Contacts of the helix formed by residues 2751 - 2772 (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 LEU2751 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2747F ILE* 5.2 7.0 - - + -
2748F PRO* 3.3 23.5 + - + +
2749F GLU 3.2 1.0 - - - -
2750F LYS* 1.3 75.6 - - - +
2752F ASP* 1.3 63.1 + - - +
2753F SER 3.2 1.6 - - - -
2754F PHE* 3.4 10.7 + - + +
2755F ILE* 3.2 22.5 + - - +
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Residues in contact with ASP2752 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2748F PRO 3.8 5.0 + - - +
2749F GLU* 3.4 15.8 + - - +
2750F LYS 3.2 0.8 - - - -
2751F LEU* 1.3 79.1 - - - +
2753F SER* 1.3 62.0 + - - +
2755F ILE* 3.5 8.0 + - - +
2756F ASN* 3.3 21.5 + - - +
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Residues in contact with SER2753 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2749F GLU 4.7 0.8 + - - -
2750F LYS 3.9 9.9 + - - -
2751F LEU 3.2 0.8 - - - -
2752F ASP* 1.3 79.9 - - - +
2754F PHE* 1.3 61.9 + - - +
2756F ASN* 3.5 5.3 + - - +
2757F LYS* 3.1 23.2 + - - +
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Residues in contact with PHE2754 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2750F LYS 4.6 1.9 + - - +
2751F LEU* 3.4 14.5 + - + +
2752F ASP 3.4 0.2 - - - -
2753F SER* 1.3 76.4 - - - +
2755F ILE* 1.3 60.8 + - - +
2757F LYS* 3.9 5.8 - - - +
2758F PHE* 3.0 30.3 + - - +
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Residues in contact with ILE2755 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2751F LEU 3.2 17.0 + - - +
2752F ASP* 3.8 9.0 - - - +
2753F SER 3.2 0.4 - - - -
2754F PHE* 1.3 78.3 - - - +
2756F ASN* 1.3 57.0 + - - +
2758F PHE* 3.5 3.7 + - - +
2759F ALA* 3.0 29.3 + - - +
2806F ARG* 5.3 11.3 - - + +
2809F ILE* 4.9 15.2 - - + +
2810F LYS* 5.9 5.6 - - + +
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Residues in contact with ASN2756 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2752F ASP 3.3 13.4 + - - +
2753F SER* 4.0 5.4 - - - +
2755F ILE* 1.3 79.4 - - - +
2757F LYS* 1.3 61.6 + - - +
2759F ALA* 3.5 6.7 + - - +
2760F GLU* 3.2 23.4 + - - +
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Residues in contact with LYS2757 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2753F SER 3.1 17.7 + - - +
2754F PHE* 3.9 7.0 - - - +
2755F ILE 3.3 0.2 - - - -
2756F ASN* 1.3 77.5 - - - +
2758F PHE* 1.3 61.0 + - - +
2760F GLU* 3.4 6.3 + - - +
2761F TYR* 3.2 22.2 + - - +
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Residues in contact with PHE2758 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2754F PHE 3.0 18.8 + - - +
2755F ILE* 4.0 3.4 - - - +
2757F LYS* 1.3 74.3 - - - +
2759F ALA* 1.3 61.5 + - - +
2761F TYR* 3.5 6.5 + - - +
2762F THR* 3.1 29.1 + - - -
2809F ILE* 4.7 15.3 - - + -
2929F PHE* 5.2 16.2 - - + -
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Residues in contact with ALA2759 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2755F ILE 3.0 18.6 + - - +
2756F ASN* 3.8 7.6 - - - +
2757F LYS 3.3 0.4 - - - -
2758F PHE* 1.3 78.4 - - - +
2760F GLU* 1.3 56.0 + - - +
2762F THR* 3.6 2.9 + - - -
2763F HIS* 3.1 29.1 + - - +
2794F TYR* 5.7 0.2 - - - -
2802F LYS* 4.9 4.9 - - + +
2805F TYR* 4.1 34.2 - - + +
2806F ARG* 4.3 9.6 - - + +
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Residues in contact with GLU2760 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2756F ASN 3.2 16.5 + - - +
2757F LYS* 3.9 5.6 - - - +
2758F PHE 3.3 0.2 - - - -
2759F ALA* 1.3 75.1 - - - +
2761F TYR* 1.3 60.8 + - - +
2763F HIS* 3.5 1.4 + - - +
2764F GLU* 3.0 30.0 + - - +
2794F TYR* 4.1 26.4 - - + +
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Residues in contact with TYR2761 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2757F LYS 3.2 16.7 + - - +
2758F PHE* 3.9 7.4 - - - +
2759F ALA 3.3 0.2 - - - -
2760F GLU* 1.3 75.0 - - - +
2762F THR* 1.3 60.4 + - - +
2764F GLU* 3.4 4.9 + - - +
2765F LYS* 3.0 29.6 + - - +
2859F PRO* 4.4 7.8 - - + +
2860F PRO 6.2 0.9 - - - -
2929F PHE* 6.2 3.4 - - + -
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Residues in contact with THR2762 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2758F PHE 3.1 17.4 + - - -
2759F ALA* 4.0 5.6 - - - -
2761F TYR* 1.3 76.2 - - - +
2763F HIS* 1.3 60.6 - - - +
2765F LYS* 3.5 5.7 + - - +
2766F TRP* 3.2 23.2 + - - +
2805F TYR* 5.1 9.0 - - - -
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Residues in contact with HIS2763 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2759F ALA 3.1 18.3 + - - +
2760F GLU* 4.0 5.4 - - - +
2761F TYR 3.3 0.2 - - - -
2762F THR* 1.3 74.2 - - - +
2764F GLU* 1.3 61.7 + - - +
2766F TRP* 3.5 5.6 + - - +
2767F ALA* 3.0 28.9 + - - +
2794F TYR* 5.1 10.8 - - + -
2805F TYR* 5.2 8.2 - - + +
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Residues in contact with GLU2764 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2760F GLU 3.0 20.0 + - - +
2761F TYR* 3.9 2.5 - - - +
2763F HIS* 1.3 75.3 - - - +
2765F LYS* 1.3 59.5 + - - +
2767F ALA* 3.4 2.2 + - - +
2768F PHE* 2.9 30.5 + - - +
2857F PRO* 4.2 23.5 - - + +
2858F GLN 5.2 0.9 - - - +
2859F PRO* 3.8 23.1 - - + +
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Residues in contact with LYS2765 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2761F TYR 3.0 17.6 + - - +
2762F THR* 3.9 6.3 - - - +
2764F GLU* 1.3 77.7 - - - +
2766F TRP* 1.3 61.9 + - - +
2768F PHE* 3.4 4.9 + - - +
2769F ASP* 3.2 22.7 + - - +
2859F PRO* 4.0 11.6 - - + +
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Residues in contact with TRP2766 (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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2762F THR 3.2 15.4 + - - +
2763F HIS* 4.0 4.9 - - - +
2764F GLU 3.3 0.2 - - - -
2765F LYS* 1.3 77.9 - - - +
2767F ALA* 1.3 62.3 + - - +
2769F ASP* 3.5 4.9 + - - +
2770F LYS* 3.1 24.0 + - - +
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Residues in contact with ALA2767 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2763F HIS 3.0 19.2 + - - +
2764F GLU* 3.9 5.6 - - - +
2766F TRP* 1.3 74.5 - - - +
2768F PHE* 1.3 61.5 + - - +
2770F LYS* 3.9 5.1 - - - +
2771F ILE* 3.0 30.0 + - - +
2790F MET 5.3 4.0 - - - +
2791F LEU* 5.2 15.0 - - + -
2792F ARG 5.6 5.2 - - - +
2857F PRO* 4.7 10.5 - - + -
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Residues in contact with PHE2768 (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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2764F GLU 2.9 18.3 + - - +
2765F LYS* 3.8 7.0 - - - +
2766F TRP 3.3 0.2 - - - -
2767F ALA* 1.3 78.1 - - - +
2769F ASP* 1.3 62.3 + - - +
2771F ILE* 3.4 14.0 + - - +
2772F GLN* 3.5 12.3 + - - +
2857F PRO* 4.4 18.3 - - - +
2859F PRO* 5.5 5.8 - - + -
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Residues in contact with ASP2769 (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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2765F LYS 3.2 13.9 + - - +
2766F TRP* 3.5 5.6 + - - +
2768F PHE* 1.3 79.6 - - - +
2770F LYS* 1.3 61.7 + - - +
2772F GLN* 3.4 17.4 + - - +
2773F ASN* 4.1 5.0 + - - +
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Residues in contact with LYS2770 (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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2766F TRP 3.1 17.9 + - - +
2767F ALA* 4.0 6.7 - - - +
2768F PHE 3.3 0.2 - - - -
2769F ASP* 1.3 74.9 - - - +
2771F ILE* 1.3 64.8 + - - +
2773F ASN* 3.2 15.3 + - - +
2775F TRP* 3.3 26.1 - - + +
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Residues in contact with ILE2771 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2767F ALA 3.0 17.9 + - - +
2768F PHE* 3.8 7.9 - - - +
2769F ASP 3.3 0.4 - - - -
2770F LYS* 1.3 76.9 - - - +
2772F GLN* 1.3 61.4 + - - +
2773F ASN 3.1 0.7 + - - -
2774F ASN* 3.4 12.1 + - - -
2775F TRP* 4.1 14.2 + - - +
2855F TYR 5.9 3.1 - - - +
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Residues in contact with GLN2772 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2768F PHE 3.5 8.2 + - - +
2769F ASP* 3.4 13.8 + - - +
2770F LYS 3.2 0.8 - - - -
2771F ILE* 1.3 77.8 - - - +
2773F ASN* 1.3 56.3 + - - +
2774F ASN 3.3 3.8 + - - -
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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