Contacts of the helix formed by residues 37 - 55 (chain D) in PDB entry 2EWC
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 ASP 37 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D GLN* 1.3 80.7 - - - +
38D ILE* 1.3 68.0 + - + +
39D GLU* 3.6 9.1 + - - +
40D SER* 2.9 32.0 + - - -
41D GLN* 2.9 20.4 + - - +
111D LEU* 4.2 3.8 - - - -
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Residues in contact with ILE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ASP* 1.3 75.0 - - + +
39D GLU* 1.3 61.5 + - + +
41D GLN* 3.2 3.2 + - + -
42D ILE* 2.9 51.0 + - + +
70D PHE* 4.7 1.8 - - + -
75D ASN* 3.8 41.7 - - + +
78D VAL* 4.2 16.4 - - + -
111D LEU* 3.8 31.4 - - + +
112D PHE* 3.9 28.9 - - + -
107I PRO* 6.3 0.2 - - + -
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Residues in contact with GLU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ASP* 3.3 9.7 + - - +
38D ILE* 1.3 82.7 - - + +
40D SER* 1.3 62.5 + - - +
42D ILE* 3.3 5.5 + - - +
43D ASN* 3.0 27.5 + - - +
78D VAL* 4.2 17.9 - - + +
81D LYS* 4.7 11.1 + - - +
82D MSE 3.4 36.0 - - + +
85D GLU* 5.4 0.9 - - - +
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Residues in contact with SER 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ASN* 2.8 17.9 + - - +
36D GLN* 3.5 38.2 + - - +
37D ASP* 2.9 22.8 + - - -
39D GLU* 1.3 76.7 - - - +
41D GLN* 1.3 53.7 + - - +
43D ASN* 3.4 5.7 + - - -
44D GLY 2.7 30.0 + - - -
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Residues in contact with GLN 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D GLY 3.6 13.9 + - - +
33D ASN 3.3 17.9 - - - +
34D VAL* 5.0 1.3 - - - -
35D GLY 3.6 5.9 - - - +
36D GLN 2.8 28.7 + - - +
37D ASP 2.9 17.6 + - - +
38D ILE* 3.7 5.4 - - - +
40D SER* 1.3 73.2 - - - +
42D ILE* 1.3 60.6 + - - +
45D ALA* 3.0 28.1 + - - +
109D GLY 2.8 25.1 + - - -
110D LEU* 3.7 10.4 - - - +
111D LEU* 2.8 34.1 + - + +
112D PHE* 3.6 18.0 + - + +
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Residues in contact with ILE 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ILE* 2.9 34.9 + - + +
39D GLU 3.7 3.6 - - - +
41D GLN* 1.3 74.6 - - - +
43D ASN* 1.3 62.8 + - - +
45D ALA* 3.3 3.5 + - - +
46D PHE* 3.1 49.8 + - + -
70D PHE* 4.8 2.5 - - + -
78D VAL* 3.8 17.0 - - + +
79D MSE 3.7 39.0 - - + +
82D MSE 3.7 16.4 - - + -
112D PHE* 3.7 30.2 - - + -
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Residues in contact with ASN 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ASN* 4.6 4.3 - - - +
39D GLU* 3.0 22.0 + - - +
40D SER* 3.7 7.4 - - - +
42D ILE* 1.3 77.8 - - - +
44D GLY* 1.3 55.6 + - - +
46D PHE* 3.4 1.4 + - - -
47D ASP* 2.9 36.5 + - - +
82D MSE 3.4 32.4 - - - +
85D GLU* 5.1 2.8 + - - +
86D ARG* 3.0 41.3 + - - +
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Residues in contact with GLY 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D GLY* 3.7 24.2 - - - -
33D ASN* 3.5 15.0 - - - +
40D SER 2.7 20.8 + - - -
41D GLN 3.5 1.8 + - - -
42D ILE 3.3 0.2 - - - -
43D ASN* 1.3 70.5 - - - +
45D ALA* 1.3 63.2 + - - +
47D ASP* 3.5 9.3 + - - +
48D GLU* 3.2 18.9 + - - +
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Residues in contact with ALA 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D CYS* 3.3 32.4 - - - +
31D VAL* 4.0 13.0 - - - +
32D GLY 3.8 0.6 - - - +
41D GLN 3.0 17.3 + - - +
42D ILE 3.3 4.7 + - - +
44D GLY* 1.3 72.8 - - - +
46D PHE* 1.3 62.7 + - - +
48D GLU 3.2 1.8 + - - +
49D MSE 3.0 24.4 + - - +
112D PHE* 3.8 12.3 - - + +
113D GLN* 4.9 0.4 - - - -
114D VAL* 3.7 16.3 - - + +
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Residues in contact with PHE 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ILE* 3.1 42.7 + - + +
43D ASN* 3.8 2.2 - - - +
45D ALA* 1.3 73.7 - - - +
47D ASP* 1.3 58.3 + - - +
49D MSE 3.2 15.0 + - - +
50D GLU* 2.9 31.5 + - - +
60D LEU* 4.8 5.3 - - + +
66D MSE 3.9 26.2 - - + -
79D MSE 4.3 8.7 - - + -
82D MSE 4.2 8.5 - - + -
83D ILE* 3.7 34.5 - - + -
86D ARG* 3.7 37.9 - - + +
87D PHE* 4.1 13.5 - + - -
112D PHE* 4.8 1.6 - + - -
114D VAL* 4.2 20.2 - - + -
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Residues in contact with ASP 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ASN* 4.6 6.4 + - - +
43D ASN* 2.9 22.3 + - - +
44D GLY* 3.6 12.1 + - - +
46D PHE* 1.3 74.6 - - - +
48D GLU* 1.3 58.4 + - - +
50D GLU* 3.3 6.6 + - - +
51D ARG* 2.9 29.0 + - - +
86D ARG* 2.6 36.4 + - - +
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Residues in contact with GLU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D CYS* 4.0 8.7 - - + -
31D VAL* 3.8 20.2 - - - +
44D GLY 3.2 10.8 + - - +
45D ALA 3.2 7.8 + - - +
47D ASP* 1.3 76.8 - - - +
49D MSE 1.3 64.5 + - - +
51D ARG* 2.8 49.1 + - - +
52D ARG* 3.0 49.0 + - - +
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Residues in contact with MSE 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D LEU* 3.9 27.3 - - + +
30D CYS* 3.7 14.2 - - - -
45D ALA 3.0 13.3 + - - +
46D PHE* 3.5 15.9 - - - +
48D GLU* 1.3 75.9 - - - +
50D GLU* 1.3 55.9 + - - +
52D ARG* 3.4 1.7 + - - +
53D LEU* 2.9 37.3 + - + +
60D LEU* 3.8 24.7 - - + -
63D VAL* 4.2 9.6 - - + -
66D MSE 4.0 25.4 - - + +
114D VAL* 4.0 18.4 - - + -
115D ASP* 3.8 31.9 - - - +
116D GLY* 4.6 0.4 - - - -
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Residues in contact with GLU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D PHE 2.9 16.3 + - - +
47D ASP* 3.6 6.3 - - - +
48D GLU 3.2 0.2 - - - -
49D MSE 1.3 72.7 - - - +
51D ARG* 1.3 61.8 - - - +
53D LEU* 3.8 6.3 - - - +
54D ALA* 2.9 31.7 + - - +
58D LEU 4.7 1.2 - - - +
59D THR* 5.8 3.6 - - - +
60D LEU* 3.4 38.5 + - + +
86D ARG* 2.7 31.6 + - - +
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Residues in contact with ARG 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ASP* 2.9 44.0 + - - +
47D ASP 2.9 17.2 + - - +
48D GLU* 2.8 48.4 + - - +
50D GLU* 1.3 77.1 - - - +
52D ARG* 1.3 70.4 + - - +
54D ALA* 3.5 12.0 + - - +
55D LEU* 3.5 24.1 + - + +
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Residues in contact with ARG 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ASP* 2.8 33.5 + - + +
15D HIS* 4.3 11.5 - - - -
17D GLY* 3.4 28.9 - - - +
18D LEU* 3.5 20.7 - - + +
27D LEU* 3.8 20.4 - - + -
28D ASN* 3.4 19.6 + - - -
29D TYR 2.8 28.9 + - - -
30D CYS* 3.5 13.2 - - - +
48D GLU* 3.0 33.6 + - - +
49D MSE 3.8 0.2 - - - +
51D ARG* 1.3 85.5 - - - +
53D LEU* 1.3 62.7 + - - +
55D LEU* 3.2 27.1 + - + +
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Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 4.6 12.8 - - + -
25D TYR* 5.0 0.4 - - + -
27D LEU* 4.3 12.8 - - + -
49D MSE 2.9 32.3 + - + +
50D GLU* 3.9 4.7 - - - +
52D ARG* 1.3 76.7 - - - +
54D ALA* 1.3 59.5 + - - +
56D VAL* 3.1 15.5 + - + +
58D LEU* 2.9 49.6 + - + +
59D THR* 3.6 24.5 - - - +
60D LEU* 4.2 4.9 - - + +
63D VAL* 3.7 20.0 - - + -
118D ALA* 3.8 25.8 - - + -
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Residues in contact with ALA 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D GLU 2.9 18.7 + - - +
51D ARG* 3.8 7.2 - - - +
52D ARG 3.3 0.2 - - - -
53D LEU* 1.3 73.0 - - - +
55D LEU* 1.3 65.4 + - - +
57D GLY* 3.1 14.8 + - - +
58D LEU 3.5 9.6 + - - +
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D TYR* 4.1 28.4 - - + -
8D ASP* 3.9 32.3 - - + +
18D LEU* 5.0 0.4 - - + -
51D ARG* 3.5 16.5 + - + +
52D ARG* 3.2 22.7 - - - +
53D LEU 3.2 0.6 - - - -
54D ALA* 1.3 78.4 - - - +
56D VAL* 1.3 62.3 + - + +
57D GLY 4.0 0.2 + - - -
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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