Contacts of the helix formed by residues 35 - 46 (chain J) in PDB entry 1DM0
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 ASN 35 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33J ARG* 2.8 3.6 + - + -
34J TRP* 1.3 78.0 - - - +
36J LEU* 1.3 61.6 + - - +
37J GLN 3.2 1.3 - - - -
38J SER* 3.3 14.6 + - - -
39J LEU* 3.7 13.4 + - - +
14K TYR* 3.7 11.2 - - + +
34K TRP* 3.3 35.0 + - + +
37K GLN* 2.3 39.7 + - - +
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Residues in contact with LEU 36 (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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31J THR* 4.1 26.0 - - + +
33J ARG* 3.2 15.0 + - + +
35J ASN* 1.3 73.6 - - - +
37J GLN* 1.3 60.9 + - - +
38J SER 3.2 0.2 - - - -
39J LEU* 3.9 6.1 - - + -
40J LEU* 2.7 43.8 + - + +
63J PHE* 4.2 15.3 - - + -
64J SER* 4.2 10.8 - - - +
66J VAL* 4.2 11.0 - - + -
68J PHE* 4.1 25.4 - - + -
14K TYR* 4.0 42.8 - - + -
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Residues in contact with GLN 37 (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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35I ASN* 4.4 18.6 - - - +
39I LEU* 4.7 10.6 - - + +
14J TYR* 4.4 13.8 - - - -
18J ASP 4.0 17.8 + - - -
20J PHE* 3.3 54.9 - - + +
31J THR* 5.5 0.8 - - - +
33J ARG 3.7 7.2 + - - +
34J TRP* 3.7 33.6 - - - +
35J ASN 3.2 0.8 - - - -
36J LEU* 1.3 81.0 - - - +
38J SER* 1.3 62.4 + - - +
41J LEU* 3.2 22.9 + - - +
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Residues in contact with SER 38 (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 LEU* 5.1 9.9 - - - +
34J TRP 4.4 2.6 + - - -
35J ASN* 3.3 10.0 + - - -
36J LEU 3.2 0.6 - - - -
37J GLN* 1.3 78.7 - - - +
39J LEU* 1.3 69.3 + - - +
41J LEU* 3.9 2.8 + - - +
42J SER* 2.9 31.0 + - - -
38K SER* 5.3 5.9 + - - -
287L MET 5.2 8.0 + - - -
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Residues in contact with LEU 39 (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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35J ASN* 3.7 14.6 - - - +
36J LEU* 3.8 7.9 - - + +
38J SER* 1.3 82.7 - - - +
40J LEU* 1.3 63.3 + - - +
42J SER* 3.3 3.8 + - - -
43J ALA* 3.0 22.3 + - - +
68J PHE* 3.7 25.2 - - + -
14K TYR* 4.4 10.1 - - + -
20K PHE* 3.9 30.3 - - + -
37K GLN* 4.1 18.6 - - + +
38K SER* 4.4 26.9 - - - +
41K LEU* 3.5 24.1 - - + +
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Residues in contact with LEU 40 (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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9J VAL* 4.7 11.6 - - + +
12J THR* 4.9 6.1 - - + -
20J PHE* 4.1 24.7 - - + -
22J VAL* 4.6 16.4 - - + -
31J THR* 4.6 1.1 - - + -
36J LEU* 2.7 37.2 + - + +
39J LEU* 1.3 71.9 - - - +
41J LEU* 1.3 57.3 + - - +
43J ALA* 3.0 6.5 + - + +
44J GLN* 2.8 26.1 + - - +
50J VAL* 4.9 7.9 - - + -
52J ILE* 5.1 2.0 - - + -
63J PHE* 3.5 34.8 - - + -
66J VAL* 4.3 15.5 - - + -
68J PHE* 4.2 16.2 - - + -
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Residues in contact with LEU 41 (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 LEU* 4.2 38.8 - - + +
42I SER* 4.8 2.2 - - - -
43I ALA 5.8 0.2 - - - +
48I MET* 5.0 3.4 - - + -
68I PHE* 3.9 30.3 - - + -
12J THR* 3.5 24.5 - - - +
20J PHE* 4.4 9.5 - - + -
37J GLN 3.2 16.8 + - - +
38J SER 4.6 1.6 - - - +
39J LEU 3.4 0.2 - - - -
40J LEU* 1.3 77.6 - - - +
42J SER* 1.4 50.7 + - - +
44J GLN* 2.9 16.2 + - + +
45J ILE* 2.8 61.6 + - + +
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Residues in contact with SER 42 (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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38J SER* 2.9 22.8 + - - -
39J LEU* 3.3 5.1 + - - +
41J LEU* 1.4 73.1 - - - +
43J ALA* 1.3 64.1 + - - +
45J ILE* 3.9 8.7 - - - +
46J THR* 2.9 34.8 + - - +
41K LEU* 4.6 11.9 - - - +
45K ILE* 4.3 2.7 - - - +
285L ILE* 4.4 9.7 + - - -
286L LEU* 4.0 29.0 + - - +
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Residues in contact with ALA 43 (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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9J VAL* 4.9 4.0 - - + +
39J LEU 3.0 12.2 + - - +
40J LEU* 3.0 11.3 + - - +
42J SER* 1.3 76.7 - - - +
44J GLN* 1.3 66.3 + - - +
46J THR* 4.2 0.2 - - - -
47J GLY* 3.2 2.6 + - - -
48J MET* 2.9 45.4 + - + +
50J VAL* 4.0 15.3 - - + -
68J PHE* 3.8 26.7 - - + -
41K LEU* 5.4 0.6 - - + +
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Residues in contact with GLN 44 (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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48I MET* 5.1 7.0 - - - -
68I PHE* 3.0 27.0 + - - +
69I ARG* 4.1 8.9 + - - -
9J VAL* 3.7 34.2 + - + +
10J GLU 4.0 5.1 + - - -
11J TYR* 3.4 16.0 - - - +
12J THR* 2.5 27.2 + - - +
40J LEU 2.8 12.1 + - - +
41J LEU* 2.9 21.1 + - + +
43J ALA* 1.3 82.4 - - - +
45J ILE* 1.3 67.4 + - + +
47J GLY* 3.0 8.1 + - - -
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Residues in contact with ILE 45 (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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42I SER* 4.5 20.6 - - - +
46I THR* 4.3 7.0 - - + +
48I MET* 4.1 27.4 - - + -
41J LEU* 2.8 44.7 + - + +
42J SER* 4.4 4.3 - - - +
43J ALA 3.5 0.2 - - - -
44J GLN* 1.3 71.8 - - - +
46J THR* 1.3 58.4 + - + +
47J GLY* 2.3 21.5 + - - -
220L ARG* 3.6 20.8 + - - +
277L TRP* 3.6 16.4 - - + -
285L ILE* 3.0 43.3 - - + +
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Residues in contact with THR 46 (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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42J SER* 2.9 24.6 + - - +
45J ILE* 1.3 79.8 - - + +
47J GLY* 1.3 58.9 + - - +
48J MET* 3.6 19.2 + - - +
45K ILE* 3.8 30.8 - - + +
272L HIS* 4.2 13.1 - - - +
275L ILE* 4.0 9.4 - - - +
277L TRP* 3.8 24.9 + - - +
282L LEU* 4.3 17.0 - - + -
285L ILE* 4.5 3.1 - - + -
286L LEU* 4.3 8.3 - - + -
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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