Contacts of the helix formed by residues 2912 - 2933 (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 THR2912 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2910F THR 3.9 0.2 + - - -
2911F LEU* 1.3 78.4 - - - +
2913F ALA* 1.3 65.4 + - - +
2914F LYS* 3.4 8.5 - - - -
2915F GLU* 4.0 11.4 - - - +
2916F LYS* 3.2 23.0 + - - +
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Residues in contact with ALA2913 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2912F THR* 1.3 73.3 - - - +
2914F LYS* 1.3 64.3 + - - +
2916F LYS* 3.5 5.7 + - - +
2917F ALA* 3.4 20.4 + - - +
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Residues in contact with LYS2914 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2912F THR* 3.4 4.3 - - - -
2913F ALA* 1.3 80.2 - - - +
2915F GLU* 1.3 60.9 + - - +
2917F ALA* 3.4 17.8 + - - +
2918F ARG* 4.4 1.7 + - - +
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Residues in contact with GLU2915 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2911F LEU* 4.4 10.3 - - + -
2912F THR* 3.6 21.0 + - - +
2913F ALA 3.3 0.4 - - - -
2914F LYS* 1.3 80.2 - - - +
2916F LYS* 1.3 61.6 + - - +
2917F ALA 3.4 0.5 + - - -
2918F ARG* 3.7 14.9 + - - +
2919F ASP* 4.6 2.3 + - - +
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Residues in contact with LYS2916 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2879F ALA* 5.5 0.5 - - - +
2908F TYR 5.7 2.5 - - - +
2911F LEU* 4.9 8.5 - - + +
2912F THR 3.2 19.2 + - - +
2913F ALA* 3.5 7.1 + - - +
2914F LYS 3.3 0.4 - - - -
2915F GLU* 1.3 73.8 - - - +
2917F ALA* 1.3 57.9 + - - +
2918F ARG 3.2 1.3 - - - -
2919F ASP* 3.4 6.8 + - + +
2920F ARG* 3.0 31.1 + - + +
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Residues in contact with ALA2917 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2913F ALA 3.4 10.7 + - - +
2914F LYS* 3.6 14.6 - - - +
2915F GLU 3.2 1.4 - - - -
2916F LYS* 1.3 77.9 - - - +
2918F ARG* 1.3 61.1 + - - +
2920F ARG* 4.3 6.0 - - - +
2921F GLU* 3.1 26.0 + - - +
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Residues in contact with ARG2918 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2914F LYS 4.4 1.5 + - - +
2915F GLU 3.7 11.9 + - - +
2916F LYS 3.2 0.8 - - - -
2917F ALA* 1.3 81.3 - - - +
2919F ASP* 1.3 60.8 + - - +
2921F GLU* 3.9 7.5 + - - +
2922F LYS* 3.9 11.1 + - - +
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Residues in contact with ASP2919 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2879F ALA* 3.4 40.6 - - + +
2882F TYR* 4.8 10.5 - - + +
2883F HIS* 5.1 8.3 - - + +
2915F GLU 4.6 1.5 + - - +
2916F LYS* 3.4 10.3 + - - +
2917F ALA 3.3 0.2 - - - -
2918F ARG* 1.3 76.8 - - - +
2920F ARG* 1.3 64.7 + - - +
2921F GLU 3.3 0.8 + - - -
2922F LYS* 3.5 6.6 + - - +
2923F ALA 3.4 15.1 + - - -
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Residues in contact with ARG2920 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2875F ALA* 5.6 2.0 - - + +
2879F ALA* 3.9 11.4 - - + +
2916F LYS* 3.0 20.4 + - + +
2917F ALA* 4.3 5.4 - - - +
2919F ASP* 1.3 74.9 - - - +
2921F GLU* 1.3 59.8 + - - +
2923F ALA* 3.9 2.7 - - - +
2924F GLN* 2.9 31.6 + - - +
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Residues in contact with GLU2921 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2917F ALA 3.1 19.9 + - - +
2918F ARG* 4.2 6.1 - - - +
2919F ASP 3.3 0.4 - - - -
2920F ARG* 1.3 78.9 - - - +
2922F LYS* 1.3 57.5 + - - +
2924F GLN* 3.5 4.4 + - - +
2925F GLU* 3.0 30.0 + - - +
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Residues in contact with LYS2922 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2882F TYR* 5.8 6.7 - - + -
2918F ARG 3.9 9.2 + - - +
2919F ASP* 3.5 9.0 + - - +
2920F ARG 3.3 0.4 - - - -
2921F GLU* 1.3 78.5 - - - +
2923F ALA* 1.3 62.5 + - - +
2925F GLU* 3.6 5.8 + - - +
2926F LEU* 3.4 21.3 + - - +
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Residues in contact with ALA2923 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2875F ALA* 3.4 35.1 - - + +
2878F LEU* 3.9 20.9 - - + -
2879F ALA* 3.9 4.7 - - + +
2919F ASP 3.4 14.4 + - - +
2920F ARG* 3.5 3.3 + - - +
2921F GLU 3.3 0.2 - - - -
2922F LYS* 1.3 77.6 - - - +
2924F GLN* 1.3 65.0 + - - +
2926F LEU* 3.4 5.8 + - - +
2927F LEU* 3.2 23.0 + - - +
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Residues in contact with GLN2924 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2875F ALA* 4.9 6.6 - - + +
2920F ARG 2.9 18.2 + - - +
2921F GLU* 4.1 5.2 - - - +
2923F ALA* 1.3 74.5 - - - +
2925F GLU* 1.3 60.5 + - - +
2927F LEU* 4.0 5.6 - - - +
2928F LYS* 2.9 32.1 + - - +
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Residues in contact with GLU2925 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2862F LEU* 6.4 1.1 - - - -
2921F GLU 3.0 18.8 + - - +
2922F LYS* 3.9 6.7 - - - +
2923F ALA 3.3 0.2 - - - -
2924F GLN* 1.3 78.7 - - - +
2926F LEU* 1.3 61.0 + - - +
2928F LYS* 4.1 4.8 - - - +
2929F PHE* 3.2 24.8 + - - +
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Residues in contact with LEU2926 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2812F SER* 5.4 12.8 - - - -
2922F LYS 3.4 14.3 + - - +
2923F ALA* 3.9 5.6 - - - +
2924F GLN 3.3 0.4 - - - -
2925F GLU* 1.3 77.1 - - - +
2927F LEU* 1.3 63.3 + - - +
2929F PHE* 3.6 5.2 + - - +
2930F LEU* 3.3 22.5 + - - +
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Residues in contact with LEU2927 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2871F LEU* 5.3 18.4 - - + +
2875F ALA* 5.6 4.5 - - + -
2923F ALA 3.2 16.5 + - - +
2924F GLN* 4.0 6.1 - - - +
2926F LEU* 1.3 74.9 - - - +
2928F LYS* 1.3 66.1 + - - +
2930F LEU* 3.4 5.2 + - - +
2931F GLN* 3.1 24.8 + - - +
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Residues in contact with LYS2928 (chain F).
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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2862F LEU* 4.5 18.6 - - + +
2865F VAL* 4.2 26.0 - - + +
2924F GLN 2.9 18.8 + - - +
2925F GLU* 4.1 4.7 - - - +
2926F LEU 3.4 0.2 - - - -
2927F LEU* 1.3 78.3 - - - +
2929F PHE* 1.3 59.8 + - - +
2931F GLN* 3.6 5.2 + - - +
2932F MET* 3.1 24.6 + - - +
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Residues in contact with PHE2929 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2758F PHE* 5.2 15.9 - - + -
2925F GLU 3.2 18.6 + - - +
2926F LEU* 4.0 5.8 - - - +
2927F LEU 3.3 0.2 - - - -
2928F LYS* 1.3 76.7 - - - +
2930F LEU* 1.3 62.2 + - - +
2932F MET* 3.6 6.1 + - - +
2933F ASN* 3.4 21.5 + - - +
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Residues in contact with LEU2930 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2926F LEU 3.3 15.9 + - - +
2927F LEU* 3.9 6.1 - - - +
2929F PHE* 1.3 76.8 - - - +
2931F GLN* 1.3 62.0 + - - +
2933F ASN* 3.3 8.7 + - - -
2934F GLY 3.3 0.2 + - - -
2935F TYR* 2.8 48.4 + - + +
2937F VAL* 5.9 7.0 - - + -
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Residues in contact with GLN2931 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2927F LEU 3.1 17.4 + - - +
2928F LYS* 4.1 5.4 - - - +
2930F LEU* 1.3 76.8 - - - +
2932F MET* 1.3 63.7 + - - +
2934F GLY* 3.3 11.3 + - - +
2935F TYR 4.0 9.4 + - - +
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Residues in contact with MET2932 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2828F GLU 4.5 0.5 - - - +
2829F GLY* 3.4 1.7 - - - -
2830F GLU* 2.9 37.6 + - + +
2928F LYS 3.1 18.6 + - - +
2929F PHE* 3.9 7.2 - - - +
2930F LEU 3.2 0.2 - - - -
2931F GLN* 1.3 78.5 - - - +
2933F ASN* 1.3 56.7 + - - +
2934F GLY 3.2 0.7 + - - -
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Residues in contact with ASN2933 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2754F PHE* 6.2 4.0 - - + -
2825F LYS* 5.3 3.8 - - - +
2827F ARG 3.6 7.4 - - - +
2829F GLY* 3.7 17.5 + - - -
2929F PHE 3.4 13.2 + - - +
2930F LEU* 3.3 6.8 + - - +
2931F GLN 3.3 0.8 - - - -
2932F MET* 1.3 76.9 - - - +
2934F GLY* 1.3 60.6 + - - +
2935F TYR* 3.4 4.6 + - + +
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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
------------------------------------------------------------
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