Contacts of the helix formed by residues 2868 - 2897 (chain F) 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 SER2868 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2866F THR 4.1 1.6 + - - -
2867F LEU* 1.3 76.2 - - - +
2869F ARG* 1.3 61.9 + - - +
2870F GLU* 3.3 8.3 - - - -
2871F LEU* 3.9 10.4 - - - +
2872F GLN* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2869 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2868F SER* 1.3 75.7 - - - +
2870F GLU* 1.3 61.0 + - - +
2872F GLN* 3.9 5.5 - - - +
2873F ALA* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2870 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2868F SER* 3.3 5.8 - - - -
2869F ARG* 1.3 79.0 - - - +
2871F LEU* 1.3 57.0 + - - +
2873F ALA* 3.4 5.3 + - - +
2874F MET* 3.1 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2871 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2867F LEU* 4.2 11.2 - - + -
2868F SER* 3.5 20.9 + - - +
2869F ARG 3.4 0.2 - - - -
2870F GLU* 1.3 79.6 - - - +
2872F GLN* 1.3 58.2 + - - +
2874F MET* 3.5 5.8 + - - +
2875F ALA* 3.0 28.1 + - - +
2927F LEU* 5.3 14.4 - - + +
2937F VAL 6.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2872 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2867F LEU* 4.7 9.4 - - + +
2868F SER 3.0 19.0 + - - +
2869F ARG* 3.9 6.3 - - - +
2871F LEU* 1.3 76.3 - - - +
2873F ALA* 1.3 62.2 + - - +
2875F ALA* 3.4 14.9 + - - +
2876F GLU* 3.5 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2873 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2869F ARG 3.0 18.7 + - - +
2870F GLU* 3.9 5.6 - - - +
2872F GLN* 1.3 77.1 - - - +
2874F MET* 1.3 60.7 + - - +
2876F GLU* 3.3 19.0 + - - +
2877F GLN* 3.9 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET2874 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2870F GLU 3.1 17.8 + - - +
2871F LEU* 3.9 6.5 - - - +
2873F ALA* 1.3 74.3 - - - +
2875F ALA* 1.3 65.1 + - - +
2877F GLN* 3.3 17.0 + - - +
2878F LEU* 3.5 11.1 + - - +
2937F VAL* 6.5 1.6 - - + -
2939F ARG* 6.2 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2875 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2871F LEU 3.0 17.3 + - - +
2872F GLN* 3.6 10.3 - - - +
2873F ALA 3.2 0.6 - - - -
2874F MET* 1.3 75.8 - - - +
2876F GLU* 1.3 59.3 + - - +
2878F LEU* 3.4 3.2 + - - +
2879F ALA* 2.9 26.2 + - - +
2920F ARG* 5.6 1.5 - - + +
2923F ALA* 3.4 31.1 - - + +
2924F GLN* 4.9 5.6 - - + +
2927F LEU* 5.6 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2876 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2872F GLN 3.5 7.0 + - - +
2873F ALA* 3.3 13.8 + - - +
2874F MET 3.2 0.8 - - - -
2875F ALA* 1.3 79.3 - - - +
2877F GLN* 1.3 57.1 + - - +
2879F ALA* 3.9 5.6 - - - +
2880F GLU* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2877 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2873F ALA 3.9 4.0 + - - +
2874F MET* 3.3 12.2 + - - +
2875F ALA 3.3 0.6 - - - -
2876F GLU* 1.3 79.2 - - - +
2878F LEU* 1.3 57.2 + - - +
2880F GLU* 3.4 5.9 + - - +
2881F ASN* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2878 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2812F SER* 6.3 2.7 - - - -
2874F MET 3.5 8.7 + - - +
2875F ALA* 3.4 8.6 + - - +
2876F GLU 3.3 0.2 - - - -
2877F GLN* 1.3 76.7 - - - +
2879F ALA* 1.3 66.6 + - - +
2881F ASN* 3.4 7.2 + - - +
2882F TYR* 3.2 21.0 + - - +
2923F ALA* 3.9 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2879 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2875F ALA 2.9 17.6 + - - +
2876F GLU* 3.9 7.0 - - - +
2878F LEU* 1.3 77.7 - - - +
2880F GLU* 1.3 61.5 + - - +
2882F TYR* 3.4 2.7 + - - +
2883F HIS* 3.3 17.8 + - - +
2916F LYS 5.5 0.4 - - - +
2919F ASP* 3.4 48.2 - - + +
2920F ARG* 3.9 9.6 - - + +
2923F ALA* 3.9 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2880 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2876F GLU 2.9 18.4 + - - +
2877F GLN* 3.9 5.6 - - - +
2878F LEU 3.3 0.2 - - - -
2879F ALA* 1.3 73.2 - - - +
2881F ASN* 1.3 60.1 + - - +
2883F HIS* 3.4 4.1 + - - +
2884F ASN* 3.0 28.1 + - - +
2908F TYR* 4.1 27.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2881 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2739F PRO* 5.1 3.4 - - - +
2740F VAL* 5.7 9.6 - - + +
2815F ALA* 5.2 14.8 - - + -
2877F GLN 3.0 16.8 + - - +
2878F LEU* 3.7 8.5 - - - +
2879F ALA 3.3 0.4 - - - -
2880F GLU* 1.3 75.2 - - - +
2882F TYR* 1.3 59.8 + - - +
2884F ASN* 3.4 6.5 + - - +
2885F THR* 2.9 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR2882 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2878F LEU 3.2 11.6 + - - +
2879F ALA* 3.7 10.3 - - - +
2880F GLU 3.3 0.2 - - - -
2881F ASN* 1.3 78.5 - - - +
2883F HIS* 1.3 58.6 + - - +
2885F THR* 3.8 5.5 - - - -
2886F TRP* 3.0 31.0 + - - +
2919F ASP* 4.8 10.5 - - + +
2922F LYS* 5.8 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS2883 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2737F PRO* 5.2 0.2 - - - +
2879F ALA 3.3 10.1 + - - +
2880F GLU* 3.8 9.9 - - - +
2881F ASN 3.3 0.4 - - - -
2882F TYR* 1.3 79.0 - - - +
2884F ASN* 1.3 54.7 + - - +
2886F TRP* 4.2 3.5 - - - +
2887F GLY* 2.7 31.7 + - - -
2908F TYR* 5.0 12.8 - - + -
2919F ASP* 5.1 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2884 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2737F PRO* 3.4 17.0 - - + +
2738F ARG 4.1 23.8 - - - +
2739F PRO* 4.2 12.9 - - + +
2880F GLU 3.0 17.0 + - - +
2881F ASN* 3.8 6.7 - - - +
2882F TYR 3.3 0.2 - - - -
2883F HIS* 1.3 74.8 - - - +
2885F THR* 1.3 60.7 + - - +
2888F ARG* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR2885 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2739F PRO* 4.1 16.7 - - - +
2881F ASN 2.9 17.9 + - - -
2882F TYR* 3.8 6.1 - - - -
2884F ASN* 1.3 77.5 - - - +
2886F TRP* 1.3 61.7 + - - +
2888F ARG* 3.5 2.8 + - - +
2889F LYS* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP2886 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2882F TYR 3.0 18.3 + - - +
2883F HIS* 4.2 3.8 - - - +
2885F THR* 1.3 75.4 - - - +
2887F GLY* 1.3 59.3 + - - +
2889F LYS* 3.5 5.7 + - - +
2890F LYS* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY2887 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2737F PRO* 4.3 8.7 - - - -
2883F HIS 2.7 23.2 + - - -
2884F ASN 4.0 0.7 - - - -
2886F TRP* 1.3 75.6 - - - +
2888F ARG* 1.3 59.9 + - - +
2890F LYS* 3.5 5.5 + - - +
2891F LYS* 3.2 23.4 + - - +
2904F LEU 5.9 2.5 - - - -
2905F LEU* 6.1 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2888 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2737F PRO* 3.9 16.9 - - + +
2739F PRO* 5.3 6.5 - - + -
2884F ASN 3.0 18.8 + - - +
2885F THR* 3.9 4.5 - - - +
2886F TRP 3.3 0.2 - - - -
2887F GLY* 1.3 77.7 - - - +
2889F LYS* 1.3 62.1 + - - +
2891F LYS* 3.5 6.7 + - - +
2892F GLN* 3.3 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2889 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2885F THR 3.2 17.4 + - - +
2886F TRP* 4.0 5.8 - - - +
2888F ARG* 1.3 75.1 - - - +
2890F LYS* 1.3 59.3 + - - +
2892F GLN* 3.5 5.6 + - - +
2893F GLU* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2890 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2886F TRP 3.0 18.6 + - - +
2887F GLY* 3.9 6.5 - - - +
2888F ARG 3.3 0.2 - - - -
2889F LYS* 1.3 74.5 - - - +
2891F LYS* 1.3 60.9 + - - +
2893F GLU* 4.0 5.1 - - - +
2894F LEU* 3.0 30.8 + - - +
2902F HIS* 5.8 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2891 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2887F GLY 3.2 16.1 + - - +
2888F ARG* 3.8 6.7 - - - +
2889F LYS 3.3 0.2 - - - -
2890F LYS* 1.3 78.5 - - - +
2892F GLN* 1.3 60.8 + - - +
2894F LEU* 4.1 3.9 - - - +
2895F GLU* 3.2 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2892 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2888F ARG 3.3 13.5 + - - +
2889F LYS* 4.1 5.4 - - - +
2890F LYS 3.3 0.4 - - - -
2891F LYS* 1.3 77.0 - - - +
2893F GLU* 1.3 64.2 + - - +
2895F GLU* 3.7 4.3 + - - +
2896F ALA* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2893 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2889F LYS 3.0 18.8 + - - +
2890F LYS* 3.5 6.0 + - - +
2892F GLN* 1.3 76.5 - - - +
2894F LEU* 1.3 63.4 + - - +
2896F ALA* 3.5 6.3 + - - +
2897F LYS* 3.4 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2894 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2890F LYS 3.0 18.1 + - - +
2891F LYS* 4.1 5.2 - - - +
2893F GLU* 1.3 76.1 - - - +
2895F GLU* 1.3 62.3 + - - +
2897F LYS* 3.2 11.4 + - - +
2898F GLY 3.5 0.5 + - - -
2899F GLY* 2.8 38.3 + - - +
2900F GLY 4.9 10.5 - - - +
2901F THR* 5.4 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2895 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2891F LYS 3.2 15.9 + - - +
2892F GLN* 4.1 5.4 - - - +
2894F LEU* 1.3 79.2 - - - +
2896F ALA* 1.3 60.8 + - - +
2897F LYS 3.4 0.3 + - - -
2898F GLY* 3.4 10.4 + - - -
2899F GLY* 3.9 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2896 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2892F GLN 3.2 19.9 + - - +
2893F GLU* 3.9 6.5 - - - +
2894F LEU 3.3 0.6 - - - -
2895F GLU* 1.3 77.3 - - - +
2897F LYS* 1.3 58.3 + - - +
2898F GLY 3.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2897 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2893F GLU 3.4 14.8 + - - +
2894F LEU* 3.2 7.3 + - - +
2895F GLU 3.2 1.2 - - - -
2896F ALA* 1.3 76.3 - - - +
2898F GLY* 1.3 58.2 + - - +
2899F GLY 3.7 3.7 - - - +
----------------------------------------------------------
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