Contacts of the helix formed by residues 22 - 35 (chain I) in PDB entry 2XEW
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 22 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20I SER 3.5 2.7 + - - +
21I ASP* 1.3 78.2 - - - +
23I ILE* 1.3 65.6 + - - +
24I GLU* 3.4 6.2 + - - +
25I ASN* 3.0 41.3 + - - +
26I VAL* 3.2 13.2 + - - +
52I ASP 3.3 12.3 - - - +
53I GLY* 3.9 17.9 - - - +
54I ARG 3.0 8.1 - - - +
55I THR* 3.9 9.6 - - + +
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Residues in contact with ILE 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I THR* 1.3 71.9 - - - +
24I GLU* 1.3 62.8 + - - +
26I VAL* 3.0 7.8 + - + +
27I LYS* 2.9 38.1 + - - +
43I LEU* 4.0 10.3 - - + -
50I LEU* 3.7 53.4 - - + +
51I GLU 3.1 24.0 - - - +
52I ASP* 3.2 3.8 + - - +
54I ARG 2.8 15.0 + - - +
55I THR 4.7 1.8 - - - +
56I LEU* 3.9 22.2 - - + -
59I TYR* 3.8 15.3 - - + -
67I LEU* 5.4 1.3 - - + -
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Residues in contact with GLU 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I THR* 3.1 5.6 - - - +
23I ILE* 1.3 76.7 - - - +
25I ASN* 1.3 59.9 + - - +
27I LYS* 3.2 9.5 + - - +
28I ALA* 2.9 29.4 + - + +
38I PRO* 3.5 17.7 - - - +
52I ASP* 2.9 47.6 + - + +
32J ASP* 2.9 44.0 - - - +
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Residues in contact with ASN 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I SER 4.7 0.6 + - - -
21I ASP* 3.6 23.4 + - + +
22I THR* 3.0 41.4 + - - +
24I GLU* 1.3 77.7 - - - +
26I VAL* 1.3 62.0 + - - +
28I ALA* 3.1 9.5 + - - +
29I LYS* 3.0 31.9 + - - +
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Residues in contact with VAL 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I ILE* 4.7 2.0 - - + -
5I VAL* 4.7 0.7 - - + -
15I LEU* 3.7 20.9 - - + -
17I VAL* 4.4 11.7 - - + -
21I ASP* 4.7 3.4 - - + -
22I THR 3.2 12.5 + - - +
23I ILE* 3.0 10.6 + - + +
25I ASN* 1.3 78.4 - - - +
27I LYS* 1.3 61.9 + - - +
29I LYS* 3.1 10.7 + - + +
30I ILE* 3.0 25.7 + - + +
43I LEU* 3.8 19.1 - - + -
56I LEU* 4.1 33.2 - - + -
67I LEU* 4.5 13.5 - - + -
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Residues in contact with LYS 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I ILE* 2.9 25.2 + - - +
24I GLU* 3.2 14.3 + - - +
26I VAL* 1.3 76.1 - - - +
28I ALA* 1.3 57.5 + - - +
30I ILE* 3.4 1.0 + - - -
31I GLN* 3.0 15.4 + - - +
38I PRO* 3.7 31.3 + - + +
41I GLN* 2.9 67.2 + - - +
42I ARG* 4.8 2.4 - - - +
43I LEU* 3.7 19.5 - - + +
50I LEU 4.7 6.1 + - - -
52I ASP* 2.7 34.5 + - - +
72I ARG* 5.4 5.9 - - - +
32J ASP 5.9 0.4 + - - +
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Residues in contact with ALA 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I GLU* 2.9 17.7 + - + +
25I ASN* 3.3 13.2 - - - +
26I VAL 3.1 0.2 - - - -
27I LYS* 1.3 73.3 - - - +
29I LYS* 1.3 60.6 + - + +
31I GLN* 3.2 11.2 + - - +
32I ASP* 2.8 37.6 + - - +
38I PRO* 4.6 6.9 - - + +
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Residues in contact with LYS 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I LEU* 3.8 20.9 - - + -
16I GLU* 3.0 23.9 + - - +
17I VAL* 3.9 17.9 - - + +
21I ASP* 3.8 22.8 + - - -
25I ASN* 3.0 22.3 + - - +
26I VAL* 3.1 10.1 + - - +
28I ALA* 1.3 72.3 - - + +
30I ILE* 1.3 60.0 + - - +
32I ASP* 3.2 15.1 + - - +
33I LYS* 2.9 34.0 + - + +
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Residues in contact with ILE 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I VAL* 3.9 19.1 - - + -
13I ILE* 4.1 17.5 - - + -
15I LEU* 4.1 15.0 - - + -
26I VAL* 3.0 17.5 + - + +
27I LYS 3.6 2.0 - - - +
29I LYS* 1.3 73.1 - - - +
31I GLN* 1.3 60.4 + - - +
33I LYS* 4.8 3.6 - - - -
34I GLU* 2.8 30.5 + - - +
36I ILE* 4.4 10.0 + - + -
41I GLN* 3.3 35.0 - - - +
43I LEU* 3.8 29.6 - - + -
69I LEU* 4.1 17.3 - - + -
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Residues in contact with GLN 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I LYS 3.0 13.5 + - - +
28I ALA* 3.2 13.3 + - - +
30I ILE* 1.3 75.9 - - - +
32I ASP* 1.3 64.5 + - - +
35I GLY* 2.7 29.6 + - - -
36I ILE 3.3 22.9 - - - +
37I PRO* 3.5 24.4 - - - +
38I PRO* 3.7 18.6 - - + +
41I GLN* 3.8 0.2 - - - +
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Residues in contact with ASP 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I ALA* 2.8 26.3 + - - +
29I LYS* 3.3 19.3 - - - +
31I GLN* 1.3 81.8 - - - +
33I LYS* 1.3 63.5 + - + +
35I GLY 4.9 0.2 + - - -
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Residues in contact with LYS 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I ILE* 4.0 9.2 - - + -
14I THR 2.8 25.4 + - - +
15I LEU* 3.7 24.8 - - + +
16I GLU 5.6 0.8 - - - +
29I LYS* 2.9 17.2 + - + +
30I ILE 4.1 1.8 - - - +
32I ASP* 1.3 81.2 - - + +
34I GLU* 1.3 79.9 + - + +
35I GLY 3.9 0.2 - - - -
74L ARG* 3.8 16.3 - - - +
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Residues in contact with GLU 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I THR 5.4 0.3 - - - +
13I ILE* 3.6 37.8 - - + +
30I ILE 2.8 16.2 + - - +
33I LYS* 1.3 96.1 - - + +
35I GLY* 1.3 61.5 + - - +
36I ILE* 3.4 22.7 + - + +
40L GLN* 4.1 10.6 - - - +
72L ARG 5.2 2.8 - - - +
73L LEU* 3.4 23.2 - - + +
74L ARG* 2.9 48.5 + - - +
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Residues in contact with GLY 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I GLN* 2.7 31.2 + - - +
33I LYS 3.9 0.2 - - - -
34I GLU* 1.3 72.9 - - - +
36I ILE* 1.3 59.4 + - - +
37I PRO* 3.4 8.3 - - - +
37L PRO* 5.6 0.2 - - - +
40L GLN* 2.9 18.1 - - - +
74L ARG* 5.9 1.3 - - - -
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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