Contacts of the helix formed by residues 35 - 46 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33Y ASP 3.2 2.6 + - - -
34Y GLU* 1.3 74.0 - - - +
36Y VAL* 1.3 69.7 + - - +
37Y GLY* 4.1 3.5 + - - -
38Y THR* 2.6 37.2 + - - -
39Y MET* 3.0 2.6 + - - -
79Y PHE* 4.0 24.5 - - - -
107Y LYS* 4.2 12.2 - - - +
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Residues in contact with VAL 36 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Y GLU 3.7 2.4 + - - -
35Y SER* 1.3 69.9 - - - +
37Y GLY* 1.3 68.7 + - - +
38Y THR 2.9 0.5 + - - -
39Y MET* 2.9 18.0 + - - +
40Y GLY 3.0 9.4 + - - -
50Y ASN* 3.9 8.9 - - - +
55Y ARG* 3.8 39.0 - - - +
79Y PHE* 3.7 23.4 - - + -
81Y GLU* 4.3 4.0 - - + +
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Residues in contact with GLY 37 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Y SER* 3.1 6.2 + - - -
36Y VAL* 1.3 82.1 - - - +
38Y THR* 1.3 54.2 + - - +
40Y GLY* 3.4 2.1 + - - -
41Y ASN* 2.5 33.9 + - - -
50Y ASN* 5.0 2.7 - - - -
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Residues in contact with THR 38 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Y GLU* 3.9 14.1 - - + -
35Y SER* 2.6 36.8 + - - -
37Y GLY* 1.3 67.2 - - - -
39Y MET* 1.3 58.1 + - - +
40Y GLY 3.0 1.1 - - - -
41Y ASN* 2.7 36.2 + - - +
42Y ARG* 3.0 39.8 + - - +
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Residues in contact with MET 39 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Y GLU* 3.9 22.2 - - + +
35Y SER 3.0 4.8 + - - +
36Y VAL* 2.9 8.7 + - - +
38Y THR* 1.3 78.5 - - - +
40Y GLY* 1.3 58.0 + - - +
42Y ARG* 3.2 24.5 - - + +
43Y LEU* 3.0 45.4 + - + +
55Y ARG* 3.5 26.9 - - + -
58Y PHE* 4.6 10.8 - - + -
59Y ARG* 3.0 41.5 - - - +
306Y GLN* 4.8 2.5 - - - +
310Y LEU* 4.0 11.7 - - + -
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Residues in contact with GLY 40 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Y VAL 3.0 9.3 + - - -
37Y GLY 3.4 3.3 + - - -
38Y THR 2.9 1.4 + - - -
39Y MET* 1.3 74.1 - - - +
41Y ASN* 1.3 55.3 + - - +
42Y ARG 3.0 1.6 - - - -
43Y LEU* 3.6 3.1 - - - +
44Y GLN* 2.6 38.9 + - - +
48Y VAL 4.9 0.5 - - - +
50Y ASN* 3.2 34.4 + - - +
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Residues in contact with ASN 41 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Y GLY 2.5 31.4 + - - -
38Y THR* 2.7 18.7 + - + +
40Y GLY* 1.3 71.0 - - - +
42Y ARG* 1.3 66.6 + - - +
44Y GLN* 3.3 21.2 - - - +
45Y ARG* 3.3 37.5 + - - +
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Residues in contact with ARG 42 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Y GLU* 4.4 17.0 + - - +
38Y THR* 3.0 36.9 + - + +
39Y MET* 3.2 30.5 - - + +
40Y GLY 3.0 0.2 - - - -
41Y ASN* 1.3 76.9 - - - +
43Y LEU* 1.3 61.3 + - - +
45Y ARG* 2.8 59.0 + - - +
46Y ILE* 3.6 7.1 + - - +
303Y ARG* 3.6 41.0 - - - +
306Y GLN* 6.4 1.6 - - - -
310Y LEU* 3.9 16.4 - - + +
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Residues in contact with LEU 43 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39Y MET* 3.0 26.2 + - + +
40Y GLY* 3.8 3.8 - - - +
42Y ARG* 1.3 78.7 - - - +
44Y GLN* 1.3 57.9 + - - +
46Y ILE* 2.8 39.0 + - + +
48Y VAL* 2.8 39.0 + - + +
49Y GLU 3.9 15.7 - - - +
50Y ASN* 4.2 16.8 - - - +
54Y ASN* 4.2 16.4 - - + -
55Y ARG* 4.3 13.0 - - + +
58Y PHE* 5.1 3.6 - - + -
310Y LEU* 3.8 11.0 - - + -
313Y TRP* 3.7 18.4 - - + -
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Residues in contact with GLN 44 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40Y GLY 2.6 24.3 + - - +
41Y ASN* 3.3 24.3 - - - +
42Y ARG 3.0 0.2 - - - -
43Y LEU* 1.3 73.8 - - - +
45Y ARG* 1.3 56.2 + - - +
47Y LYS* 3.0 20.4 + - - +
48Y VAL 3.9 6.5 + - - +
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Residues in contact with ARG 45 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41Y ASN* 3.3 23.0 + - - +
42Y ARG* 2.8 43.5 + - - +
44Y GLN* 1.3 77.6 - - - +
46Y ILE* 1.3 61.2 + - + +
47Y LYS* 3.1 11.0 + - - +
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Residues in contact with ILE 46 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42Y ARG 4.2 5.8 - - - +
43Y LEU* 2.8 40.3 + - + +
45Y ARG* 1.3 81.2 - - + +
47Y LYS* 1.3 74.9 + - - +
48Y VAL* 3.3 23.9 - - + +
310Y LEU* 3.4 52.9 - - + +
311Y ALA* 3.9 16.8 - - + +
313Y TRP* 3.8 7.9 - - + -
314Y GLY* 4.2 12.8 - - - +
315Y GLY 4.3 1.6 - - - +
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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