Contacts of the helix formed by residues 3786 - 3800 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3785D THR* 1.3 75.1 - - - +
3787D ALA* 1.3 67.5 + - - -
3788D MET* 3.2 3.6 - - - -
3789D VAL* 3.2 21.9 + - - +
3790D SER* 3.5 10.6 + - - -
3875D PHE* 5.2 3.7 - - - -
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Residues in contact with ALA3787 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3714D GLU* 5.5 7.0 - - - +
3719D MET* 6.1 0.9 - - - -
3786D GLY* 1.3 71.9 - - - -
3788D MET* 1.3 58.2 + - - +
3790D SER* 2.9 19.2 + - - +
3791D SER* 2.9 19.0 + - - +
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Residues in contact with MET3788 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3712D LEU* 4.6 8.3 - - + -
3713D ASP* 3.4 28.0 - - + +
3714D GLU 3.9 21.3 - - - +
3715D ASP* 4.0 10.1 - - - +
3718D TYR* 3.7 36.8 - - + -
3719D MET* 5.7 6.1 - - + +
3777D MET* 3.7 28.0 - - + +
3786D GLY* 3.2 0.8 - - - -
3787D ALA* 1.3 75.3 - - - +
3789D VAL* 1.3 69.3 + - + +
3791D SER* 3.3 9.6 + - - -
3792D THR* 3.2 24.7 + - + +
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Residues in contact with VAL3789 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3777D MET* 6.5 0.7 - - + -
3778D ILE* 4.8 10.3 - - + -
3781D CYS* 4.4 18.4 - - + -
3784D GLU* 3.4 25.1 - - + +
3786D GLY* 3.2 21.2 + - - +
3788D MET* 1.3 83.5 - - + +
3790D SER* 1.3 59.6 + - - +
3792D THR* 3.0 18.3 + - - -
3793D LEU* 3.4 18.5 + - + +
3830D LEU* 4.3 24.7 - - + -
3875D PHE* 4.4 12.8 - - + -
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Residues in contact with SER3790 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3786D GLY 3.5 7.1 + - - -
3787D ALA* 2.9 20.3 + - - +
3788D MET 3.3 0.2 - - - -
3789D VAL* 1.3 77.9 - - - +
3791D SER* 1.3 63.8 + - - +
3793D LEU* 3.7 5.7 + - - +
3794D LYS* 3.1 22.5 + - - +
3874D GLU 5.1 9.6 - - - -
3875D PHE* 4.3 22.8 - - - -
3878D ASP* 6.0 0.5 - - - +
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Residues in contact with SER3791 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3718D TYR* 6.5 0.4 - - - -
3719D MET* 4.0 20.1 - - - +
3722D ALA* 4.3 24.6 - - - +
3787D ALA 2.9 16.1 + - - -
3788D MET* 3.3 10.5 + - - -
3789D VAL 3.3 0.4 - - - -
3790D SER* 1.3 78.5 + - - +
3792D THR* 1.3 65.7 + - - +
3794D LYS* 3.3 15.5 + - - +
3795D LEU* 3.3 13.2 + - - +
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Residues in contact with THR3792 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3718D TYR* 3.4 42.0 - - + +
3722D ALA* 5.8 1.8 - - + -
3774D VAL* 4.7 15.4 - - + +
3777D MET* 3.7 19.6 - - + +
3778D ILE* 4.0 17.1 - - - +
3788D MET 3.2 11.6 + - - +
3789D VAL* 3.0 19.2 + - - -
3791D SER* 1.3 77.7 - - - +
3793D LEU* 1.3 57.6 + - - +
3795D LEU* 3.4 7.3 + - - +
3796D GLY* 3.1 22.0 + - - -
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Residues in contact with LEU3793 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3778D ILE* 3.8 25.4 - - + -
3789D VAL* 3.4 23.0 + - + +
3790D SER* 4.1 5.4 - - - +
3791D SER 3.3 0.4 - - - -
3792D THR* 1.3 76.3 + - - +
3794D LYS* 1.3 63.7 + - - +
3796D GLY* 3.8 2.4 - - - +
3797D ILE* 3.3 29.5 + - - +
3830D LEU* 4.9 5.2 - - + -
3875D PHE* 4.7 19.5 - - + +
3878D ASP* 4.9 14.5 - - + +
3879D LEU* 4.7 28.5 - - + +
3882D PHE* 4.6 27.8 - - + -
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Residues in contact with LYS3794 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3723D ASP* 6.2 3.4 - - - -
3726D ALA* 4.2 11.7 - - + +
3790D SER 3.1 15.8 + - - +
3791D SER* 3.5 12.8 - - - +
3792D THR 3.2 0.4 - - - -
3793D LEU* 1.3 77.5 - - - +
3795D LEU* 1.3 59.7 + - - +
3797D ILE* 3.3 32.5 - - + +
3798D SER* 3.7 8.7 + - - -
3877D GLN* 5.6 8.5 - - - +
3878D ASP* 5.5 4.7 - - + +
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Residues in contact with LEU3795 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3722D ALA* 3.5 31.6 - - + +
3725D MET* 3.8 36.1 - - + -
3726D ALA* 3.8 18.8 - - + +
3765D LEU* 5.1 2.5 - - + -
3770D ALA* 5.3 6.5 - - + +
3774D VAL* 3.9 23.6 - - + -
3791D SER 3.3 9.4 + - - +
3792D THR* 3.9 7.9 - - - +
3793D LEU 3.3 0.2 - - - -
3794D LYS* 1.3 76.8 - - - +
3796D GLY* 1.3 64.4 - - - +
3798D SER* 3.4 10.2 + - - -
3799D ILE* 3.5 24.8 - - + +
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Residues in contact with GLY3796 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3774D VAL* 4.9 12.3 - - - -
3792D THR 3.1 14.8 + - - -
3793D LEU 3.5 1.7 + - - -
3794D LYS 3.4 0.4 - - - -
3795D LEU* 1.3 80.7 - - - +
3797D ILE* 1.3 60.5 + - - +
3798D SER 3.3 0.5 + - - -
3799D ILE* 3.4 14.1 + - - +
3800D LEU* 3.5 20.8 - - - +
3882D PHE* 3.9 21.3 - - - -
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Residues in contact with ILE3797 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3793D LEU 3.3 14.8 + - - +
3794D LYS* 3.3 34.3 - - + +
3796D GLY* 1.3 75.7 - - - +
3798D SER* 1.3 62.4 + - - +
3799D ILE 3.3 0.2 - - - -
3800D LEU* 3.8 4.3 + - - +
3801D ASN* 3.3 25.1 + - - +
3877D GLN* 5.6 5.4 - - - +
3878D ASP* 4.1 17.3 - - + +
3881D ARG* 4.5 17.7 - - + +
3882D PHE* 3.8 38.6 - - + +
3885D LEU* 4.5 7.6 - - + +
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Residues in contact with SER3798 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3726D ALA* 3.2 30.3 + - - -
3729D CYS* 3.2 27.9 - - - +
3730D HIS* 3.8 11.8 + - - +
3758D LEU* 5.8 2.4 - - - +
3794D LYS 3.7 9.6 + - - -
3795D LEU* 3.4 11.6 + - - -
3796D GLY 3.2 1.4 - - - -
3797D ILE* 1.3 83.3 - - - +
3799D ILE* 1.3 61.4 + - - +
3801D ASN* 3.9 14.1 - - - +
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Residues in contact with ILE3799 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3726D ALA* 6.5 0.2 - - - -
3729D CYS* 3.9 17.3 - - + -
3758D LEU* 5.4 2.1 - - - +
3762D GLN* 3.9 28.3 - - + +
3765D LEU* 3.7 36.3 - - + -
3766D HIS* 5.6 3.6 - - + +
3770D ALA* 6.1 1.3 - - + -
3771D ALA* 6.1 0.9 - - + -
3774D VAL* 6.3 0.9 - - + -
3795D LEU* 3.5 25.6 - - + +
3796D GLY* 3.4 8.0 + - - +
3797D ILE 3.3 0.6 - - - -
3798D SER* 1.3 81.6 - - - +
3800D LEU* 1.3 60.5 - - + +
3801D ASN 3.2 4.8 + - - -
3802D GLY 4.6 2.3 + - - -
3804D ASN* 3.7 11.8 + - - +
3807D VAL* 3.9 31.9 - - + -
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Residues in contact with LEU3800 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3796D GLY* 3.5 19.1 + - - +
3797D ILE* 3.8 3.1 + - - +
3799D ILE* 1.3 79.0 - - + +
3801D ASN* 1.3 63.0 + - - +
3802D GLY 3.3 2.9 - - - -
3803D GLY* 3.1 15.3 + - - +
3804D ASN* 4.2 12.6 - - - +
3807D VAL* 3.7 26.7 - - + -
3808D GLN* 5.0 9.0 - - + -
3811D MET* 4.2 18.8 - - + -
3882D PHE* 4.7 9.0 - - + +
3885D LEU* 3.1 47.2 - - + +
3886D LEU* 3.9 24.5 - - + +
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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
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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