Contacts of the helix formed by residues 2798 - 2819 (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 SER2798 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2796D THR 3.9 1.0 + - - -
2797D PHE* 1.3 76.5 - - - +
2799D GLU* 1.3 61.2 + - - +
2800D LYS* 3.3 8.5 - - - -
2801D ASP* 3.9 9.4 - - - +
2802D LYS* 3.0 27.3 + - - +
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Residues in contact with GLU2799 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2798D SER* 1.3 76.3 - - - +
2800D LYS* 1.3 62.0 + - - +
2802D LYS* 3.6 5.0 + - - +
2803D GLU* 3.2 23.7 + - - +
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Residues in contact with LYS2800 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2798D SER* 3.3 5.8 - - - -
2799D GLU* 1.3 77.2 - - - +
2801D ASP* 1.3 63.8 + - - +
2803D GLU* 3.5 14.1 + - - +
2804D ILE* 3.8 9.0 + - - +
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Residues in contact with ASP2801 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2797D PHE* 3.8 23.3 - - + -
2798D SER* 3.5 10.9 + - - +
2799D GLU 3.4 0.2 - - - -
2800D LYS* 1.3 79.4 - - - +
2802D LYS* 1.3 62.2 + - - +
2804D ILE* 3.4 18.8 + - - +
2805D TYR* 4.4 2.6 + - - +
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Residues in contact with LYS2802 (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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2759D ALA* 4.9 4.5 - - + +
2794D TYR 5.7 2.2 - - - +
2797D PHE* 4.4 9.8 - - + +
2798D SER 3.0 18.6 + - - +
2799D GLU* 4.1 4.9 - - - +
2801D ASP* 1.3 76.9 - - - +
2803D GLU* 1.3 57.7 + - - +
2804D ILE 3.2 0.6 + - - -
2805D TYR* 3.5 5.3 + - - +
2806D ARG* 3.2 27.6 + - - +
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Residues in contact with GLU2803 (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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2799D GLU 3.2 18.7 + - - +
2800D LYS* 3.8 8.7 - - - +
2801D ASP 3.3 0.6 - - - -
2802D LYS* 1.3 74.7 - - - +
2804D ILE* 1.3 63.6 + - - +
2805D TYR 3.3 0.2 - - - -
2806D ARG* 3.8 8.7 - - - -
2807D TRP* 3.2 25.8 + - - +
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Residues in contact with ILE2804 (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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2800D LYS 3.8 6.6 + - - +
2801D ASP* 3.4 13.8 + - - +
2802D LYS 3.2 0.8 - - - -
2803D GLU* 1.3 80.1 - - - +
2805D TYR* 1.3 58.5 + - - +
2807D TRP* 4.2 8.1 + - - +
2808D PRO* 4.6 5.2 - - - +
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Residues in contact with TYR2805 (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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2759D ALA* 4.1 32.1 - - + +
2762D THR* 5.1 9.6 - - - -
2763D HIS* 5.2 7.6 - - + +
2801D ASP 4.4 1.9 + - - +
2802D LYS* 3.5 5.1 + - - +
2804D ILE* 1.3 78.2 - - + +
2806D ARG* 1.3 63.3 + - - +
2807D TRP 3.3 1.2 + - - -
2808D PRO* 3.8 12.9 - - - +
2809D ILE* 3.8 10.9 + - - +
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Residues in contact with ARG2806 (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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2755D ILE* 5.3 11.3 - - + +
2756D ASN* 6.5 0.2 - - - -
2759D ALA* 4.3 12.3 - - + +
2802D LYS* 3.2 18.7 + - + +
2803D GLU* 3.7 6.9 + - - -
2805D TYR* 1.3 75.6 - - - +
2807D TRP* 1.3 60.3 + - - +
2808D PRO 3.3 0.2 - - - -
2809D ILE* 3.5 5.3 + - - +
2810D LYS* 3.0 31.0 + - - +
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Residues in contact with TRP2807 (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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2803D GLU 3.2 18.9 + - - +
2804D ILE* 4.3 5.6 - - - +
2805D TYR 3.3 0.4 - - - -
2806D ARG* 1.3 77.9 - - - +
2808D PRO* 1.3 57.8 - - - +
2810D LYS* 4.0 4.6 - - - +
2811D GLU* 3.0 29.8 + - - +
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Residues in contact with PRO2808 (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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2804D ILE 4.6 5.0 - - - +
2805D TYR* 3.8 9.7 - - - +
2806D ARG 3.3 0.6 - - - -
2807D TRP* 1.3 79.5 - - - +
2809D ILE* 1.3 59.7 + - - +
2811D GLU* 4.0 5.4 - - + +
2812D SER* 3.3 23.0 + - - -
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Residues in contact with ILE2809 (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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2755D ILE* 4.9 15.9 - - + +
2758D PHE* 4.7 19.7 - - + -
2759D ALA 5.5 1.6 - - - +
2805D TYR 3.8 9.6 + - - +
2806D ARG* 3.5 8.4 + - - +
2807D TRP 3.3 0.4 - - - -
2808D PRO* 1.3 75.7 - - - +
2810D LYS* 1.3 60.2 + - - +
2812D SER* 3.5 4.8 + - - -
2813D LEU* 3.0 28.8 + - - +
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Residues in contact with LYS2810 (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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2755D ILE* 5.9 4.9 - - + +
2806D ARG 3.0 18.9 + - - +
2807D TRP* 4.0 5.4 - - - +
2809D ILE* 1.3 75.8 - - - +
2811D GLU* 1.3 59.2 + - - +
2813D LEU* 3.4 5.2 + - - +
2814D LYS* 2.9 31.8 + - - +
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Residues in contact with GLU2811 (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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2742D THR* 4.8 9.1 - - - -
2807D TRP 3.0 19.0 + - - +
2808D PRO* 4.0 5.8 - - + +
2809D ILE 3.3 0.2 - - - -
2810D LYS* 1.3 78.1 - - - +
2812D SER* 1.3 60.3 + - - +
2814D LYS* 3.6 5.4 + - - +
2815D ALA* 3.2 22.5 + - - +
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Residues in contact with SER2812 (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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2808D PRO 3.3 17.0 + - - -
2809D ILE* 3.5 5.8 + - - -
2811D GLU* 1.3 77.2 - - - +
2813D LEU* 1.3 62.9 + - - +
2815D ALA* 3.5 6.6 + - - +
2816D MET* 3.4 20.4 + - - +
2878D LEU* 6.3 2.7 - - - -
2926D LEU* 5.4 12.3 - - - -
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Residues in contact with LEU2813 (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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2751D LEU* 6.3 3.6 - - + -
2809D ILE 3.0 18.5 + - - +
2810D LYS* 3.9 5.6 - - - +
2812D SER* 1.3 75.7 - - - +
2814D LYS* 1.3 63.2 + - - +
2816D MET* 3.4 7.2 + - - +
2817D ILE* 3.2 22.3 + - - +
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Residues in contact with LYS2814 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2741D GLU 5.2 0.2 - - - +
2742D THR* 3.8 22.0 - - - +
2745D VAL* 3.8 31.2 - - + +
2810D LYS 2.9 19.0 + - - +
2811D GLU* 3.6 2.9 + - - +
2812D SER 3.3 0.2 - - - -
2813D LEU* 1.3 72.7 - - - +
2815D ALA* 1.3 64.8 + - - +
2817D ILE* 3.4 7.2 + - - +
2818D ALA* 3.3 19.4 + - - +
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Residues in contact with ALA2815 (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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2740D VAL* 4.8 19.0 - - + +
2741D GLU 6.0 0.2 - - - -
2742D THR* 4.8 5.1 - - - -
2811D GLU 3.2 17.7 + - - +
2812D SER* 3.8 7.2 - - - +
2813D LEU 3.3 0.4 - - - -
2814D LYS* 1.3 79.2 - - - +
2816D MET* 1.3 60.6 + - - +
2818D ALA* 3.4 14.1 + - - +
2819D TRP* 3.5 11.4 + - - +
2881D ASN* 5.2 14.1 - - + -
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Residues in contact with MET2816 (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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2812D SER 3.4 11.5 + - - +
2813D LEU* 3.4 8.9 + - - +
2814D LYS 3.3 0.2 - - - -
2815D ALA* 1.3 76.7 - - - +
2817D ILE* 1.3 64.5 - - - +
2819D TRP* 3.3 13.4 + - - +
2821D TRP* 3.3 32.9 + - + +
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Residues in contact with ILE2817 (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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2745D VAL* 5.2 7.0 - - + -
2746D ILE 5.3 7.4 - - - +
2813D LEU 3.2 16.6 + - - +
2814D LYS* 3.7 9.0 - - - +
2815D ALA 3.3 0.4 - - - -
2816D MET* 1.3 78.0 - - - +
2818D ALA* 1.3 61.0 + - - +
2820D GLU* 3.4 12.0 + - - -
2821D TRP 4.5 6.4 + - - +
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Residues in contact with ALA2818 (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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2740D VAL* 5.2 8.7 - - + -
2741D GLU 4.5 14.6 - - - +
2745D VAL* 5.7 3.1 - - + +
2814D LYS 3.3 10.3 + - - +
2815D ALA* 3.8 10.1 - - - +
2816D MET 3.3 0.8 - - - -
2817D ILE* 1.3 80.6 - - - +
2819D TRP* 1.3 56.3 + - - +
2820D GLU* 3.2 5.6 + - - +
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Residues in contact with TRP2819 (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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2815D ALA 3.5 8.8 + - - +
2816D MET* 3.3 12.2 + - - +
2817D ILE 3.2 0.8 - - - -
2818D ALA* 1.3 77.0 - - - +
2820D GLU* 1.3 70.2 + - - +
2821D TRP* 3.3 5.7 + - + +
2939D ARG* 5.4 5.0 - - - +
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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
------------------------------------------------------------
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