3.3 0.8 - - - -
3772B GLU* 1.3 81.2 - - - +
3774B VAL* 1.3 61.9 - - + +
3776B GLN* 3.6 7.0 + - - +
3777B MET* 3.3 25.5 + - - +
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Residues in contact with VAL3774 (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* 5.3 5.4 - - - +
3770B ALA 3.5 13.0 - - - +
3771B ALA* 3.3 21.8 - - - +
3773B MET* 1.3 77.9 - - + +
3775B LEU* 1.3 71.0 + - + +
3777B MET* 4.2 4.1 - - - +
3778B ILE* 3.2 27.7 + - - +
3792B THR* 4.7 19.3 - - + +
3795B LEU* 3.9 27.1 - - + -
3796B GLY* 4.9 12.3 - - - -
3799B ILE* 6.3 0.9 - - + -
3811B MET* 4.5 8.7 - - + -
3823B PHE* 4.8 0.2 - - - -
3882B PHE* 5.3 7.1 - - + -
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Residues in contact with LEU3775 (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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3771B ALA 3.5 16.8 - - - +
3772B GLU* 3.5 10.2 + - - +
3773B MET 3.2 0.4 - - - -
3774B VAL* 1.3 91.9 - - + +
3776B GLN* 1.3 65.1 + - - +
3777B MET 3.3 0.2 - - - -
3778B ILE 3.5 0.3 + - - -
3779B SER* 3.5 8.7 + - - -
3811B MET* 3.8 53.2 - - + +
3814B TYR* 4.5 17.3 - - + -
3815B LEU* 4.4 20.2 - - + -
3823B PHE* 3.2 47.1 - - + -
3882B PHE* 5.2 5.4 - - + -
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Residues in contact with GLN3776 (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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462B GLU* 4.1 17.6 + - - -
3702B SER* 4.1 21.8 - - - +
3705B ALA* 4.4 7.1 - - + +
3706B LEU* 3.4 32.6 - - + +
3772B GLU* 3.3 25.0 + - - +
3773B MET* 3.6 5.2 + - - +
3774B VAL 3.6 0.2 - - - -
3775B LEU* 1.3 76.4 - - - +
3777B MET* 1.3 59.0 + - - +
3779B SER* 3.5 7.3 + - - +
3780B ALA* 3.1 26.0 + - - +
3814B TYR* 2.9 40.2 + - + +
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Residues in contact with MET3777 (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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3701B PHE* 5.9 1.1 - - - +
3704B THR* 5.8 2.7 - - - -
3705B ALA* 4.5 15.4 - - + +
3712B LEU* 5.8 4.3 - - + -
3718B TYR* 3.8 20.9 - - + +
3773B MET 3.3 18.7 + - - +
3774B VAL 4.6 2.5 - - - +
3775B LEU 3.3 0.2 - - - -
3776B GLN* 1.3 76.3 - - - +
3778B ILE* 1.3 65.6 + - - +
3780B ALA* 3.2 26.3 + - + -
3781B CYS* 3.4 14.3 + - + +
3788B MET* 3.7 29.2 - - + +
3789B VAL* 6.5 0.7 - - + -
3792B THR* 3.7 33.4 - - + +
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Residues in contact with ILE3778 (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 3.2 18.8 + - - +
3775B LEU 3.5 0.8 + - - +
3776B GLN 3.3 0.6 - - - -
3777B MET* 1.3 77.9 - - - +
3779B SER* 1.3 59.5 + - - +
3781B CYS* 3.2 21.1 - - - -
3789B VAL* 4.8 11.4 - - + -
3792B THR* 4.0 19.5 - - - +
3793B LEU* 3.8 32.5 - - + -
3823B PHE* 3.8 31.2 - - + +
3826B SER* 3.1 30.8 + - - +
3827B ILE* 4.8 7.2 - - + -
3830B LEU* 5.4 7.2 - - + -
3882B PHE* 6.3 3.1 - - + -
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Residues in contact with SER3779 (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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3775B LEU 3.5 8.5 + - - -
3776B GLN* 3.5 10.0 + - - -
3777B MET 3.3 0.4 - - - -
3778B ILE* 1.3 78.9 - - - +
3780B ALA* 1.3 60.4 + - - +
3781B CYS 3.3 0.6 + - - -
3782B LYS* 3.6 11.4 + - - +
3821B VAL 4.6 2.8 + - - -
3822B GLY* 3.7 25.9 - - - +
3823B PHE* 3.7 24.8 + - - +
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Residues in contact with ALA3780 (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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3705B ALA* 3.9 24.7 - - + +
3710B SER 4.5 3.3 - - - +
3711B LYS* 2.9 20.5 - - - +
3776B GLN 3.1 17.4 + - - +
3777B MET* 3.2 24.6 + - + +
3779B SER* 1.3 75.8 - - - +
3781B CYS* 1.3 61.2 + - - +
3782B LYS* 3.2 4.7 + - - +
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Residues in contact with CYS3781 (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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3711B LYS* 4.1 9.9 - - - +
3712B LEU* 5.2 5.1 - - + +
3777B MET* 3.4 13.9 + - + +
3778B ILE* 3.2 22.4 - - - +
3779B SER 3.3 1.2 - - - -
3780B ALA* 1.3 78.3 - - - +
3782B LYS* 1.3 65.5 + - - +
3783B GLY* 3.2 19.0 + - - -
3784B GLU* 3.4 39.3 + - + +
3789B VAL* 4.4 19.7 - - + -
3826B SER* 3.7 11.7 - - - -
3830B LEU* 5.3 6.1 - - - -
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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