Contacts of the helix formed by residues 886 - 906 (chain M) in PDB entry 2DFS
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 THR 886 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881M VAL* 2.7 32.4 + - + +
882M HIS* 2.8 20.3 + - - -
885M ARG* 1.3 80.7 - - + +
887M LEU* 1.4 59.4 + - - +
888M LYS 3.3 2.2 - - - -
889M ALA* 2.8 24.5 + - - +
890M ILE* 3.0 18.8 + - - +
89S PHE* 4.7 3.3 - - + -
90S ARG 5.1 2.9 - - - +
91S VAL* 3.9 29.2 - - + -
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Residues in contact with LEU 887 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882M HIS 3.0 22.0 + - - +
883M TYR* 4.0 10.3 - - + +
886M THR* 1.4 76.3 - - - +
888M LYS* 1.3 58.4 + - + +
890M ILE* 3.1 20.7 + - + +
891M VAL* 2.9 36.1 + - + +
18R LEU* 3.7 50.9 - - + -
112S LEU* 4.9 4.9 - - + -
113S GLY* 4.6 16.8 - - - +
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Residues in contact with LYS 888 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883M TYR* 3.3 28.2 + - + +
884M HIS* 5.4 3.1 - - - +
886M THR 3.3 0.6 - - - -
887M LEU* 1.3 77.5 - - + +
889M ALA* 1.3 59.6 + - - +
891M VAL* 3.3 21.2 - - + +
892M TYR* 2.8 66.9 + - + -
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Residues in contact with ALA 889 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885M ARG* 4.0 14.7 - - - +
886M THR 2.8 15.4 + - - +
888M LYS* 1.3 71.8 - - - +
890M ILE* 1.4 62.0 + - - +
892M TYR* 4.1 8.1 - - - +
893M LEU* 3.3 22.5 + - - +
88S ALA* 5.5 1.4 - - - -
89S PHE* 3.6 28.0 + - + +
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Residues in contact with ILE 890 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886M THR* 3.0 21.4 + - - +
887M LEU* 3.1 22.9 + - + +
889M ALA* 1.4 74.3 - - - +
891M VAL* 1.4 63.0 + - - +
893M LEU* 3.3 5.4 + - - +
894M GLN* 3.1 40.2 + - - +
89S PHE* 3.6 32.1 - - + -
91S VAL* 5.2 2.7 - - + -
108S VAL* 3.9 24.9 - - + +
109S MET* 4.3 2.0 - - + -
112S LEU* 3.6 38.1 - - + -
113S GLY* 4.3 3.1 - - - +
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Residues in contact with VAL 891 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887M LEU* 2.9 25.4 + - + +
888M LYS* 3.3 31.4 - - + +
890M ILE* 1.4 71.0 - - - +
892M TYR* 1.4 75.8 + - + +
894M GLN* 3.1 9.8 + - - +
895M CYS* 3.0 30.0 + - - -
113S GLY* 3.5 25.4 - - - -
114S GLU* 3.9 16.4 - - + +
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Residues in contact with TYR 892 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888M LYS* 2.8 59.8 + - + +
889M ALA* 4.1 7.6 - - - +
890M ILE 3.4 0.2 - - - -
891M VAL* 1.4 83.4 - - + +
893M LEU* 1.3 61.6 + - - +
895M CYS* 3.4 14.9 - - - +
896M CYS* 3.3 26.5 + - - -
44S THR* 6.2 1.3 - - + -
85S ILE* 4.3 16.4 - - + -
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Residues in contact with LEU 893 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889M ALA 3.3 12.4 + - - +
890M ILE 3.3 10.2 + - - +
892M TYR* 1.3 78.9 - - - +
894M GLN* 1.3 56.2 + - - +
896M CYS* 3.2 7.8 + - + +
897M TYR* 2.9 41.2 + - + +
85S ILE* 4.5 10.2 - - + +
87S GLU 4.4 5.4 - - - +
88S ALA* 3.3 39.9 - - + -
89S PHE* 3.8 21.3 - - + -
90S ARG* 4.6 6.3 - - - +
109S MET* 4.2 5.6 - - + -
145S MET* 3.5 32.3 - - + -
146S THR* 5.8 3.8 - - + -
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Residues in contact with GLN 894 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890M ILE* 3.1 22.3 + - - +
891M VAL* 3.1 8.1 + - - +
893M LEU* 1.3 71.2 - - - +
895M CYS* 1.3 64.9 + - - +
897M TYR* 3.3 8.8 - - - +
898M ARG* 3.0 28.6 + - - +
108S VAL 4.0 2.6 + - - -
109S MET* 3.0 42.5 + - + -
112S LEU 2.8 23.8 + - - -
113S GLY* 3.2 8.7 - - - -
114S GLU* 2.8 38.0 + - + +
115S LYS* 3.6 5.1 - - - +
116S LEU* 4.0 13.4 - - + +
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Residues in contact with CYS 895 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891M VAL* 3.0 31.3 + - - -
892M TYR* 3.4 17.5 - - - +
894M GLN* 1.3 73.8 - - - +
896M CYS* 1.3 58.1 + - - +
898M ARG* 3.3 7.4 + - - +
899M ARG* 3.1 31.5 + - - +
42S ASN 3.7 12.6 - - - +
43S PRO 4.2 3.6 - - - +
44S THR* 3.4 34.5 - - + +
82S GLU* 5.2 2.7 - - - +
114S GLU* 3.6 21.0 + - - -
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Residues in contact with CYS 896 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892M TYR 3.3 14.3 + - - -
893M LEU* 3.2 13.1 + - + +
895M CYS* 1.3 73.6 - - - +
897M TYR* 1.3 58.8 + - - +
899M ARG* 3.3 2.1 + - - +
900M MET* 2.8 29.5 + - - +
42S ASN* 3.4 44.0 - - - +
82S GLU* 4.2 4.5 - - - -
85S ILE* 3.5 28.0 - - + -
145S MET* 5.5 8.1 - - + +
146S THR* 6.1 4.5 - - + -
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Residues in contact with TYR 897 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893M LEU* 2.9 25.1 + - + +
894M GLN* 3.3 13.0 - - - +
896M CYS* 1.3 72.4 - - - +
898M ARG* 1.4 59.6 + - - +
900M MET* 3.2 8.0 + - - +
901M MET* 2.9 47.0 + - + +
90S ARG* 6.1 0.2 - - - -
105S LEU* 3.9 6.1 - - - +
109S MET* 3.5 31.9 - - + +
116S LEU* 3.4 29.2 - - + -
120S GLU 5.5 0.2 - - - -
121S VAL* 5.6 2.5 - - + -
124S MET* 3.6 37.6 - - + +
141S PHE* 3.4 25.5 - + - -
145S MET* 3.6 34.3 - - + -
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Residues in contact with ARG 898 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894M GLN 3.0 10.1 + - - +
895M CYS* 3.3 10.1 + - - +
897M TYR* 1.4 79.1 - - - +
899M ARG* 1.3 58.4 + - + +
901M MET* 3.3 10.8 - - - +
902M ALA 3.2 15.2 + - - -
37S ARG* 3.2 32.4 + - - +
43S PRO 5.4 0.2 - - - +
44S THR 5.8 1.1 - - - +
45S GLU* 3.6 26.5 + - - +
114S GLU* 2.7 46.8 + - - +
115S LYS 3.0 20.4 + - - -
116S LEU* 3.4 14.2 - - + +
117S THR* 5.4 1.4 - - - +
120S GLU* 2.8 42.7 + - - +
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Residues in contact with ARG 899 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895M CYS 3.1 9.4 + - - +
896M CYS 3.8 2.2 - - - +
897M TYR 3.1 0.4 - - - -
898M ARG* 1.3 76.0 - - - +
900M MET* 1.3 62.3 + - - +
901M MET 3.3 0.2 - - - -
903M LYS* 3.3 10.0 + - - +
33S GLY* 4.0 6.0 - - - -
36S MET* 3.1 30.5 - - - +
37S ARG* 2.8 59.4 - - - +
40S GLY 4.7 1.0 - - - +
41S GLN 3.0 24.9 - - - +
42S ASN* 3.3 17.0 - - + -
43S PRO* 2.7 39.8 + - - +
44S THR 2.7 19.3 + - - -
47S GLU* 2.6 32.7 + - - -
48S LEU* 3.8 10.5 - - - +
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Residues in contact with MET 900 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896M CYS 2.8 16.9 + - - +
897M TYR* 3.2 7.4 + - - +
899M ARG* 1.3 76.9 - - - +
901M MET* 1.4 61.9 + - - +
903M LYS* 3.4 30.2 + - - +
904M ARG* 3.3 44.5 + - - +
40S GLY 6.0 0.7 - - - +
42S ASN* 5.2 1.5 + - - +
124S MET* 5.3 4.5 - - + -
127S GLU* 5.1 1.1 - - - +
144S MET 4.1 5.2 - - - +
145S MET* 3.5 34.3 - - + +
147S ALA 3.6 23.8 - - - +
148S LYS* 4.8 14.6 - - + -
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Residues in contact with MET 901 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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897M TYR* 2.9 44.2 + - + +
898M ARG* 3.3 14.6 - - - +
899M ARG 3.3 0.4 - - - -
900M MET* 1.4 75.1 - - - +
902M ALA* 1.3 63.6 + - + +
904M ARG* 3.1 27.8 + - - +
905M GLU* 3.4 8.9 + - - +
116S LEU* 4.3 3.4 - - + -
120S GLU* 3.5 63.5 - - + +
123S GLU* 5.1 13.5 - - + +
124S MET* 4.1 11.9 - - + +
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Residues in contact with ALA 902 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898M ARG 3.2 4.8 + - - +
899M ARG 3.9 0.6 + - - -
900M MET 3.5 0.2 - - - -
901M MET* 1.3 79.4 - - + +
903M LYS* 1.4 55.3 + - - +
904M ARG 3.1 0.4 - - - -
905M GLU* 2.9 24.0 + - + +
906M LEU 3.1 4.3 + - - -
34S THR* 3.2 35.8 - - + +
37S ARG* 3.1 35.0 - - - +
38S SER* 3.1 13.3 - - - -
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Residues in contact with LYS 903 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899M ARG 3.3 11.0 + - - +
900M MET* 3.4 28.7 - - - +
901M MET 3.2 0.4 - - - -
902M ALA* 1.4 74.5 - - - +
904M ARG* 1.3 56.8 + - + +
907M LYS* 4.0 19.4 - - - +
11S GLU* 3.7 22.5 + - - +
37S ARG* 3.1 18.7 - - - +
38S SER* 2.8 45.4 + - - +
39S LEU* 2.7 25.5 + - - +
40S GLY* 4.1 8.1 - - - +
148S LYS* 5.3 11.4 - - + -
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Residues in contact with ARG 904 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900M MET* 3.3 44.6 + - - +
901M MET* 3.1 10.6 + - - +
902M ALA 3.1 0.4 - - - -
903M LYS* 1.3 80.9 - - + +
905M GLU* 1.3 64.8 + - + +
906M LEU 3.4 0.7 - - - -
907M LYS* 3.2 15.1 + - - +
908M LYS* 3.5 16.8 + - - +
123S GLU* 2.6 43.5 + - - +
124S MET* 3.8 15.2 - - - +
126S ARG* 4.8 7.2 - - - +
127S GLU* 2.6 48.2 + - - +
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Residues in contact with GLU 905 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901M MET 3.4 10.7 + - - +
902M ALA* 2.9 19.4 + - + +
904M ARG* 1.3 78.2 - - + +
906M LEU* 1.3 56.3 + - - +
908M LYS* 2.6 64.7 + - - +
909M LEU* 3.1 20.8 + - - +
19S PHE* 5.2 7.7 - - + -
34S THR* 4.8 11.4 - - + +
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Residues in contact with LEU 906 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902M ALA 3.1 7.4 + - - +
905M GLU* 1.3 72.1 - - - +
907M LYS* 1.3 63.2 + - - +
908M LYS 3.8 0.2 - - - -
909M LEU 3.4 10.1 - - - +
12S PHE* 4.2 2.9 - - + -
15S ALA* 3.2 60.4 - - + +
16S PHE* 3.6 7.0 - - - +
18S LEU* 6.0 0.2 - - - -
19S PHE* 3.9 22.2 - - + -
34S THR 4.4 2.2 - - - +
35S VAL* 3.5 30.3 - - + +
38S SER* 3.1 50.8 + - - +
39S LEU 3.9 1.1 - - - +
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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
------------------------------------------------------------
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