Contacts of the helix formed by residues 22 - 35 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20J SER 4.5 2.5 - - - +
21J ASP* 1.3 78.7 - - - +
23J ILE* 1.3 65.1 + - - +
24J GLU* 3.4 6.9 + - - +
25J ASN* 3.0 41.3 + - - +
26J VAL* 3.2 14.4 + - - +
52J ASP 3.3 12.0 + - - -
53J GLY* 3.8 18.8 - - - +
54J ARG 3.1 7.6 - - - +
55J THR* 4.0 10.3 - - + +
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Residues in contact with ILE 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J THR* 1.3 72.2 - - - +
24J GLU* 1.3 56.9 + - - +
26J VAL* 3.2 7.5 + - + +
27J LYS* 2.9 37.1 + - - +
43J LEU* 4.0 16.6 - - + -
50J LEU* 3.8 48.2 - - + +
51J GLU 3.1 26.9 - - - +
52J ASP* 3.3 2.0 + - - +
54J ARG 2.9 10.7 + - - +
56J LEU* 3.4 29.2 - - + +
59J TYR* 4.0 16.2 - - + -
61J ILE* 4.7 0.2 - - + -
67J LEU* 5.5 2.0 - - + -
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Residues in contact with GLU 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J THR* 3.1 8.5 - - - +
23J ILE* 1.3 74.7 - - - +
25J ASN* 1.3 61.8 + - - +
27J LYS* 3.3 8.3 + - - +
28J ALA* 2.8 30.8 + - + +
38J PRO* 3.5 31.6 - - - +
52J ASP* 3.0 45.1 + - + +
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Residues in contact with ASN 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J SER 4.7 0.8 + - - -
21J ASP* 3.5 24.5 + - + +
22J THR* 3.0 41.8 + - - +
24J GLU* 1.3 75.8 - - - +
26J VAL* 1.3 58.1 + - - +
28J ALA* 3.2 8.9 + - - +
29J LYS* 2.9 37.1 + - - +
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Residues in contact with VAL 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J ILE* 4.6 2.9 - - + -
5J VAL* 4.6 0.7 - - + -
15J LEU* 3.8 20.0 - - + -
17J VAL* 4.4 10.8 - - + -
21J ASP* 4.8 2.9 - - + -
22J THR 3.2 13.8 + - - +
23J ILE* 3.4 9.2 - - + +
24J GLU 3.2 0.2 - - - -
25J ASN* 1.3 76.8 - - - +
27J LYS* 1.3 58.1 + - - +
29J LYS* 3.0 10.9 + - - +
30J ILE* 2.9 30.8 + - + +
43J LEU* 3.8 20.0 - - + -
56J LEU* 3.9 34.1 - - + -
67J LEU* 4.5 12.8 - - + -
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Residues in contact with LYS 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J ILE* 2.9 23.4 + - - +
24J GLU* 3.3 15.0 + - - +
26J VAL* 1.3 75.2 - - - +
28J ALA* 1.3 56.9 + - - +
30J ILE* 3.2 1.4 + - - -
31J GLN* 2.9 24.6 + - - +
38J PRO* 3.9 25.3 + - + +
41J GLN* 3.0 62.5 + - + +
42J ARG* 4.6 2.6 - - - +
43J LEU* 3.5 24.0 - - + +
50J LEU 4.4 7.8 + - - -
52J ASP* 2.9 30.8 + - - +
72J ARG* 5.5 4.9 - - - +
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Residues in contact with ALA 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J GLU* 2.8 18.7 + - + +
25J ASN* 3.4 12.3 - - - +
26J VAL 3.2 0.2 - - - -
27J LYS* 1.3 75.8 - - - +
29J LYS* 1.3 52.3 + - + +
31J GLN* 3.2 14.7 + - - +
32J ASP* 2.8 43.5 + - - +
38J PRO* 4.6 4.6 - - + +
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Residues in contact with LYS 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53I GLY* 5.7 4.8 - - - -
15J LEU* 4.0 18.8 - - + -
16J GLU* 3.2 32.5 + - - +
17J VAL* 3.9 13.0 - - + -
21J ASP* 3.8 21.8 - - - -
25J ASN* 2.9 21.7 + - - +
26J VAL* 3.4 9.9 - - - +
28J ALA* 1.3 73.6 - - + +
30J ILE* 1.3 60.9 + - - +
32J ASP* 3.3 13.1 + - - +
33J LYS* 3.0 35.4 + - + +
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Residues in contact with ILE 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J VAL* 3.7 33.9 - - + -
13J ILE* 4.4 12.1 - - + -
15J LEU* 4.0 15.3 - - + -
26J VAL* 2.9 17.2 + - + +
27J LYS 3.5 2.0 - - - +
29J LYS* 1.3 71.8 - - - +
31J GLN* 1.3 60.5 + - - +
33J LYS* 3.3 3.9 + - - +
34J GLU* 2.8 31.4 + - + +
36J ILE* 4.4 11.6 + - + -
41J GLN* 3.4 36.6 - - - +
43J LEU* 3.8 19.1 - - + -
69J LEU* 4.2 16.8 - - + -
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Residues in contact with GLN 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I PRO* 6.0 0.3 - - - +
39I ASP* 3.9 2.9 + - - +
27J LYS 2.9 12.8 + - - +
28J ALA* 3.3 14.1 - - - +
30J ILE* 1.3 78.2 - - - +
32J ASP* 1.3 64.1 + - - +
35J GLY* 2.8 31.4 + - - +
36J ILE 3.3 21.5 + - - +
37J PRO* 3.7 21.4 - - - +
38J PRO* 3.7 18.2 - - + +
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Residues in contact with ASP 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I GLU* 2.9 44.9 - - - +
27I LYS* 5.9 0.5 + - - +
38I PRO* 3.5 16.7 - - - +
39I ASP* 3.0 27.9 + - - -
52I ASP* 4.8 3.9 - - - +
72I ARG* 4.8 0.3 + - - -
28J ALA* 2.8 24.5 + - - +
29J LYS* 3.4 17.7 - - - +
31J GLN* 1.3 79.0 - - - +
33J LYS* 1.3 60.6 + - + +
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Residues in contact with LYS 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I ASP* 3.5 4.0 - - - +
52I ASP* 3.7 36.0 - - - +
72I ARG* 2.9 34.2 + - - +
13J ILE* 4.3 9.2 - - + -
14J THR 2.9 24.3 + - - +
15J LEU* 3.8 22.0 - - + +
16J GLU 5.1 2.7 - - - +
29J LYS* 3.0 19.9 + - - +
30J ILE 4.1 0.4 - - - +
32J ASP* 1.3 80.0 - - + +
34J GLU* 1.3 79.4 + - + +
74K ARG* 3.7 1.4 - - - +
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Residues in contact with GLU 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I ASP* 3.4 7.2 - - - -
72I ARG* 4.3 6.7 + - - -
74I ARG* 2.9 28.6 + - - -
12J THR 5.4 0.3 - - - +
13J ILE* 3.6 40.2 - - + +
30J ILE 2.8 14.9 + - - +
33J LYS* 1.3 92.8 - - + +
35J GLY* 1.3 60.7 + - - +
36J ILE* 3.2 24.3 + - + +
40K GLN* 3.9 1.0 - - - +
73K LEU* 3.3 23.2 - - + +
74K ARG* 2.8 31.8 + - - +
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Residues in contact with GLY 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I ASP* 3.4 20.4 - - - -
74I ARG* 4.4 0.7 - - - -
31J GLN* 2.8 23.0 + - - +
34J GLU* 1.3 77.6 - - - +
36J ILE* 1.3 61.0 - - - +
37J PRO* 3.5 8.3 - - - +
37K PRO* 5.5 0.3 - - - +
40K GLN* 2.9 16.5 - - - +
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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