Contacts of the helix formed by residues 35 - 46 (chain X) in PDB entry 1XDM
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 SER 35 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33X ASP 3.0 5.1 + - - -
34X GLU* 1.3 79.7 - - - +
36X VAL* 1.3 71.0 + - - +
37X GLY 4.3 1.8 + - - -
38X THR* 2.5 42.1 + - - -
39X MET* 3.1 4.2 + - - +
79X PHE* 3.4 18.4 - - - -
107X LYS* 3.2 16.3 + - - +
109X ASP 6.6 0.2 - - - -
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Residues in contact with VAL 36 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34X GLU 3.5 1.1 + - - -
35X SER* 1.3 72.7 - - - +
37X GLY* 1.3 64.7 - - - +
39X MET* 3.8 4.3 + - - +
40X GLY 3.6 4.7 + - - -
50X ASN* 3.4 17.9 - - - +
55X ARG* 4.0 33.9 + - - +
79X PHE* 3.2 33.7 - - + -
81X GLU* 4.6 2.2 - - + +
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Residues in contact with GLY 37 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X SER* 3.2 3.4 + - - -
36X VAL* 1.3 76.5 - - - +
38X THR* 1.3 70.2 + - - +
40X GLY* 2.8 13.9 + - - -
41X ASN* 3.1 15.9 - - - +
50X ASN* 4.9 2.5 - - - -
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Residues in contact with THR 38 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34X GLU* 3.3 27.1 - - + -
35X SER* 2.5 38.6 + - - -
37X GLY* 1.3 68.6 - - - +
39X MET* 1.3 67.8 + - - +
40X GLY 2.8 0.3 + - - -
41X ASN* 2.7 32.6 + - - +
42X ARG* 3.4 27.8 + - - +
107X LYS* 5.3 0.3 + - - -
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Residues in contact with MET 39 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34X GLU* 3.7 17.5 - - - +
35X SER 3.1 9.3 + - - +
36X VAL 3.9 4.9 - - - +
38X THR* 1.3 78.8 - - - +
40X GLY* 1.3 55.1 + - - +
42X ARG* 2.6 71.9 + - + +
43X LEU* 2.9 31.2 + - + +
55X ARG* 3.7 29.4 - - + -
58X PHE* 5.1 6.7 - - + -
59X ARG* 3.0 39.5 - - - +
306X GLN* 5.1 5.4 - - - +
310X LEU* 4.1 11.4 - - + -
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Residues in contact with GLY 40 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36X VAL 3.6 3.6 + - - -
37X GLY 2.8 13.0 + - - -
38X THR 2.8 4.2 + - - -
39X MET* 1.3 73.8 - - - +
41X ASN* 1.3 56.7 + - - -
43X LEU* 3.1 7.7 + - - +
44X GLN* 3.0 26.9 + - - +
48X VAL 5.0 1.0 - - - +
50X ASN* 3.4 30.5 + - - +
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Residues in contact with ASN 41 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37X GLY* 3.1 9.9 - - - +
38X THR* 2.7 34.1 + - - +
40X GLY* 1.3 71.7 - - - -
42X ARG* 1.3 63.0 + - - +
44X GLN* 2.9 32.4 - - + +
45X ARG* 2.9 31.5 + - - +
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Residues in contact with ARG 42 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34X GLU* 3.7 20.3 + - - +
38X THR* 3.8 24.5 + - + +
39X MET* 2.6 53.0 + - + +
41X ASN* 1.3 74.4 - - - +
43X LEU* 1.3 56.7 + - + -
44X GLN 2.9 7.5 + - - -
45X ARG* 2.9 50.7 + - - +
46X ILE* 4.0 6.8 - - - +
303X ARG* 3.1 49.0 - - - +
306X GLN* 6.2 1.8 - - - -
310X LEU* 4.1 18.0 - - + +
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Residues in contact with LEU 43 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39X MET* 2.9 47.1 + - + +
40X GLY 3.5 6.1 - - - +
42X ARG* 1.3 75.8 - - - +
44X GLN* 1.3 58.6 + - - +
45X ARG 3.5 0.2 - - - -
46X ILE* 3.6 13.1 - - + +
47X LYS 3.4 2.1 + - - -
48X VAL* 2.7 53.8 + - + +
49X GLU 3.9 16.2 - - - +
50X ASN* 4.1 22.0 - - - +
54X ASN* 4.1 17.0 - - + -
55X ARG* 4.4 6.1 - - + +
58X PHE* 5.7 2.2 - - + -
310X LEU* 4.5 15.9 - - + -
313X TRP* 5.7 5.2 - - + -
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Residues in contact with GLN 44 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40X GLY 3.0 6.1 + - - +
41X ASN* 2.9 36.4 - - + +
43X LEU* 1.3 76.7 - - - +
45X ARG* 1.3 57.1 + - + +
47X LYS* 2.7 30.1 + - - +
48X VAL 4.7 3.4 - - - -
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Residues in contact with ARG 45 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41X ASN* 2.9 34.1 + - - +
42X ARG* 2.9 47.5 + - - +
44X GLN* 1.3 81.6 - - + +
46X ILE* 1.3 62.8 + - + +
47X LYS* 3.3 11.1 + - - +
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Residues in contact with ILE 46 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42X ARG 4.0 3.1 - - - +
43X LEU* 3.6 24.9 - - + +
45X ARG* 1.3 74.9 - - + +
47X LYS* 1.3 73.2 + - - +
48X VAL* 3.4 27.3 - - + +
310X LEU* 3.0 55.6 - - + +
311X ALA* 3.5 19.7 - - + +
313X TRP* 4.5 7.6 - - + -
314X GLY* 4.0 21.5 - - - +
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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