Contacts of the helix formed by residues 2751 - 2772 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2747B ILE* 5.2 6.5 - - + -
2748B PRO* 3.3 23.7 + - + +
2749B GLU 3.2 1.2 - - - -
2750B LYS* 1.3 75.4 - - - +
2752B ASP* 1.3 62.8 + - - +
2753B SER 3.2 1.6 - - - -
2754B PHE* 3.4 11.4 + - + +
2755B ILE* 3.2 21.8 + - - +
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Residues in contact with ASP2752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2748B PRO 3.8 4.6 + - - +
2749B GLU* 3.4 17.1 + - - +
2750B LYS 3.2 1.6 - - - -
2751B LEU* 1.3 77.7 - - - +
2753B SER* 1.3 61.7 + - - +
2755B ILE* 3.5 6.8 + - - +
2756B ASN* 3.3 22.3 + - - +
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Residues in contact with SER2753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2749B GLU 4.7 0.6 + - - -
2750B LYS 3.9 10.1 + - - -
2751B LEU 3.2 0.4 - - - -
2752B ASP* 1.3 78.5 - - - +
2754B PHE* 1.3 63.6 + - - +
2756B ASN* 3.5 5.4 + - - +
2757B LYS* 3.1 22.7 + - - +
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Residues in contact with PHE2754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2750B LYS 4.6 1.7 + - - +
2751B LEU* 3.4 14.1 + - + +
2752B ASP 3.4 0.4 - - - -
2753B SER* 1.3 76.0 - - - +
2755B ILE* 1.3 61.5 + - - +
2757B LYS* 3.9 5.9 - - - +
2758B PHE* 3.0 30.7 + - - +
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Residues in contact with ILE2755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2751B LEU 3.2 15.9 + - - +
2752B ASP* 3.8 9.0 - - - +
2753B SER 3.2 0.4 - - - -
2754B PHE* 1.3 78.1 - - - +
2756B ASN* 1.3 57.9 + - - +
2758B PHE* 3.5 4.5 + - - +
2759B ALA* 3.0 28.9 + - - +
2806B ARG* 5.3 11.0 - - + +
2809B ILE* 4.9 14.8 - - + +
2810B LYS* 5.9 5.6 - - + +
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Residues in contact with ASN2756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2752B ASP 3.3 12.6 + - - +
2753B SER* 3.5 6.0 + - - +
2755B ILE* 1.3 78.9 - - - +
2757B LYS* 1.3 61.8 + - - +
2759B ALA* 3.5 5.8 + - - +
2760B GLU* 3.2 23.0 + - - +
2806B ARG* 6.5 0.2 - - - -
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Residues in contact with LYS2757 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2753B SER 3.1 17.9 + - - +
2754B PHE* 3.9 7.2 - - - +
2756B ASN* 1.3 77.9 - - - +
2758B PHE* 1.3 62.3 + - - +
2760B GLU* 3.4 6.2 + - - +
2761B TYR* 3.2 22.3 + - - +
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Residues in contact with PHE2758 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2754B PHE 3.0 19.0 + - - +
2755B ILE* 4.0 3.1 - - - +
2757B LYS* 1.3 74.3 - - - +
2759B ALA* 1.3 60.8 + - - +
2761B TYR* 3.9 6.3 - - - +
2762B THR* 3.1 29.3 + - - -
2809B ILE* 4.7 16.2 - - + -
2929B PHE* 5.2 15.3 - - + -
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Residues in contact with ALA2759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2755B ILE 3.0 18.2 + - - +
2756B ASN* 3.8 7.2 - - - +
2757B LYS 3.3 0.2 - - - -
2758B PHE* 1.3 78.7 - - - +
2760B GLU* 1.3 56.7 + - - +
2762B THR* 3.6 3.1 + - - -
2763B HIS* 3.1 28.8 + - - +
2794B TYR* 5.7 0.2 - - - -
2802B LYS* 4.9 4.5 - - + +
2805B TYR* 4.1 35.5 - - + +
2806B ARG* 4.3 9.6 - - + +
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Residues in contact with GLU2760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2756B ASN 3.2 17.0 + - - +
2757B LYS* 3.9 6.1 - - - +
2758B PHE 3.3 0.2 - - - -
2759B ALA* 1.3 74.2 - - - +
2761B TYR* 1.3 59.4 + - - +
2763B HIS* 4.0 1.5 - - - +
2764B GLU* 3.0 30.7 + - - +
2794B TYR* 4.1 26.6 - - + +
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Residues in contact with TYR2761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2757B LYS 3.2 17.4 + - - +
2758B PHE* 3.5 6.5 + - - +
2759B ALA 3.3 0.2 - - - -
2760B GLU* 1.3 75.5 - - - +
2762B THR* 1.3 59.6 + - - +
2764B GLU* 3.9 5.0 - - - +
2765B LYS* 3.0 30.0 + - - +
2859B PRO* 4.4 8.1 - - + +
2860B PRO 6.2 1.3 - - - -
2929B PHE* 6.2 3.8 - - + -
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Residues in contact with THR2762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2758B PHE 3.1 17.7 + - - -
2759B ALA* 4.0 5.4 - - - -
2761B TYR* 1.3 76.0 - - - +
2763B HIS* 1.3 63.1 + - - +
2765B LYS* 3.5 5.7 + - - +
2766B TRP* 3.2 23.2 + - - +
2805B TYR* 5.1 9.2 - - - -
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Residues in contact with HIS2763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2759B ALA 3.1 18.8 + - - +
2760B GLU* 4.0 5.6 - - - +
2761B TYR 3.3 0.2 - - - -
2762B THR* 1.3 73.9 - - - +
2764B GLU* 1.3 61.2 + - - +
2766B TRP* 3.5 5.0 + - - +
2767B ALA* 3.0 28.9 + - - +
2794B TYR* 5.1 10.3 - - + -
2805B TYR* 5.2 8.0 - - + +
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Residues in contact with GLU2764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2760B GLU 3.0 19.2 + - - +
2761B TYR* 3.9 2.2 - - - +
2762B THR 3.3 0.2 - - - -
2763B HIS* 1.3 74.8 - - - +
2765B LYS* 1.3 59.7 + - - +
2767B ALA* 3.8 3.0 - - - +
2768B PHE* 2.9 30.5 + - - +
2857B PRO* 4.2 22.2 - - + +
2858B GLN 5.2 0.9 - - - +
2859B PRO* 3.8 24.3 - - + +
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Residues in contact with LYS2765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2761B TYR 3.0 17.9 + - - +
2762B THR* 3.9 7.2 - - - +
2763B HIS 3.3 0.2 - - - -
2764B GLU* 1.3 77.5 - - - +
2766B TRP* 1.3 60.4 + - - +
2768B PHE* 3.4 5.5 + - - +
2769B ASP* 3.2 23.0 + - - +
2859B PRO* 4.0 10.9 - - + +
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Residues in contact with TRP2766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2762B THR 3.2 14.4 + - - +
2763B HIS* 4.0 5.6 - - - +
2765B LYS* 1.3 79.6 - - - +
2767B ALA* 1.3 62.3 + - - +
2769B ASP* 3.5 5.3 + - - +
2770B LYS* 3.1 23.7 + - - +
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Residues in contact with ALA2767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2763B HIS 3.0 19.0 + - - +
2764B GLU* 3.9 5.8 - - - +
2766B TRP* 1.3 75.1 - - - +
2768B PHE* 1.3 61.2 + - - +
2770B LYS* 3.5 5.9 + - - +
2771B ILE* 3.0 30.0 + - - +
2790B MET 5.3 4.0 - - - +
2791B LEU* 5.2 15.7 - - + -
2792B ARG 5.6 4.7 - - - +
2857B PRO* 4.7 11.0 - - + -
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Residues in contact with PHE2768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2764B GLU 2.9 18.8 + - - +
2765B LYS* 3.8 6.7 - - - +
2766B TRP 3.3 0.4 - - - -
2767B ALA* 1.3 77.5 - - - +
2769B ASP* 1.3 60.6 + - - +
2771B ILE* 3.4 13.8 + - - +
2772B GLN* 3.5 12.3 + - - +
2857B PRO* 4.4 17.9 - - - +
2859B PRO* 5.5 4.9 - - + -
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Residues in contact with ASP2769 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2765B LYS 3.2 13.7 + - - +
2766B TRP* 4.0 5.2 - - - +
2768B PHE* 1.3 78.7 - - - +
2770B LYS* 1.3 62.4 + - - +
2772B GLN* 3.4 17.6 + - - +
2773B ASN* 4.1 5.2 + - - +
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Residues in contact with LYS2770 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2766B TRP 3.1 18.8 + - - +
2767B ALA* 4.0 6.1 - - - +
2768B PHE 3.3 0.2 - - - -
2769B ASP* 1.3 75.2 - - - +
2771B ILE* 1.3 64.8 + - - +
2773B ASN* 3.2 15.7 + - - +
2775B TRP* 3.3 26.0 - - + +
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Residues in contact with ILE2771 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2767B ALA 3.0 17.9 + - - +
2768B PHE* 3.8 8.3 - - - +
2769B ASP 3.3 0.6 - - - -
2770B LYS* 1.3 75.8 - - - +
2772B GLN* 1.3 61.3 + - - +
2773B ASN 3.3 0.9 + - - -
2774B ASN* 3.4 12.4 + - - -
2775B TRP 4.1 14.0 + - - +
2855B TYR 5.9 3.1 - - - +
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Residues in contact with GLN2772 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2768B PHE 3.5 9.1 + - - +
2769B ASP* 3.4 13.6 + - - +
2770B LYS 3.2 1.2 - - - -
2771B ILE* 1.3 78.1 - - - +
2773B ASN* 1.3 55.8 + - - +
2774B ASN 3.3 4.3 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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