Contacts of the helix formed by residues 2795 - 2811 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2597B PRO* 3.6 12.3 - - - -
2598B GLY* 3.6 15.3 - - - -
2738B TYR* 3.9 0.2 - - - -
2777B TYR* 3.2 14.4 + - - -
2794B TYR* 1.3 80.1 - - - +
2796B PRO* 1.3 67.1 - - - +
2797B ARG* 2.9 26.0 + - - +
2798B GLU* 2.6 57.4 + - - +
2799B MET 3.7 0.5 + - - -
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Residues in contact with PRO2796 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2598B GLY 3.3 21.1 - - - +
2599B SER* 5.0 0.7 - - - +
2738B TYR* 3.7 5.8 - - + -
2739B PRO* 4.0 26.5 - - + -
2744B LEU* 4.9 7.0 - - + -
2748B TYR* 2.8 27.8 + - - +
2777B TYR* 3.2 15.3 - - + +
2795B SER* 1.3 81.7 - - - +
2797B ARG* 1.3 55.3 + - - +
2798B GLU 3.2 0.2 - - - -
2799B MET* 3.2 9.3 + - + -
2800B THR* 2.9 22.2 + - - -
4804B ADP 3.1 28.3 - - + +
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Residues in contact with ARG2797 (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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2597B PRO* 3.7 13.1 - - - +
2598B GLY* 3.2 18.3 - - - +
2793B ILE* 5.1 6.9 - - - +
2795B SER* 2.9 16.5 + - - +
2796B PRO* 1.3 77.1 - - - +
2798B GLU* 1.3 65.2 + - - +
2800B THR* 3.2 3.8 + - - -
2801B ARG* 2.9 48.7 + - - +
2836B ARG* 6.1 0.8 - - - +
3086B PHE 4.4 5.5 + - - -
3087B ASN* 3.4 42.9 + - - +
3088B ARG* 6.1 2.5 - - - +
4804B ADP 3.0 66.0 + - + +
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Residues in contact with GLU2798 (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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2777B TYR* 5.2 1.1 - - + -
2793B ILE 3.4 21.8 - - - +
2794B TYR* 3.6 19.0 - - + -
2795B SER* 2.6 48.9 + - - +
2797B ARG* 1.3 82.2 + - - +
2799B MET* 1.3 56.5 + - + +
2801B ARG* 3.2 18.9 + - - +
2802B TRP* 2.9 26.1 + - - +
2832B LEU* 3.1 25.4 - - + +
2833B PHE* 4.3 18.6 - - + -
2836B ARG* 4.1 15.2 + - - +
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Residues in contact with MET2799 (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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2744B LEU* 5.2 5.8 - - + -
2748B TYR* 3.3 52.7 - - + +
2773B MET* 3.6 35.4 - - + -
2774B VAL* 4.6 12.3 - - + +
2777B TYR* 3.4 44.6 - - + -
2796B PRO* 3.2 5.4 + - + +
2798B GLU* 1.3 76.3 - - - +
2800B THR* 1.3 59.0 + - - +
2802B TRP* 3.1 25.1 - - - +
2803B VAL* 2.9 32.1 + - - +
2833B PHE* 5.2 0.4 - - - -
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Residues in contact with THR2800 (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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2563B ALA* 3.4 30.3 - - + +
2564B ALA 5.1 2.9 - - - +
2748B TYR* 3.5 8.4 + - - -
2751B PHE* 5.1 0.8 - - + -
2796B PRO 2.9 10.7 + - - -
2797B ARG 3.2 5.8 + - - -
2799B MET* 1.3 74.1 - - - +
2801B ARG* 1.3 59.0 + - + +
2803B VAL* 3.1 11.9 - - - +
2804B ARG* 2.9 31.5 + - + +
4804B ADP 2.6 44.9 + - - +
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Residues in contact with ARG2801 (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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2797B ARG* 2.9 34.5 + - - +
2798B GLU* 3.4 22.8 - - - +
2800B THR* 1.3 76.4 - - - +
2802B TRP* 1.3 57.2 - - - +
2804B ARG* 3.2 9.8 + - - +
2805B GLY* 2.9 26.2 + - - -
2828B GLU* 4.1 2.6 - - - +
2832B LEU* 3.8 20.1 - - + +
2836B ARG* 4.6 16.0 - - - +
2928B GLN* 5.3 13.0 - - - +
3087B ASN 3.7 21.4 + - - -
3088B ARG* 3.7 14.6 + - - +
3089B CYS 4.6 4.6 + - - -
3090B VAL* 4.6 22.6 - - - +
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Residues in contact with TRP2802 (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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2773B MET* 3.5 31.6 - - + -
2776B PHE* 3.4 31.4 - + + -
2777B TYR 5.2 0.2 - - - -
2798B GLU 2.9 9.0 + - - +
2799B MET* 3.1 27.4 - - - +
2801B ARG* 1.3 74.7 - - - +
2803B VAL* 1.3 59.8 + - - +
2805B GLY* 3.2 2.3 + - - -
2806B ILE* 2.9 43.0 + - + +
2825B TRP* 3.1 51.8 + + - -
2828B GLU* 3.4 22.3 - - + +
2829B ALA* 3.4 23.1 - - + -
2832B LEU* 3.3 10.9 - - + +
2833B PHE* 3.5 33.9 - + - -
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Residues in contact with VAL2803 (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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2562B VAL* 5.4 2.5 - - + -
2563B ALA* 3.6 28.3 - - + -
2748B TYR* 4.4 11.9 - - + -
2751B PHE* 4.5 13.5 - - + -
2752B ASN* 4.4 18.8 - - - +
2755B MET* 3.4 18.3 - - + +
2773B MET* 3.9 20.6 - - + -
2799B MET 2.9 18.6 + - - +
2800B THR* 3.1 24.2 - - - +
2802B TRP* 1.3 76.9 - - - +
2804B ARG* 1.3 55.8 + - - +
2806B ILE* 3.2 7.0 + - + -
2807B PHE* 2.9 25.9 + - - +
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Residues in contact with ARG2804 (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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2560B HIS 4.8 5.3 + - - -
2561B LYS* 5.4 0.2 - - - +
2562B VAL* 4.2 23.6 - - - +
2563B ALA* 3.6 22.4 - - - +
2564B ALA* 4.4 20.9 - - - +
2565B PRO* 5.8 3.8 - - - +
2800B THR* 2.9 21.4 + - + +
2801B ARG* 3.4 11.4 - - - +
2803B VAL* 1.3 77.8 - - + +
2805B GLY* 1.3 55.3 + - - +
2807B PHE* 3.2 20.8 + - - +
2808B GLU* 2.9 49.5 + - + +
2811B ARG* 6.1 0.6 - - - +
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Residues in contact with GLY2805 (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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2801B ARG 2.9 11.0 + - - -
2802B TRP 3.2 4.9 + - - -
2804B ARG* 1.3 75.1 - - - +
2806B ILE* 1.3 57.3 - - - +
2808B GLU* 3.2 9.5 + - - +
2809B ALA* 2.9 28.6 + - - +
2828B GLU* 3.6 26.4 - - - +
2881B TYR* 5.9 1.4 - - - -
2924B ARG* 6.2 1.3 - - - -
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Residues in contact with ILE2806 (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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2752B ASN* 5.1 1.6 - - - +
2755B MET* 3.5 27.4 - - + -
2756B LEU* 5.2 1.8 - - + -
2769B LEU* 5.2 7.0 - - + -
2773B MET* 4.6 9.9 - - - -
2802B TRP* 2.9 43.1 + - + +
2803B VAL* 3.5 11.0 - - - +
2805B GLY* 1.3 75.4 - - - +
2807B PHE* 1.3 55.8 + - - +
2809B ALA* 3.2 3.8 + - - +
2810B LEU* 2.9 29.9 + - + +
2821B LEU* 4.4 14.6 - - + -
2824B ILE* 4.1 23.7 - - + +
2825B TRP* 4.4 20.9 - - + -
2828B GLU* 4.5 6.1 - - + -
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Residues in contact with PHE2807 (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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2559B THR* 3.2 35.0 - - - -
2560B HIS* 3.8 16.4 - - - -
2562B VAL* 3.6 25.8 - - + -
2755B MET* 3.5 23.5 - - + -
2758B LEU* 5.6 5.6 - - + -
2803B VAL 2.9 12.8 + - - +
2804B ARG* 3.3 22.7 - - - +
2806B ILE* 1.3 74.4 - - - +
2808B GLU* 1.3 66.9 + - - +
2810B LEU* 3.2 6.2 + - + +
2811B ARG* 2.7 82.6 + - + +
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Residues in contact with GLU2808 (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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2804B ARG* 2.9 30.8 + - + +
2805B GLY* 3.4 11.2 - - - +
2807B PHE* 1.3 94.6 - - + +
2809B ALA* 1.3 61.3 + - - +
2811B ARG* 4.6 12.5 + - - +
2812B PRO* 3.1 24.8 - - - +
2881B TYR* 4.8 10.8 - - + +
2927B ARG* 4.3 21.7 + - - +
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Residues in contact with ALA2809 (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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2805B GLY 2.9 11.8 + - - +
2806B ILE 3.4 3.1 - - - +
2808B GLU* 1.3 76.4 - - - +
2810B LEU* 1.3 63.1 + - - +
2812B PRO* 3.9 4.7 - - - +
2813B LEU* 4.1 14.4 - - - +
2816B LEU* 4.9 2.8 - - + +
2824B ILE* 3.2 41.7 - - + -
2828B GLU* 6.4 0.7 - - + -
2873B TYR* 6.0 0.7 - - + -
2881B TYR* 4.2 32.3 - - + +
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Residues in contact with LEU2810 (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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2755B MET* 3.2 44.2 - - + +
2756B LEU* 4.7 9.0 - - + -
2758B LEU* 4.0 20.1 - - + +
2759B ILE* 3.3 37.5 - - + +
2762B LEU* 4.6 7.4 - - + -
2806B ILE* 2.9 14.6 + - + +
2807B PHE* 3.5 10.1 - - + +
2809B ALA* 1.3 77.2 - - - +
2811B ARG* 1.3 66.2 + - - +
2812B PRO 3.4 0.2 - - - -
2813B LEU* 2.9 17.2 + - - +
2814B GLU* 3.6 9.5 + - - +
2816B LEU* 4.0 15.0 - - + -
2821B LEU* 5.8 4.5 - - + -
2824B ILE* 4.9 1.3 - - + +
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Residues in contact with ARG2811 (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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2560B HIS* 5.4 11.4 + - - -
2758B LEU* 4.5 17.0 - - + +
2804B ARG* 6.1 0.6 - - - +
2807B PHE* 2.7 59.5 + - + +
2808B GLU* 4.1 14.8 + - - +
2810B LEU* 1.3 73.0 - - - +
2812B PRO* 1.3 70.7 - - + +
2814B 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