Contacts of the helix formed by residues 2751 - 2772 (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 LEU2751 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2747D ILE* 5.2 7.0 - - + -
2748D PRO* 3.3 23.3 + - + +
2749D GLU 3.2 0.8 - - - -
2750D LYS* 1.3 76.1 - - - +
2752D ASP* 1.3 62.9 + - - +
2753D SER 3.2 1.8 - - - -
2754D PHE* 3.4 10.9 + - + +
2755D ILE* 3.2 22.0 + - - +
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Residues in contact with ASP2752 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2748D PRO 3.8 4.6 + - - +
2749D GLU* 3.4 16.7 + - - +
2750D LYS 3.2 1.6 - - - -
2751D LEU* 1.3 79.5 - - - +
2753D SER* 1.3 60.0 + - - +
2755D ILE* 3.5 7.8 + - - +
2756D ASN* 3.3 21.5 + - - +
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Residues in contact with SER2753 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2749D GLU 4.7 0.4 + - - -
2750D LYS 3.9 10.1 + - - -
2751D LEU 3.2 0.8 - - - -
2752D ASP* 1.3 77.8 - - - +
2754D PHE* 1.3 62.5 + - - +
2756D ASN* 3.5 6.0 + - - +
2757D LYS* 3.1 23.0 + - - +
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Residues in contact with PHE2754 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2750D LYS 4.6 2.1 + - - +
2751D LEU* 3.4 13.7 + - + +
2752D ASP 3.4 0.4 - - - -
2753D SER* 1.3 77.0 - - - +
2755D ILE* 1.3 60.8 + - - +
2757D LYS* 3.9 6.1 - - - +
2758D PHE* 3.0 31.0 + - - +
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Residues in contact with ILE2755 (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 3.2 17.0 + - - +
2752D ASP* 3.8 8.7 - - - +
2753D SER 3.2 0.2 - - - -
2754D PHE* 1.3 77.8 - - - +
2756D ASN* 1.3 57.4 + - - +
2758D PHE* 3.5 4.0 + - - +
2759D ALA* 3.0 29.5 + - - +
2806D ARG* 5.3 10.4 - - + +
2809D ILE* 4.9 15.4 - - + +
2810D LYS* 5.9 4.9 - - + +
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Residues in contact with ASN2756 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2752D ASP 3.3 13.5 + - - +
2753D SER* 4.0 5.2 - - - +
2755D ILE* 1.3 78.3 - - - +
2757D LYS* 1.3 62.3 + - - +
2759D ALA* 3.5 6.2 + - - +
2760D GLU* 3.2 23.0 + - - +
2806D ARG* 6.5 0.2 - - - -
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Residues in contact with LYS2757 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2753D SER 3.1 17.4 + - - +
2754D PHE* 3.9 7.0 - - - +
2755D ILE 3.3 0.2 - - - -
2756D ASN* 1.3 77.7 - - - +
2758D PHE* 1.3 61.5 + - - +
2760D GLU* 3.4 5.8 + - - +
2761D TYR* 3.2 22.5 + - - +
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Residues in contact with PHE2758 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2754D PHE 3.0 18.3 + - - +
2755D ILE* 4.0 3.6 - - - +
2757D LYS* 1.3 75.6 - - - +
2759D ALA* 1.3 60.0 + - - +
2761D TYR* 3.5 5.7 + - - +
2762D THR* 3.1 29.5 + - - -
2809D ILE* 4.7 16.2 - - + -
2929D PHE* 5.2 15.7 - - + -
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Residues in contact with ALA2759 (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 3.0 19.4 + - - +
2756D ASN* 3.8 7.2 - - - +
2757D LYS 3.3 0.2 - - - -
2758D PHE* 1.3 77.9 - - - +
2760D GLU* 1.3 55.7 + - - +
2762D THR* 3.6 3.3 + - - -
2763D HIS* 3.1 27.9 + - - +
2794D TYR* 5.7 0.7 - - - -
2802D LYS* 4.9 4.3 - - + +
2805D TYR* 4.1 35.3 - - + +
2806D ARG* 4.3 9.6 - - + +
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Residues in contact with GLU2760 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2756D ASN 3.2 16.8 + - - +
2757D LYS* 3.9 5.6 - - - +
2758D PHE 3.3 0.2 - - - -
2759D ALA* 1.3 74.8 - - - +
2761D TYR* 1.3 59.9 + - - +
2763D HIS* 3.5 1.9 + - - +
2764D GLU* 3.0 30.0 + - - +
2794D TYR* 4.1 27.5 - - + +
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Residues in contact with TYR2761 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2757D LYS 3.2 17.0 + - - +
2758D PHE* 3.5 7.2 + - - +
2759D ALA 3.3 0.2 - - - -
2760D GLU* 1.3 75.2 - - - +
2762D THR* 1.3 59.8 + - - +
2764D GLU* 3.4 4.9 + - - +
2765D LYS* 3.0 29.8 + - - +
2859D PRO* 4.4 7.5 - - + +
2860D PRO 6.2 1.1 - - - -
2929D PHE* 6.2 3.6 - - + -
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Residues in contact with THR2762 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2758D PHE 3.1 18.3 + - - -
2759D ALA* 4.0 5.4 - - - -
2761D TYR* 1.3 75.9 - - - +
2763D HIS* 1.3 62.2 + - - +
2765D LYS* 3.5 6.3 + - - +
2766D TRP* 3.2 22.9 + - - +
2805D TYR* 5.1 8.3 - - - -
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Residues in contact with HIS2763 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2759D ALA 3.1 18.6 + - - +
2760D GLU* 4.0 5.6 - - - +
2762D THR* 1.3 74.9 - - - +
2764D GLU* 1.3 61.0 + - - +
2766D TRP* 3.5 5.2 + - - +
2767D ALA* 3.0 29.1 + - - +
2794D TYR* 5.1 10.3 - - + -
2805D TYR* 5.2 7.8 - - + +
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Residues in contact with GLU2764 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2760D GLU 3.0 18.1 + - - +
2761D TYR* 3.9 2.7 - - - +
2763D HIS* 1.3 74.6 - - - +
2765D LYS* 1.3 60.6 + - - +
2767D ALA* 3.8 2.3 - - - +
2768D PHE* 2.9 30.5 + - - +
2857D PRO* 4.2 23.0 - - + +
2858D GLN 5.2 0.9 - - - +
2859D PRO* 3.8 23.0 - - + +
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Residues in contact with LYS2765 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2761D TYR 3.0 18.1 + - - +
2762D THR* 3.9 6.3 - - - +
2763D HIS 3.3 0.2 - - - -
2764D GLU* 1.3 77.5 - - - +
2766D TRP* 1.3 61.1 + - - +
2768D PHE* 3.4 4.7 + - - +
2769D ASP* 3.2 22.9 + - - +
2859D PRO* 4.0 12.0 - - + +
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Residues in contact with TRP2766 (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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2762D THR 3.2 15.0 + - - +
2763D HIS* 4.0 5.4 - - - +
2765D LYS* 1.3 79.5 - - - +
2767D ALA* 1.3 62.4 + - - +
2769D ASP* 3.5 5.5 + - - +
2770D LYS* 3.1 23.6 + - - +
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Residues in contact with ALA2767 (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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2763D HIS 3.0 18.1 + - - +
2764D GLU* 3.9 6.7 - - - +
2766D TRP* 1.3 74.9 - - - +
2768D PHE* 1.3 59.5 + - - +
2770D LYS* 3.5 5.8 + - - +
2771D ILE* 3.0 29.1 + - - +
2790D MET 5.3 3.1 - - - +
2791D LEU* 5.2 16.4 - - + -
2792D ARG 5.6 4.5 - - - +
2857D PRO* 4.7 11.4 - - + -
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Residues in contact with PHE2768 (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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2764D GLU 2.9 19.4 + - - +
2765D LYS* 3.8 6.5 - - - +
2766D TRP 3.3 0.2 - - - -
2767D ALA* 1.3 76.9 - - - +
2769D ASP* 1.3 61.5 + - - +
2771D ILE* 3.4 13.0 + - - +
2772D GLN* 3.5 12.1 + - - +
2857D PRO* 4.4 17.4 - - - +
2859D PRO* 5.5 5.4 - - + -
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Residues in contact with ASP2769 (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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2765D LYS 3.2 14.1 + - - +
2766D TRP* 4.0 5.2 - - - +
2767D ALA 3.4 0.2 - - - -
2768D PHE* 1.3 78.4 - - - +
2770D LYS* 1.3 61.6 + - - +
2772D GLN* 3.4 18.6 + - - +
2773D ASN* 4.1 5.2 + - - +
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Residues in contact with LYS2770 (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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2766D TRP 3.1 18.1 + - - +
2767D ALA* 4.0 6.5 - - - +
2769D ASP* 1.3 74.9 - - - +
2771D ILE* 1.3 65.2 + - - +
2773D ASN* 3.2 16.4 + - - +
2775D TRP* 3.3 25.5 - - + +
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Residues in contact with ILE2771 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2767D ALA 3.0 18.6 + - - +
2768D PHE* 3.8 7.6 - - - +
2769D ASP 3.3 0.4 - - - -
2770D LYS* 1.3 77.4 - - - +
2772D GLN* 1.3 61.6 + - - +
2773D ASN 3.1 1.1 + - - -
2774D ASN* 3.4 12.0 + - - -
2775D TRP 4.1 14.5 + - - +
2855D TYR 5.9 3.1 - - - +
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Residues in contact with GLN2772 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2768D PHE 3.5 8.9 + - - +
2769D ASP* 3.4 13.4 + - - +
2770D LYS 3.2 0.8 - - - -
2771D ILE* 1.3 77.7 - - - +
2773D ASN* 1.3 56.7 + - - +
2774D ASN 3.3 4.5 + - - -
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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