Contacts of the helix formed by residues 2912 - 2933 (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 THR2912 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2910B THR 3.9 0.4 + - - -
2911B LEU* 1.3 79.1 - - - +
2913B ALA* 1.3 65.5 + - - +
2914B LYS* 3.4 7.6 - - - -
2915B GLU* 4.0 12.0 - - - +
2916B LYS* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2913 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2912B THR* 1.3 73.5 - - - +
2914B LYS* 1.3 64.7 + - - +
2916B LYS* 3.5 6.1 + - - +
2917B ALA* 3.4 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2914 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2912B THR* 3.4 4.8 - - - -
2913B ALA* 1.3 79.2 - - - +
2915B GLU* 1.3 61.7 + - - +
2917B ALA* 3.4 17.8 + - - +
2918B ARG* 4.4 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2915 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2911B LEU* 4.4 9.9 - - + -
2912B THR* 3.6 21.6 + - - +
2913B ALA 3.4 0.2 - - - -
2914B LYS* 1.3 79.2 - - - +
2916B LYS* 1.3 60.0 + - - +
2917B ALA 3.4 0.7 + - - -
2918B ARG* 3.7 15.8 + - - +
2919B ASP* 4.6 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2916 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2879B ALA* 5.5 0.2 - - - +
2908B TYR 5.7 2.5 - - - +
2911B LEU* 4.9 7.8 - - + +
2912B THR 3.2 19.8 + - - +
2913B ALA* 3.5 6.5 + - - +
2914B LYS 3.3 0.2 - - - -
2915B GLU* 1.3 74.8 - - - +
2917B ALA* 1.3 58.8 + - - +
2918B ARG 3.2 1.6 - - - -
2919B ASP* 3.4 7.5 + - + +
2920B ARG* 3.0 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2917 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2913B ALA 3.4 11.3 + - - +
2914B LYS* 3.6 14.6 - - - +
2915B GLU 3.2 1.8 - - - -
2916B LYS* 1.3 76.9 - - - +
2918B ARG* 1.3 61.2 + - - +
2920B ARG* 4.4 5.8 - - - -
2921B GLU* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2918 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2914B LYS 4.4 1.5 + - - +
2915B GLU 3.7 11.9 + - - +
2916B LYS 3.2 0.8 - - - -
2917B ALA* 1.3 80.6 - - - +
2919B ASP* 1.3 59.2 + - - +
2921B GLU* 3.9 7.2 + - - +
2922B LYS* 3.9 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2919 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2879B ALA* 3.4 42.9 - - + +
2882B TYR* 4.8 10.9 - - + +
2883B HIS* 5.1 7.6 - - + +
2915B GLU 4.6 1.7 + - - +
2916B LYS* 3.4 10.0 + - - +
2917B ALA 3.3 0.2 - - - -
2918B ARG* 1.3 76.8 - - - +
2920B ARG* 1.3 65.3 + - - +
2921B GLU 3.3 0.4 - - - -
2922B LYS* 3.5 6.2 + - - +
2923B ALA 3.4 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2920 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2875B ALA* 5.6 1.8 - - - +
2879B ALA* 3.9 11.6 - - + +
2916B LYS* 3.0 19.3 + - + +
2917B ALA* 4.3 5.4 - - - +
2918B ARG 3.5 0.2 - - - -
2919B ASP* 1.3 75.6 - - - +
2921B GLU* 1.3 60.7 + - - +
2922B LYS 3.3 0.2 - - - -
2923B ALA* 3.9 2.9 - - - +
2924B GLN* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2921 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2917B ALA 3.1 18.7 + - - +
2918B ARG* 4.2 5.4 - - - +
2919B ASP 3.3 0.4 - - - -
2920B ARG* 1.3 78.8 - - - +
2922B LYS* 1.3 57.9 + - - +
2924B GLN* 4.0 4.4 - - - +
2925B GLU* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2922 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2882B TYR* 5.8 6.5 - - + -
2918B ARG 3.9 9.4 + - - +
2919B ASP* 3.5 8.9 + - - +
2920B ARG 3.3 0.4 - - - -
2921B GLU* 1.3 77.7 - - - +
2923B ALA* 1.3 62.7 + - - +
2925B GLU* 3.6 5.4 + - - +
2926B LEU* 3.4 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2923 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2875B ALA* 3.4 35.0 - - + +
2878B LEU* 3.9 20.9 - - + -
2879B ALA* 3.9 3.8 - - + +
2919B ASP 3.4 14.1 + - - +
2920B ARG* 4.0 4.0 - - - +
2921B GLU 3.3 0.2 - - - -
2922B LYS* 1.3 78.1 - - - +
2924B GLN* 1.3 63.0 + - - +
2926B LEU* 3.4 5.7 + - - +
2927B LEU* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2924 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2875B ALA* 4.9 6.9 - - + +
2920B ARG 2.9 19.6 + - - +
2921B GLU* 4.1 4.9 - - - +
2923B ALA* 1.3 74.3 - - - +
2925B GLU* 1.3 59.7 + - - +
2927B LEU* 3.4 5.1 + - - +
2928B LYS* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2925 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2862B LEU* 6.4 1.1 - - - -
2921B GLU 3.0 18.8 + - - +
2922B LYS* 3.9 6.5 - - - +
2923B ALA 3.3 0.2 - - - -
2924B GLN* 1.3 76.8 - - - +
2926B LEU* 1.3 61.7 + - - +
2928B LYS* 4.1 4.8 - - - +
2929B PHE* 3.2 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2926 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2812B SER* 5.4 11.9 - - - -
2922B LYS 3.4 14.5 + - - +
2923B ALA* 3.4 5.6 + - - +
2924B GLN 3.3 0.2 - - - -
2925B GLU* 1.3 78.1 - - - +
2927B LEU* 1.3 63.4 + - - +
2929B PHE* 3.6 4.6 + - - +
2930B LEU* 3.3 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2927 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2871B LEU* 5.3 17.9 - - + +
2875B ALA* 5.6 4.5 - - + -
2923B ALA 3.2 17.0 + - - +
2924B GLN* 4.0 5.6 - - - +
2925B GLU 3.4 0.2 - - - -
2926B LEU* 1.3 75.0 - - - +
2928B LYS* 1.3 64.6 + - - +
2930B LEU* 3.4 5.8 + - - +
2931B GLN* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2928 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2862B LEU* 4.5 18.2 - - + +
2865B VAL* 4.2 26.3 - - + +
2924B GLN 2.9 18.8 + - - +
2925B GLU* 4.1 4.3 - - - +
2927B LEU* 1.3 78.9 - - - +
2929B PHE* 1.3 60.3 + - - +
2931B GLN* 3.6 5.0 + - - +
2932B MET* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2929 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2758B PHE* 5.2 16.4 - - + -
2925B GLU 3.2 18.3 + - - +
2926B LEU* 4.0 5.6 - - - +
2927B LEU 3.3 0.2 - - - -
2928B LYS* 1.3 77.4 - - - +
2930B LEU* 1.3 61.4 + - - +
2932B MET* 3.6 6.1 + - - +
2933B ASN* 3.4 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2930 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2926B LEU 3.3 15.9 + - - +
2927B LEU* 3.9 5.4 - - - +
2928B LYS 3.3 0.4 - - - -
2929B PHE* 1.3 77.7 - - - +
2931B GLN* 1.3 63.1 + - - +
2933B ASN* 3.3 8.3 + - - -
2935B TYR* 2.8 46.9 + - + +
2937B VAL* 5.9 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2931 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2927B LEU 3.1 17.0 + - - +
2928B LYS* 4.1 5.6 - - - +
2930B LEU* 1.3 76.8 - - - +
2932B MET* 1.3 60.5 + - - +
2934B GLY* 3.3 11.1 + - - +
2935B TYR 4.0 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET2932 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2828B GLU 4.5 0.9 - - - +
2829B GLY* 3.4 2.1 - - - -
2830B GLU* 2.9 36.9 + - + +
2928B LYS 3.1 18.1 + - - +
2929B PHE* 3.9 7.6 - - - +
2930B LEU 3.2 0.4 - - - -
2931B GLN* 1.3 79.3 - - - +
2933B ASN* 1.3 57.2 + - - +
2934B GLY 3.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2933 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2754B PHE* 6.2 4.0 - - + -
2825B LYS* 5.3 4.0 - - - +
2827B ARG 3.6 7.6 - - - +
2829B GLY* 3.7 18.1 + - - -
2929B PHE 3.4 13.5 + - - +
2930B LEU* 3.3 5.9 + - - +
2931B GLN 3.3 0.4 - - - -
2932B MET* 1.3 77.0 - - - +
2934B GLY* 1.3 61.2 + - - +
2935B TYR* 3.4 4.2 - - + +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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