Contacts of the helix formed by residues 2912 - 2933 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2910H THR 3.9 0.2 + - - -
2911H LEU* 1.3 78.5 - - - +
2913H ALA* 1.3 65.7 + - - +
2914H LYS* 3.4 8.3 - - - -
2915H GLU* 4.0 11.1 - - - +
2916H LYS* 3.2 22.9 + - - +
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Residues in contact with ALA2913 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2912H THR* 1.3 73.7 - - - +
2914H LYS* 1.3 64.4 + - - +
2916H LYS* 3.5 5.7 + - - +
2917H ALA* 3.4 20.1 + - - +
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Residues in contact with LYS2914 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2912H THR* 3.4 4.7 - - - -
2913H ALA* 1.3 80.3 - - - +
2915H GLU* 1.3 60.7 + - - +
2917H ALA* 3.4 17.5 + - - +
2918H ARG* 4.4 2.1 + - - +
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Residues in contact with GLU2915 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2911H LEU* 4.4 9.2 - - + -
2912H THR* 3.6 22.0 + - - +
2913H ALA 3.3 0.2 - - - -
2914H LYS* 1.3 79.4 - - - +
2916H LYS* 1.3 60.4 + - - +
2917H ALA 3.4 0.7 + - - -
2918H ARG* 3.7 15.4 + - - +
2919H ASP* 4.6 1.7 + - - +
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Residues in contact with LYS2916 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2879H ALA* 5.5 0.3 - - - +
2908H TYR 5.7 2.0 - - - +
2911H LEU* 4.9 8.5 - - + +
2912H THR 3.2 18.5 + - - +
2913H ALA* 4.0 6.7 - - - +
2914H LYS 3.3 0.6 - - - -
2915H GLU* 1.3 73.2 - - - +
2917H ALA* 1.3 59.0 + - - +
2918H ARG 3.2 1.3 - - - -
2919H ASP* 3.4 8.8 + - - +
2920H ARG* 3.0 30.5 + - + +
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Residues in contact with ALA2917 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2913H ALA 3.4 10.7 + - - +
2914H LYS* 3.6 14.6 - - - +
2915H GLU 3.2 1.6 - - - -
2916H LYS* 1.3 78.9 - - - +
2918H ARG* 1.3 61.8 + - - +
2920H ARG* 4.4 5.6 - - - -
2921H GLU* 3.1 26.2 + - - +
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Residues in contact with ARG2918 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2914H LYS 4.4 1.8 + - - +
2915H GLU 3.7 11.0 + - - +
2916H LYS 3.2 0.8 - - - -
2917H ALA* 1.3 80.5 - - - +
2919H ASP* 1.3 61.1 + - - +
2921H GLU* 3.9 8.1 + - - +
2922H LYS* 3.9 11.1 + - - +
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Residues in contact with ASP2919 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2879H ALA* 3.4 40.9 - - + +
2882H TYR* 4.8 9.6 - - + +
2883H HIS* 5.1 8.1 - - + +
2915H GLU 4.6 1.7 + - - +
2916H LYS* 3.4 10.5 + - + +
2918H ARG* 1.3 77.3 - - - +
2920H ARG* 1.3 63.8 + - - +
2921H GLU 3.3 0.4 - - - -
2922H LYS* 3.5 6.7 + - - +
2923H ALA 3.4 15.8 + - - -
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Residues in contact with ARG2920 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2875H ALA* 5.6 1.7 - - - +
2879H ALA* 3.9 12.1 - - + +
2916H LYS* 3.0 21.2 + - + +
2917H ALA* 4.3 4.9 - - - +
2919H ASP* 1.3 75.3 - - - +
2921H GLU* 1.3 60.3 + - - +
2923H ALA* 3.9 2.3 - - - +
2924H GLN* 2.9 31.2 + - - +
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Residues in contact with GLU2921 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2917H ALA 3.1 19.3 + - - +
2918H ARG* 4.2 5.8 - - - +
2919H ASP 3.3 0.4 - - - -
2920H ARG* 1.3 77.9 - - - +
2922H LYS* 1.3 57.0 + - - +
2924H GLN* 3.5 4.6 + - - +
2925H GLU* 3.0 29.3 + - - +
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Residues in contact with LYS2922 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2882H TYR* 5.8 6.7 - - + -
2918H ARG 3.9 8.9 + - - +
2919H ASP* 3.5 9.1 + - - +
2920H ARG 3.3 0.6 - - - -
2921H GLU* 1.3 79.5 - - - +
2923H ALA* 1.3 61.9 + - - +
2925H GLU* 3.6 5.6 + - - +
2926H LEU* 3.4 21.5 + - - +
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Residues in contact with ALA2923 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2875H ALA* 3.4 35.4 - - + +
2878H LEU* 3.9 21.0 - - + +
2879H ALA* 3.9 3.8 - - + +
2919H ASP 3.4 14.4 + - - +
2920H ARG* 4.0 3.8 - - - +
2921H GLU 3.3 0.6 - - - -
2922H LYS* 1.3 77.2 - - - +
2924H GLN* 1.3 63.5 + - - +
2926H LEU* 3.4 6.0 + - - +
2927H LEU* 3.2 22.7 + - - +
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Residues in contact with GLN2924 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2875H ALA* 4.9 6.7 - - + +
2920H ARG 2.9 19.5 + - - +
2921H GLU* 4.1 4.5 - - - +
2923H ALA* 1.3 74.7 - - - +
2925H GLU* 1.3 60.0 + - - +
2927H LEU* 4.0 4.8 - - - +
2928H LYS* 2.9 31.5 + - - +
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Residues in contact with GLU2925 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2862H LEU* 6.4 1.3 - - - -
2921H GLU 3.0 18.2 + - - +
2922H LYS* 3.9 6.7 - - - +
2923H ALA 3.3 0.2 - - - -
2924H GLN* 1.3 77.6 - - - +
2926H LEU* 1.3 59.9 - - - +
2928H LYS* 3.6 4.6 + - - +
2929H PHE* 3.2 24.1 + - - +
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Residues in contact with LEU2926 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2812H SER* 5.4 12.3 - - - -
2922H LYS 3.4 13.3 + - - +
2923H ALA* 3.9 5.8 - - - +
2924H GLN 3.3 0.8 - - - -
2925H GLU* 1.3 78.3 - - - +
2927H LEU* 1.3 63.7 + - - +
2929H PHE* 3.6 5.0 + - - +
2930H LEU* 3.3 21.8 + - - +
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Residues in contact with LEU2927 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2871H LEU* 5.3 17.9 - - + +
2875H ALA* 5.6 4.3 - - + -
2923H ALA 3.2 17.0 + - - +
2924H GLN* 4.0 5.8 - - - +
2926H LEU* 1.3 73.7 - - - +
2928H LYS* 1.3 64.3 + - - +
2930H LEU* 3.4 5.0 + - - +
2931H GLN* 3.1 25.1 + - - +
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Residues in contact with LYS2928 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2862H LEU* 4.5 18.2 - - + +
2865H VAL* 4.2 26.8 - - + +
2924H GLN 2.9 18.2 + - - +
2925H GLU* 4.1 4.5 - - - +
2927H LEU* 1.3 77.5 - - - +
2929H PHE* 1.3 61.5 + - - +
2931H GLN* 3.6 5.0 + - - +
2932H MET* 3.1 24.3 + - - +
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Residues in contact with PHE2929 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2758H PHE* 5.2 16.2 - - + -
2925H GLU 3.2 18.8 + - - +
2926H LEU* 4.0 5.2 - - - +
2927H LEU 3.3 0.2 - - - -
2928H LYS* 1.3 76.1 - - - +
2930H LEU* 1.3 61.0 + - - +
2932H MET* 3.6 6.5 + - - +
2933H ASN* 3.4 21.1 + - - +
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Residues in contact with LEU2930 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2926H LEU 3.3 16.2 + - - +
2927H LEU* 3.9 5.8 - - - +
2929H PHE* 1.3 76.5 - - - +
2931H GLN* 1.3 63.9 + - - +
2933H ASN* 3.3 8.7 + - - -
2935H TYR* 2.8 49.0 + - + +
2937H VAL* 5.9 7.2 - - + -
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Residues in contact with GLN2931 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2927H LEU 3.1 17.5 + - - +
2928H LYS* 4.1 5.8 - - - +
2930H LEU* 1.3 76.0 - - - +
2932H MET* 1.3 61.5 + - - +
2934H GLY* 3.3 10.9 + - - -
2935H TYR 4.0 10.1 + - - +
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Residues in contact with MET2932 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2828H GLU 4.5 0.9 - - - +
2829H GLY* 3.4 2.1 - - - -
2830H GLU* 2.9 37.6 + - + +
2928H LYS 3.1 18.6 + - - +
2929H PHE* 3.9 7.6 - - - +
2930H LEU 3.2 0.4 - - - -
2931H GLN* 1.3 78.8 - - - +
2933H ASN* 1.3 56.0 + - - +
2934H GLY 3.2 0.8 + - - -
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Residues in contact with ASN2933 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2754H PHE* 6.2 3.8 - - + -
2825H LYS* 5.3 4.2 - - - +
2827H ARG 3.6 7.3 - - - +
2829H GLY* 3.7 17.4 + - - -
2929H PHE 3.4 12.3 + - - +
2930H LEU* 3.3 7.4 + - - +
2931H GLN 3.3 0.6 - - - -
2932H MET* 1.3 78.3 - - - +
2934H GLY* 1.3 60.9 + - - +
2935H TYR* 3.4 3.7 + - + +
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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