Contacts of the helix formed by residues 2798 - 2819 (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 SER2798 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2796F THR 3.9 1.2 + - - -
2797F PHE* 1.3 77.7 - - - +
2799F GLU* 1.3 62.0 + - - +
2800F LYS* 3.3 8.3 - - - -
2801F ASP* 3.9 8.8 - - - +
2802F LYS* 3.0 26.9 + - - +
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Residues in contact with GLU2799 (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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2798F SER* 1.3 76.3 - - - +
2800F LYS* 1.3 61.4 + - - +
2802F LYS* 4.0 4.5 - - - +
2803F GLU* 3.2 24.1 + - - +
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Residues in contact with LYS2800 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2798F SER* 3.3 5.2 - - - -
2799F GLU* 1.3 77.9 - - - +
2801F ASP* 1.3 63.9 + - - +
2803F GLU* 3.5 14.3 + - - +
2804F ILE* 3.8 8.8 + - - +
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Residues in contact with ASP2801 (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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2797F PHE* 3.8 24.0 - - + -
2798F SER* 3.5 10.6 + - - +
2800F LYS* 1.3 78.3 - - - +
2802F LYS* 1.3 61.0 + - - +
2804F ILE* 3.4 18.8 + - - +
2805F TYR* 4.4 2.6 + - - +
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Residues in contact with LYS2802 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2759F ALA* 4.9 4.7 - - + +
2794F TYR 5.7 2.2 - - - +
2797F PHE* 4.4 10.0 - - + +
2798F SER 3.0 18.4 + - - +
2799F GLU* 4.1 5.6 - - - +
2800F LYS 3.3 0.2 - - - -
2801F ASP* 1.3 77.8 - - - +
2803F GLU* 1.3 56.9 + - - +
2804F ILE 3.4 0.3 + - - -
2805F TYR* 3.5 5.5 + - - +
2806F ARG* 3.2 27.7 + - + +
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Residues in contact with GLU2803 (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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2799F GLU 3.2 18.2 + - - +
2800F LYS* 3.8 8.5 - - - +
2801F ASP 3.3 0.8 - - - -
2802F LYS* 1.3 75.3 - - - +
2804F ILE* 1.3 63.0 + - - +
2806F ARG* 3.8 8.1 - - - -
2807F TRP* 3.2 25.6 + - - +
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Residues in contact with ILE2804 (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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2800F LYS 3.8 6.8 + - - +
2801F ASP* 3.4 14.1 + - - +
2802F LYS 3.2 1.0 - - - -
2803F GLU* 1.3 79.1 - - - +
2805F TYR* 1.3 58.7 + - + +
2807F TRP* 4.2 8.4 + - - +
2808F PRO* 4.6 5.4 - - - +
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Residues in contact with TYR2805 (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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2759F ALA* 4.1 32.7 - - + +
2762F THR* 5.1 9.9 - - - -
2763F HIS* 5.2 7.4 - - + +
2801F ASP 4.4 2.2 + - - +
2802F LYS* 3.5 5.7 + - - +
2804F ILE* 1.3 77.6 - - + +
2806F ARG* 1.3 62.7 + - - +
2807F TRP 3.3 1.3 + - - -
2808F PRO* 3.8 12.9 - - - +
2809F ILE* 3.8 10.7 + - - +
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Residues in contact with ARG2806 (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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2755F ILE* 5.3 11.5 - - + +
2759F ALA* 4.3 11.8 - - + +
2802F LYS* 3.2 19.4 + - + +
2803F GLU* 3.7 6.9 + - - -
2804F ILE 3.5 0.2 - - - -
2805F TYR* 1.3 75.6 - - - +
2807F TRP* 1.3 60.9 + - - +
2808F PRO 3.3 0.2 - - - -
2809F ILE* 3.5 6.5 + - - +
2810F LYS* 3.0 31.5 + - - +
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Residues in contact with TRP2807 (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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2803F GLU 3.2 19.6 + - - +
2804F ILE 4.3 5.8 - - - +
2805F TYR 3.3 0.4 - - - -
2806F ARG* 1.3 77.6 - - - +
2808F PRO* 1.3 57.7 - - - +
2810F LYS* 4.0 4.3 - - - +
2811F GLU* 3.0 30.3 + - - +
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Residues in contact with PRO2808 (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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2804F ILE 4.6 4.0 - - - +
2805F TYR* 3.8 11.0 - - - +
2806F ARG 3.3 0.2 - - - -
2807F TRP* 1.3 81.4 - - - +
2809F ILE* 1.3 58.8 + - - +
2811F GLU* 4.0 4.5 - - + +
2812F SER* 3.3 23.0 + - - -
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Residues in contact with ILE2809 (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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2755F ILE* 4.9 15.3 - - + +
2758F PHE* 4.7 20.0 - - + -
2759F ALA 5.5 1.3 - - - +
2805F TYR 3.8 10.1 + - - +
2806F ARG* 3.5 8.8 + - - +
2807F TRP 3.3 0.4 - - - -
2808F PRO* 1.3 77.1 - - - +
2810F LYS* 1.3 60.9 + - - +
2812F SER* 3.5 5.3 + - - +
2813F LEU* 3.0 29.3 + - - +
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Residues in contact with LYS2810 (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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2755F ILE* 5.9 5.5 - - + +
2806F ARG 3.0 18.1 + - - +
2807F TRP* 4.0 4.9 - - - +
2809F ILE* 1.3 75.9 - - - +
2811F GLU* 1.3 59.7 + - - +
2813F LEU* 3.8 5.8 - - - +
2814F LYS* 2.9 31.5 + - - +
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Residues in contact with GLU2811 (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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2742F THR* 4.8 8.3 - - - -
2807F TRP 3.0 18.2 + - - +
2808F PRO* 4.0 6.1 - - + +
2809F ILE 3.3 0.2 - - - -
2810F LYS* 1.3 77.2 - - - +
2812F SER* 1.3 60.1 + - - +
2814F LYS* 4.0 5.8 - - - +
2815F ALA* 3.2 22.9 + - - +
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Residues in contact with SER2812 (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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2808F PRO 3.3 16.1 + - - -
2809F ILE* 3.9 5.4 - - - -
2810F LYS 3.3 0.2 - - - -
2811F GLU* 1.3 78.4 - - - +
2813F LEU* 1.3 63.3 + - - +
2815F ALA* 3.5 6.8 + - - +
2816F MET* 3.4 20.8 + - - +
2878F LEU* 6.3 2.9 - - - -
2926F LEU* 5.4 12.6 - - - -
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Residues in contact with LEU2813 (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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2751F LEU* 6.3 3.6 - - + -
2809F ILE 3.0 17.6 + - - +
2810F LYS* 3.9 6.3 - - - +
2812F SER* 1.3 75.7 - - - +
2814F LYS* 1.3 63.5 + - - +
2816F MET* 3.4 7.0 + - - +
2817F ILE* 3.2 21.3 + - - +
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Residues in contact with LYS2814 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2742F THR* 3.8 22.4 - - - +
2745F VAL* 3.8 30.9 - - + +
2810F LYS 2.9 17.9 + - - +
2811F GLU* 4.0 2.9 - - - +
2813F LEU* 1.3 74.3 - - - +
2815F ALA* 1.3 65.5 + - - +
2817F ILE* 3.4 6.9 + - - +
2818F ALA* 3.3 20.3 + - - +
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Residues in contact with ALA2815 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2740F VAL* 4.8 19.0 - - + +
2741F GLU 6.0 0.4 - - - -
2742F THR* 4.8 5.3 - - - -
2811F GLU 3.2 16.8 + - - +
2812F SER* 3.8 7.6 - - - +
2813F LEU 3.3 0.4 - - - -
2814F LYS* 1.3 76.9 - - - +
2816F MET* 1.3 60.7 + - - +
2818F ALA* 3.4 15.4 + - - +
2819F TRP* 3.5 11.6 + - - +
2881F ASN* 5.2 13.7 - - + -
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Residues in contact with MET2816 (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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2812F SER 3.4 11.2 + - - +
2813F LEU* 3.4 9.2 + - - +
2814F LYS 3.3 0.4 - - - -
2815F ALA* 1.3 76.3 - - - +
2817F ILE* 1.3 64.2 + - - +
2819F TRP* 3.3 13.6 + - - +
2821F TRP* 3.3 33.4 + - + +
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Residues in contact with ILE2817 (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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2745F VAL* 5.2 6.5 - - + -
2746F ILE 5.3 8.1 - - - +
2813F LEU 3.2 16.3 + - - +
2814F LYS* 3.7 9.9 - - - +
2815F ALA 3.3 0.4 - - - -
2816F MET* 1.3 79.0 - - - +
2818F ALA* 1.3 61.0 + - - +
2820F GLU* 3.4 12.6 + - - -
2821F TRP 4.5 6.9 + - - +
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Residues in contact with ALA2818 (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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2740F VAL* 5.2 9.4 - - + -
2741F GLU 4.5 14.8 - - - +
2745F VAL* 5.7 3.5 - - + +
2814F LYS 3.3 9.7 + - - +
2815F ALA* 3.8 10.5 - - - +
2816F MET 3.3 0.8 - - - -
2817F ILE* 1.3 79.9 - - - +
2819F TRP* 1.3 54.6 + - - +
2820F GLU* 3.2 5.2 + - - +
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Residues in contact with TRP2819 (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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2815F ALA 3.5 9.4 + - - +
2816F MET* 3.3 11.8 + - - +
2817F ILE 3.2 1.0 - - - -
2818F ALA* 1.3 75.2 - - - +
2820F GLU* 1.3 69.6 + - - +
2821F TRP* 3.3 5.3 + - + +
2939F ARG* 5.4 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
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Atomic class I II III IV V VI VII VIII
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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