Contacts of the helix formed by residues 2751 - 2772 (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 LEU2751 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2747H ILE* 5.2 7.0 - - + -
2748H PRO* 3.3 24.0 + - + +
2749H GLU 3.2 1.0 - - - -
2750H LYS* 1.3 75.3 - - - +
2752H ASP* 1.3 62.9 + - - +
2753H SER 3.2 1.1 - - - -
2754H PHE* 3.4 11.1 + - + +
2755H ILE* 3.2 22.1 + - - +
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Residues in contact with ASP2752 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2748H PRO 3.8 5.0 + - - +
2749H GLU* 3.4 15.6 + - - +
2750H LYS 3.2 1.4 - - - -
2751H LEU* 1.3 78.7 - - - +
2753H SER* 1.3 60.9 + - - +
2755H ILE* 3.5 7.2 + - - +
2756H ASN* 3.3 22.0 + - - +
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Residues in contact with SER2753 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2749H GLU 4.7 0.8 + - - -
2750H LYS 3.9 10.8 + - - -
2751H LEU 3.2 0.6 - - - -
2752H ASP* 1.3 77.6 - - - +
2754H PHE* 1.3 61.8 + - - +
2756H ASN* 3.5 4.8 + - - +
2757H LYS* 3.1 23.0 + - - +
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Residues in contact with PHE2754 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2750H LYS 4.6 1.2 + - - +
2751H LEU* 3.4 14.3 + - + +
2752H ASP 3.4 0.4 - - - -
2753H SER* 1.3 76.1 - - - +
2755H ILE* 1.3 59.6 + - - +
2757H LYS* 3.9 6.5 - - - +
2758H PHE* 3.0 31.0 + - - +
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Residues in contact with ILE2755 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2751H LEU 3.2 16.6 + - - +
2752H ASP* 3.8 8.3 - - - +
2753H SER 3.2 0.2 - - - -
2754H PHE* 1.3 78.5 - - - +
2756H ASN* 1.3 56.1 + - - +
2758H PHE* 3.5 4.8 + - - +
2759H ALA* 3.0 29.1 + - - +
2806H ARG* 5.3 11.2 - - + +
2809H ILE* 4.9 14.8 - - + +
2810H LYS* 5.9 5.4 - - + +
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Residues in contact with ASN2756 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2752H ASP 3.3 13.7 + - - +
2753H SER* 4.0 4.9 - - - +
2754H PHE 3.4 0.2 - - - -
2755H ILE* 1.3 79.8 - - - +
2757H LYS* 1.3 63.2 + - - +
2759H ALA* 3.5 6.4 + - - +
2760H GLU* 3.2 23.0 + - - +
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Residues in contact with LYS2757 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2753H SER 3.1 17.5 + - - +
2754H PHE* 3.9 6.7 - - - +
2756H ASN* 1.3 78.1 - - - +
2758H PHE* 1.3 61.2 + - - +
2760H GLU* 3.4 5.5 + - - +
2761H TYR* 3.2 21.8 + - - +
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Residues in contact with PHE2758 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2754H PHE 3.0 18.5 + - - +
2755H ILE* 4.0 3.6 - - - +
2757H LYS* 1.3 74.1 - - - +
2759H ALA* 1.3 60.3 + - - +
2761H TYR* 3.5 5.7 + - - +
2762H THR* 3.1 28.6 + - - -
2809H ILE* 4.7 14.6 - - + -
2929H PHE* 5.2 15.3 - - + -
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Residues in contact with ALA2759 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2755H ILE 3.0 18.4 + - - +
2756H ASN* 3.8 7.6 - - - +
2757H LYS 3.3 0.2 - - - -
2758H PHE* 1.3 78.9 - - - +
2760H GLU* 1.3 57.1 + - - +
2762H THR* 3.6 2.7 + - - -
2763H HIS* 3.1 28.6 + - - +
2794H TYR* 5.7 0.2 - - - -
2802H LYS* 4.9 4.5 - - + +
2805H TYR* 4.1 36.1 - - + +
2806H ARG* 4.3 9.4 - - + +
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Residues in contact with GLU2760 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2756H ASN 3.2 16.5 + - - +
2757H LYS* 3.9 5.8 - - - +
2759H ALA* 1.3 75.1 - - - +
2761H TYR* 1.3 61.7 + - - +
2763H HIS* 3.9 2.1 - - - +
2764H GLU* 3.0 30.3 + - - +
2794H TYR* 4.1 26.8 - - + +
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Residues in contact with TYR2761 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2757H LYS 3.2 16.2 + - - +
2758H PHE* 3.9 6.7 - - - +
2759H ALA 3.3 0.2 - - - -
2760H GLU* 1.3 75.1 - - - +
2762H THR* 1.3 60.7 + - - +
2764H GLU* 3.4 5.2 + - - +
2765H LYS* 3.0 29.8 + - - +
2859H PRO* 4.4 7.8 - - + +
2860H PRO 6.2 1.8 - - - -
2929H PHE* 6.2 3.4 - - + -
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Residues in contact with THR2762 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2758H PHE 3.1 17.2 + - - -
2759H ALA* 4.0 5.4 - - - -
2760H GLU 3.4 0.2 - - - -
2761H TYR* 1.3 78.2 - - - +
2763H HIS* 1.3 62.0 + - - +
2765H LYS* 3.5 5.4 + - - +
2766H TRP* 3.2 23.2 + - - +
2805H TYR* 5.1 9.2 - - - -
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Residues in contact with HIS2763 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2759H ALA 3.1 18.7 + - - +
2760H GLU* 4.0 5.8 - - - +
2762H THR* 1.3 74.3 - - - +
2764H GLU* 1.3 61.1 + - - +
2766H TRP* 3.5 5.0 + - - +
2767H ALA* 3.0 29.3 + - - +
2792H ARG 6.2 0.2 - - - +
2794H TYR* 5.1 10.1 - - + -
2805H TYR* 5.2 8.2 - - + +
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Residues in contact with GLU2764 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2760H GLU 3.0 19.2 + - - +
2761H TYR* 3.9 2.5 - - - +
2763H HIS* 1.3 76.6 - - - +
2765H LYS* 1.3 59.0 + - - +
2767H ALA* 3.9 2.0 - - - +
2768H PHE* 2.9 31.2 + - - +
2857H PRO* 4.2 21.4 - - + +
2858H GLN 5.2 0.7 - - - +
2859H PRO* 3.8 23.2 - - + +
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Residues in contact with LYS2765 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2761H TYR 3.0 18.5 + - - +
2762H THR* 3.9 6.7 - - - +
2763H HIS 3.3 0.2 - - - -
2764H GLU* 1.3 77.7 - - - +
2766H TRP* 1.3 61.4 + - - +
2768H PHE* 3.4 4.9 + - - +
2769H ASP* 3.2 22.0 + - - +
2859H PRO* 4.0 11.2 - - + +
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Residues in contact with TRP2766 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2762H THR 3.2 14.1 + - - +
2763H HIS* 4.0 5.4 - - - +
2764H GLU 3.3 0.2 - - - -
2765H LYS* 1.3 78.3 - - - +
2767H ALA* 1.3 61.6 + - - +
2769H ASP* 3.5 5.5 + - - +
2770H LYS* 3.1 23.6 + - - +
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Residues in contact with ALA2767 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2763H HIS 3.0 18.5 + - - +
2764H GLU* 3.9 6.3 - - - +
2765H LYS 3.3 0.2 - - - -
2766H TRP* 1.3 74.5 - - - +
2768H PHE* 1.3 60.8 + - - +
2770H LYS* 3.9 5.6 - - - +
2771H ILE* 3.0 29.8 + - - +
2790H MET 5.3 4.0 - - - +
2791H LEU* 5.2 15.0 - - + -
2792H ARG 5.6 4.7 - - - +
2857H PRO* 4.7 11.0 - - + -
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Residues in contact with PHE2768 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2764H GLU 2.9 18.8 + - - +
2765H LYS* 3.8 6.7 - - - +
2766H TRP 3.3 0.4 - - - -
2767H ALA* 1.3 77.9 - - - +
2769H ASP* 1.3 62.2 + - - +
2771H ILE* 3.4 13.6 + - - +
2772H GLN* 3.5 11.8 + - - +
2857H PRO* 4.4 18.3 - - - +
2859H PRO* 5.5 5.2 - - + -
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Residues in contact with ASP2769 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2765H LYS 3.2 13.3 + - - +
2766H TRP* 4.0 5.4 - - - +
2768H PHE* 1.3 79.6 - - - +
2770H LYS* 1.3 61.9 + - - +
2772H GLN* 3.4 17.6 + - - +
2773H ASN* 4.1 5.0 + - - +
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Residues in contact with LYS2770 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2766H TRP 3.1 18.2 + - - +
2767H ALA* 3.5 6.3 + - - +
2769H ASP* 1.3 75.4 - - - +
2771H ILE* 1.3 65.0 + - - +
2773H ASN* 3.2 16.3 + - - +
2775H TRP* 3.3 24.8 - - + +
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Residues in contact with ILE2771 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2767H ALA 3.0 18.0 + - - +
2768H PHE* 3.8 8.1 - - - +
2769H ASP 3.3 0.4 - - - -
2770H LYS* 1.3 76.9 - - - +
2772H GLN* 1.3 61.7 + - - +
2773H ASN 3.1 0.9 + - - -
2774H ASN* 3.4 12.0 + - - -
2775H TRP* 4.1 14.6 + - - +
2855H TYR 5.9 2.7 - - - +
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Residues in contact with GLN2772 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2768H PHE 3.5 8.6 + - - +
2769H ASP* 3.4 13.8 + - - +
2770H LYS 3.2 1.2 - - - -
2771H ILE* 1.3 77.5 - - - +
2773H ASN* 1.3 55.6 + - - +
2774H 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) + - + + + + + -
------------------------------------------------------------
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