Contacts of the helix formed by residues 2795 - 2811 (chain A) in PDB entry 5NUG
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 SER2795 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2597A PRO* 3.6 12.1 - - - -
2598A GLY* 3.6 15.7 - - - -
2738A TYR* 3.9 0.4 - - - -
2777A TYR* 3.2 14.5 + - - -
2794A TYR* 1.3 79.3 - - - +
2796A PRO* 1.3 66.8 - - - +
2797A ARG* 3.1 26.0 + - - +
2798A GLU* 2.6 58.4 + - - +
2799A MET 3.7 0.2 + - - -
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Residues in contact with PRO2796 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2598A GLY 3.3 21.5 - - - +
2599A SER* 5.0 0.4 - - - -
2738A TYR* 3.7 6.1 - - + -
2739A PRO* 4.0 26.7 - - + -
2744A LEU* 4.9 6.3 - - + -
2748A TYR* 2.8 28.7 + - + +
2777A TYR* 3.2 15.3 - - + +
2795A SER* 1.3 82.6 - - - +
2797A ARG* 1.3 55.4 + - - +
2799A MET* 3.2 9.3 + - + -
2800A THR* 2.9 21.4 + - - -
4804A ADP 3.1 29.6 - - + +
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Residues in contact with ARG2797 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2597A PRO* 3.7 12.9 - - - +
2598A GLY* 3.2 18.2 - - - +
2793A ILE* 5.1 7.3 - - - +
2795A SER* 2.9 16.4 + - - +
2796A PRO* 1.3 78.0 - - - +
2798A GLU* 1.3 66.1 + - - +
2800A THR* 3.2 3.8 + - - -
2801A ARG* 2.9 48.0 + - - +
2836A ARG* 6.1 1.0 - - - +
3086A PHE 4.4 5.5 + - - -
3087A ASN* 3.4 41.9 + - - +
3088A ARG* 6.1 3.1 - - - +
4804A ADP 3.0 66.3 + - + +
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Residues in contact with GLU2798 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2777A TYR* 5.2 0.9 - - + -
2793A ILE 3.4 21.5 - - - +
2794A TYR* 3.6 20.2 - - + -
2795A SER* 2.6 48.9 + - - +
2797A ARG* 1.3 79.3 + - - +
2799A MET* 1.3 56.9 + - + +
2801A ARG* 3.2 20.2 + - - +
2802A TRP* 2.9 26.4 + - - +
2832A LEU* 3.1 24.8 - - + +
2833A PHE* 4.3 19.3 - - + -
2836A ARG* 4.1 14.8 + - - +
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Residues in contact with MET2799 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2744A LEU* 5.2 4.9 - - + -
2748A TYR* 3.3 52.5 - - + +
2773A MET* 3.6 37.0 - - + +
2774A VAL* 4.6 12.3 - - + +
2777A TYR* 3.4 46.2 - - + -
2796A PRO* 3.2 5.6 + - + +
2798A GLU* 1.3 75.7 - - - +
2800A THR* 1.3 58.1 + - - +
2802A TRP* 3.1 25.0 - - - +
2803A VAL* 2.9 31.7 + - - +
2833A PHE* 5.2 0.2 - - - -
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Residues in contact with THR2800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2563A ALA* 3.4 30.1 - - + +
2564A ALA 5.1 2.5 - - - +
2748A TYR* 3.5 7.9 + - - -
2751A PHE* 5.1 0.6 - - + -
2796A PRO 2.9 10.8 + - - -
2797A ARG 3.4 5.6 - - - -
2799A MET* 1.3 75.9 - - - +
2801A ARG* 1.3 57.7 + - - +
2803A VAL* 3.1 12.2 - - - +
2804A ARG* 2.9 32.1 + - + +
4804A ADP 2.6 44.9 + - - +
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Residues in contact with ARG2801 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2797A ARG* 2.9 34.1 + - - +
2798A GLU* 3.4 24.0 - - - +
2800A THR* 1.3 75.7 - - - +
2802A TRP* 1.3 58.4 + - - +
2804A ARG* 3.2 9.8 + - - +
2805A GLY* 2.9 26.3 + - - -
2828A GLU* 4.1 2.5 - - - +
2832A LEU* 3.8 19.2 - - + +
2836A ARG* 4.6 15.8 - - - +
2928A GLN* 5.3 13.3 - - - +
3087A ASN 3.7 21.8 + - - -
3088A ARG* 3.7 14.1 + - - +
3089A CYS 4.6 4.0 + - - -
3090A VAL* 4.6 21.5 - - - +
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Residues in contact with TRP2802 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2773A MET* 3.5 29.6 - - + -
2776A PHE* 3.4 31.0 - + + -
2777A TYR 5.2 0.7 - - - -
2798A GLU 2.9 8.8 + - - +
2799A MET* 3.1 27.8 - - - +
2801A ARG* 1.3 75.5 - - - +
2803A VAL* 1.3 59.1 + - - +
2805A GLY* 3.2 2.8 + - - -
2806A ILE* 2.9 42.9 + - + +
2825A TRP* 3.1 51.6 + + - -
2828A GLU* 3.4 23.8 - - + +
2829A ALA* 3.4 24.0 - - + -
2832A LEU* 3.3 10.5 - - + +
2833A PHE* 3.5 33.2 - + - -
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Residues in contact with VAL2803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2562A VAL* 5.4 2.9 - - + -
2563A ALA* 3.6 28.3 - - + -
2748A TYR* 4.4 12.6 - - + -
2751A PHE* 4.5 11.9 - - + -
2752A ASN* 4.4 19.1 - - - +
2755A MET* 3.4 18.5 - - + +
2773A MET* 3.9 21.1 - - + -
2799A MET 2.9 18.5 + - - +
2800A THR* 3.1 24.5 - - - +
2802A TRP* 1.3 78.6 - - - +
2804A ARG* 1.3 55.4 - - - +
2806A ILE* 3.2 6.3 + - + -
2807A PHE* 2.9 25.9 + - - +
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Residues in contact with ARG2804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2560A HIS 4.8 5.3 + - - -
2561A LYS* 5.4 0.4 - - - +
2562A VAL* 4.2 23.0 - - - +
2563A ALA* 3.6 24.0 - - - +
2564A ALA* 4.4 19.8 - - - +
2565A PRO* 5.8 3.8 - - - +
2800A THR* 2.9 21.9 + - + +
2801A ARG* 3.2 11.9 + - - +
2803A VAL* 1.3 76.3 - - - +
2805A GLY* 1.3 56.0 + - - +
2807A PHE* 3.2 20.8 + - - +
2808A GLU* 2.9 49.4 + - + +
2811A ARG* 6.1 0.8 - - - +
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Residues in contact with GLY2805 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2801A ARG 2.9 12.0 + - - -
2802A TRP 3.2 3.8 + - - -
2804A ARG* 1.3 76.2 - - - +
2806A ILE* 1.3 57.4 - - - +
2808A GLU* 3.2 9.5 + - - +
2809A ALA* 2.9 28.8 + - - +
2828A GLU* 3.6 26.9 - - - +
2881A TYR* 5.9 1.4 - - - -
2924A ARG* 6.2 1.3 - - - -
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Residues in contact with ILE2806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2752A ASN* 5.1 1.6 - - - +
2755A MET* 3.5 28.0 - - + -
2756A LEU* 5.2 2.7 - - + -
2769A LEU* 5.2 6.7 - - + -
2773A MET* 4.6 9.9 - - - -
2802A TRP* 2.9 44.4 + - + +
2803A VAL* 3.2 10.7 + - + +
2805A GLY* 1.3 76.8 - - - +
2807A PHE* 1.3 57.4 + - - +
2809A ALA* 3.2 3.8 + - - +
2810A LEU* 2.9 28.8 + - + +
2821A LEU* 4.4 13.7 - - + -
2824A ILE* 4.1 23.2 - - + +
2825A TRP* 4.4 20.2 - - + -
2828A GLU* 4.5 5.6 - - + -
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Residues in contact with PHE2807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2559A THR* 3.2 34.5 - - - -
2560A HIS* 3.8 15.9 - - - -
2562A VAL* 3.6 26.2 - - + -
2755A MET* 3.5 22.6 - - + -
2758A LEU* 5.6 6.3 - - + -
2803A VAL 2.9 13.2 + - - +
2804A ARG* 3.3 23.3 - - - +
2806A ILE* 1.3 78.0 - - - +
2808A GLU* 1.3 65.6 + - - +
2810A LEU* 3.2 6.1 + - + +
2811A ARG* 2.7 82.6 + - + +
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Residues in contact with GLU2808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2804A ARG* 2.9 31.4 + - + +
2805A GLY* 3.4 11.4 - - - +
2807A PHE* 1.3 94.3 - - + +
2809A ALA* 1.3 61.2 + - - +
2811A ARG* 4.6 13.2 + - - +
2812A PRO* 3.1 25.1 - - - +
2881A TYR* 4.8 10.5 - - + +
2927A ARG* 4.3 22.6 + - - +
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Residues in contact with ALA2809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2805A GLY 2.9 11.6 + - - +
2806A ILE 3.4 2.7 - - - +
2808A GLU* 1.3 78.2 - - - +
2810A LEU* 1.3 63.8 + - - +
2812A PRO* 3.9 4.9 - - - +
2813A LEU* 4.1 14.6 - - - +
2816A LEU* 4.9 2.6 - - + +
2824A ILE* 3.2 42.0 - - + -
2828A GLU* 6.4 0.4 - - + -
2873A TYR* 6.0 0.2 - - + -
2881A TYR* 4.2 32.4 - - + +
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Residues in contact with LEU2810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2755A MET* 3.2 42.6 - - + +
2756A LEU* 4.7 9.6 - - + -
2758A LEU* 4.0 21.5 - - + +
2759A ILE* 3.3 37.2 - - + +
2762A LEU* 4.6 7.4 - - + -
2806A ILE* 2.9 14.6 + - + +
2807A PHE* 3.5 9.9 - - + +
2809A ALA* 1.3 77.9 - - - +
2811A ARG* 1.3 67.4 + - - +
2813A LEU* 2.9 16.1 + - - +
2814A GLU* 3.6 9.3 + - - +
2816A LEU* 4.0 15.3 - - + -
2821A LEU* 5.8 4.5 - - + -
2824A ILE* 4.9 1.3 - - + +
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Residues in contact with ARG2811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2560A HIS* 5.4 11.2 + - - +
2758A LEU* 4.5 16.0 - - + +
2804A ARG* 6.1 0.6 - - - +
2807A PHE* 2.7 58.2 + - + +
2808A GLU* 4.1 14.4 + - - +
2810A LEU* 1.3 72.3 - - - +
2812A PRO* 1.3 70.8 - - + +
2813A LEU 3.5 0.2 + - - -
2814A GLU* 3.9 16.1 - - - +
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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
------------------------------------------------------------
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