Contacts of the helix formed by residues 40 - 55 (chain W) in PDB entry 2D3O
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 PRO 40 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600 A 3.8 42.8 + - + +
930 A 3.3 37.2 - - + +
940 C 4.0 17.3 - - + +
37W LEU* 3.8 7.8 - - + +
38W ALA* 3.6 7.9 - - - +
39W GLN* 1.3 87.2 - - - +
41W HIS* 1.3 59.1 + - - +
42W ARG 3.2 1.0 + - - -
43W VAL* 3.5 13.5 + - + +
44W ARG* 3.8 13.9 + - - +
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Residues in contact with HIS 41 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940 C 3.0 23.6 + - - +
950 G 2.7 64.7 + - - +
39W GLN* 3.0 13.2 + - + +
40W PRO* 1.3 75.7 - - - +
42W ARG* 1.3 78.4 + - + +
43W VAL 3.0 6.6 + - - -
44W ARG* 3.9 12.8 - - + +
45W GLN* 3.2 29.2 + - + +
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Residues in contact with ARG 42 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24W GLU* 2.5 40.7 + - - +
28W LEU* 3.4 29.3 - - + +
37W LEU* 5.7 0.7 - - + -
39W GLN* 2.8 40.9 + - + +
41W HIS* 1.3 89.1 + - + +
43W VAL* 1.3 60.6 + - + +
45W GLN* 5.3 7.1 - - - +
46W LEU* 3.1 36.2 - - - +
49W GLU* 4.9 9.5 + - - -
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Residues in contact with VAL 43 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590 G 5.3 1.8 - - - +
600 A 3.7 20.6 - - - +
25W LEU* 3.4 28.9 - - + -
28W LEU* 4.0 11.2 - - + -
37W LEU* 5.0 11.0 - - + -
39W GLN 5.0 3.1 - - - +
40W PRO 3.5 6.7 + - - +
41W HIS 3.0 0.2 - - - -
42W ARG* 1.3 84.8 - - + +
44W ARG* 1.3 65.0 + - - +
45W GLN 3.4 0.4 - - - -
46W LEU* 3.7 2.8 - - - +
47W ARG* 2.9 58.0 + - - +
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Residues in contact with ARG 44 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600 A 4.7 8.1 - - - +
730 A 2.8 50.2 + - + +
860 U 3.1 27.1 + - - +
930 A 4.6 7.7 + - - +
940 C 2.8 49.5 + - - +
950 G 4.6 12.9 + - - +
40W PRO* 3.8 9.6 + - - +
41W HIS* 3.5 16.6 + - + +
43W VAL* 1.3 80.1 - - - +
45W GLN* 1.3 62.0 - - - +
47W ARG* 4.0 10.9 - - - +
48W ARG* 3.2 21.9 + - - +
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Residues in contact with GLN 45 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950 G 6.1 0.7 - - - +
960 C 4.0 38.6 + - - +
970 U 5.7 0.8 + - - -
41W HIS* 3.2 20.3 + - + +
42W ARG* 5.3 7.6 - - - +
44W ARG* 1.3 76.7 - - - +
46W LEU* 1.3 66.5 + - - +
48W ARG* 3.1 28.3 + - - +
49W GLU* 3.0 41.7 + - + +
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Residues in contact with LEU 46 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21W ARG* 3.5 51.5 - - + +
24W GLU* 3.2 29.6 - - + +
25W LEU* 3.6 28.3 - - + +
28W LEU* 4.4 1.3 - - + -
42W ARG* 3.1 40.2 + - - +
43W VAL* 3.5 6.6 + - - +
44W ARG 3.3 0.4 - - - -
45W GLN* 1.3 78.2 - - - +
47W ARG* 1.3 58.6 + - - +
49W GLU* 2.9 25.7 + - + +
50W VAL* 3.2 13.9 + - - +
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Residues in contact with ARG 47 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580 C 3.4 8.1 + - - -
590 G 2.8 44.9 + - - -
600 A 2.5 30.5 + - - -
710 A 4.7 9.9 + - - +
730 A 4.6 17.9 + - - +
25W LEU* 3.8 25.4 - - + -
43W VAL* 2.9 34.1 + - - +
44W ARG* 4.0 10.4 - - - +
46W LEU* 1.3 79.6 - - - +
48W ARG* 1.3 61.1 + - - +
50W VAL* 3.4 24.9 + - + +
51W ALA* 3.5 9.0 + - - +
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Residues in contact with ARG 48 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740 G 4.3 15.3 + - - +
750 C 2.5 41.1 + - - +
760 C 5.3 2.5 - - - +
960 C 4.5 16.8 + - - -
1010 A 5.7 1.6 + - - -
1020 C 4.7 12.5 + - - -
44W ARG 3.2 14.5 + - - +
45W GLN* 3.1 28.4 + - - +
46W LEU 3.0 0.6 - - - -
47W ARG* 1.3 76.5 - - - +
49W GLU* 1.3 61.0 + - + +
51W ALA* 3.7 8.8 + - - +
52W GLN* 3.4 27.3 + - - +
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Residues in contact with GLU 49 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1W MET* 5.9 2.9 - - + -
21W ARG* 2.9 40.3 + - + +
42W ARG* 4.9 8.0 + - - -
45W GLN* 3.0 34.0 + - + +
46W LEU* 2.9 13.9 + - - +
48W ARG* 1.3 75.8 - - + +
50W VAL* 1.3 65.6 + - - +
51W ALA 3.2 2.0 - - - -
52W GLN* 3.0 36.0 + - - +
53W LEU* 4.0 8.1 - - - +
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Residues in contact with VAL 50 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710 A 3.2 34.8 - - - +
17W GLU 5.5 1.1 - - - +
18W ILE* 4.6 10.1 - - + +
21W ARG* 3.6 30.7 - - + +
22W LYS* 4.5 20.6 - - + +
25W LEU* 6.6 0.4 - - + -
46W LEU 3.2 9.0 + - - +
47W ARG* 3.5 17.0 - - + +
49W GLU* 1.3 78.4 - - - +
51W ALA* 1.3 53.3 + - - +
52W GLN 3.4 0.3 + - - -
53W LEU* 3.6 13.2 + - - +
54W ASN* 2.5 34.6 + - - +
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Residues in contact with ALA 51 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710 A 3.8 28.5 - - - +
740 G 5.5 0.2 - - - +
750 C 3.3 38.3 + - - +
47W ARG 3.5 5.2 + - - +
48W ARG* 4.0 4.0 - - - +
49W GLU 3.2 0.6 - - - -
50W VAL* 1.3 75.2 - - - +
52W GLN* 1.3 57.7 + - - +
53W LEU 3.1 9.0 + - - -
54W ASN* 3.4 9.0 - - - +
55W THR* 2.7 28.6 + - - -
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Residues in contact with GLN 52 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750 C 4.1 13.5 - - - +
760 C 3.1 24.6 + - - +
1W MET* 3.0 54.3 + - - +
2W LYS* 4.7 5.7 - - - +
6W MET* 4.5 3.5 - - - +
48W ARG* 3.4 26.3 + - - +
49W GLU* 3.0 23.2 + - - +
51W ALA* 1.3 77.4 - - - +
53W LEU* 1.3 70.2 + - + +
55W THR* 5.2 0.4 - - - -
56W VAL* 3.5 19.8 - - + +
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Residues in contact with LEU 53 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6W MET* 5.4 7.2 - - + -
14W PHE* 3.0 49.7 - - + +
17W GLU* 3.1 41.3 - - + +
18W ILE* 3.4 32.5 - - + +
21W ARG* 5.5 5.8 - - - +
49W GLU 4.0 10.5 - - - +
50W VAL* 3.7 10.3 - - - +
51W ALA 3.1 2.4 + - - -
52W GLN* 1.3 90.0 - - + +
54W ASN* 1.3 64.6 + - - +
55W THR 3.0 5.5 + - - -
56W VAL* 3.2 6.8 + - - -
57W LYS* 3.3 2.5 + - - -
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Residues in contact with ASN 54 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710 A 3.8 51.3 + - + +
18W ILE* 3.7 27.9 - - - +
50W VAL* 2.5 32.0 + - - +
51W ALA* 3.4 14.8 + - - +
53W LEU* 1.3 72.5 - - - +
55W THR* 1.3 57.7 + - - +
57W LYS* 3.9 24.8 + - - +
58W ALA* 3.3 22.0 + - - +
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Residues in contact with THR 55 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710 A 3.6 19.6 - - - +
750 C 3.2 27.8 + - - +
760 C 3.9 18.6 - - - +
1080 G 4.8 4.9 - - - +
1090 A 4.6 12.7 + - - +
51W ALA 2.7 24.5 + - - -
52W GLN* 5.2 0.4 - - - -
53W LEU 3.0 1.0 - - - -
54W ASN* 1.3 79.8 + - - +
56W VAL* 1.3 62.8 + - - +
58W ALA* 3.6 5.6 - - - +
59W GLU* 2.9 33.7 + - + +
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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