Contacts of the helix formed by residues 51 - 64 (chain W) 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 THR 51 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49W GLU* 2.9 9.7 + - - -
50W ASN* 1.3 72.1 - - - +
52W GLU* 1.3 65.3 + - - +
53W GLU* 3.3 13.8 + - + +
54W ASN* 2.7 50.2 - - - +
55W ARG* 3.1 27.8 + - - +
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Residues in contact with GLU 52 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51W THR* 1.3 74.8 + - - +
53W GLU* 1.3 65.1 + - - +
55W ARG* 3.2 31.9 + - - +
56W ARG* 2.8 20.4 + - - -
81W GLU* 4.0 15.9 - - + +
85W GLN* 3.5 26.3 + - - +
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Residues in contact with GLU 53 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51W THR* 3.3 10.7 + - + +
52W GLU* 1.3 78.7 - - - +
54W ASN* 1.3 57.0 + - - +
56W ARG* 2.7 51.0 + - - +
57W GLN* 2.5 57.5 + - - +
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Residues in contact with ASN 54 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43W LEU* 5.3 4.9 - - + -
48W VAL* 3.8 21.4 - - + +
49W GLU* 3.1 27.8 + - - +
51W THR* 2.7 38.0 - - + +
53W GLU* 1.3 74.2 - - - +
55W ARG* 1.3 57.6 + - + +
57W GLN* 3.1 15.1 + - - +
58W PHE* 2.8 32.6 + - - +
313W TRP* 3.8 12.4 - - + -
315W GLY* 5.7 0.9 - - - -
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Residues in contact with ARG 55 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34W GLU 5.6 0.6 + - - -
36W VAL* 3.6 29.6 - - - +
39W MET* 3.8 33.0 - - + -
43W LEU* 4.5 5.4 - - + -
50W ASN* 2.7 42.9 + - - +
51W THR* 3.1 33.3 + - - +
52W GLU* 3.3 26.5 - - - +
53W GLU 3.0 0.6 - - - -
54W ASN* 1.3 77.3 - - - +
56W ARG* 1.3 63.9 + - - +
58W PHE* 3.8 2.9 - - - +
59W ARG* 3.0 43.3 + - - +
81W GLU* 2.4 40.2 + - - +
85W GLN* 4.3 2.2 - - - -
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Residues in contact with ARG 56 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52W GLU* 2.8 8.1 + - - +
53W GLU* 2.7 49.0 + - - +
55W ARG* 1.3 74.1 - - - +
57W GLN* 1.3 57.7 + - - +
60W GLU* 3.0 64.3 + - - +
85W GLN* 3.0 47.0 - - + +
86W LYS 2.7 37.2 + - - +
87W ASP* 3.6 5.1 - - - +
88W SER* 4.5 8.9 + - - +
93W PHE* 3.2 10.2 - - + -
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Residues in contact with GLN 57 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53W GLU* 2.5 39.6 + - - +
54W ASN* 3.5 15.9 + - - +
56W ARG* 1.3 76.0 - - - +
58W PHE* 1.3 56.5 + - - +
60W GLU* 3.7 14.3 - - - +
61W ILE* 3.0 27.7 + - + +
313W TRP* 3.0 26.3 - - + -
315W GLY 4.0 6.9 - - - +
317W ALA* 4.3 17.1 - - + +
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Residues in contact with PHE 58 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39W MET* 4.0 15.7 - - + -
43W LEU* 6.1 1.3 - - + -
54W ASN 2.8 19.7 + - - +
55W ARG* 4.0 3.4 - - - +
57W GLN* 1.3 70.7 - - - +
59W ARG* 1.3 67.9 + - + +
60W GLU 3.1 1.6 - - - -
61W ILE* 3.0 23.5 + - + +
62W LEU* 3.3 27.3 + - + +
306W GLN* 3.7 24.9 - - + -
309W ALA* 4.6 0.2 - - + -
310W LEU* 3.4 58.8 - - + -
313W TRP* 3.7 35.0 - + + -
323W THR* 3.4 23.8 - - + -
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Residues in contact with ARG 59 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32W ALA* 4.4 10.2 + - + +
33W ASP 5.5 0.4 - - - -
34W GLU* 3.1 49.0 + - - +
39W MET* 3.8 28.6 - - + +
55W ARG* 3.0 30.2 + - - +
58W PHE* 1.3 84.5 - - + +
60W GLU* 1.3 62.2 + - - +
62W LEU* 3.2 13.8 + - + -
63W PHE* 3.0 42.7 + - + -
79W PHE* 5.6 1.4 - - - +
81W GLU* 3.4 21.2 + - - -
82W THR* 3.2 37.1 + - - -
85W GLN* 4.4 2.0 - - - +
93W PHE* 3.4 12.8 - - + -
306W GLN* 5.3 1.3 + - - +
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Residues in contact with GLU 60 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56W ARG* 3.0 40.6 + - - +
57W GLN* 3.7 13.1 - - - +
58W PHE 3.1 0.2 - - - -
59W ARG* 1.3 78.2 - - - +
61W ILE* 1.3 56.0 + - + +
63W PHE* 4.3 1.0 - - - +
64W SER* 2.9 40.7 + - - -
87W ASP* 3.0 12.5 - - + +
88W SER* 2.4 48.3 + - - -
89W GLN* 5.1 0.5 - - - +
93W PHE* 3.1 18.1 - - + -
96W ILE* 5.5 1.9 - - + +
320W LYS* 5.9 1.6 - - - +
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Residues in contact with ILE 61 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57W GLN* 3.0 22.7 - - + +
58W PHE* 3.1 13.0 - - + +
60W GLU* 1.3 77.8 - - + +
62W LEU* 1.3 62.0 + - - +
64W SER* 3.5 5.3 + - - -
313W TRP* 3.3 43.5 - - + +
317W ALA* 5.4 2.9 - - - +
320W LYS* 4.0 20.9 - - + +
323W THR* 3.5 21.1 - - + -
324W GLN* 2.6 54.5 + - + +
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Residues in contact with LEU 62 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30W LEU* 4.7 8.5 - - + -
32W ALA* 4.9 1.8 - - + -
58W PHE* 3.7 35.0 - - + +
59W ARG* 3.2 17.2 + - + +
60W GLU 3.2 0.6 - - - -
61W ILE* 1.3 76.7 - - - +
63W PHE* 1.3 72.4 + - + +
65W VAL* 2.9 34.0 + - - +
306W GLN* 3.8 31.2 - - + +
309W ALA* 4.5 4.5 - - + -
323W THR* 4.7 3.6 - - + -
324W GLN* 5.5 0.4 - - - -
327W PHE* 3.5 49.1 - - + -
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Residues in contact with PHE 63 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30W LEU* 4.7 9.0 - - + -
32W ALA* 4.7 6.5 - - + -
59W ARG* 3.0 24.7 + - + +
60W GLU 4.3 2.0 - - - +
62W LEU* 1.3 90.2 - - + +
64W SER* 1.3 56.6 + - - +
65W VAL* 3.1 1.9 + - - +
76W VAL* 4.2 16.4 - - + -
78W LEU* 3.3 35.2 - - + -
82W THR* 4.3 4.0 - - + -
93W PHE* 3.1 45.5 - + + -
96W ILE* 3.2 15.1 - - + +
97W LEU* 3.8 31.2 - - + +
100W LYS* 3.1 30.8 + - - +
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Residues in contact with SER 64 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60W GLU* 2.9 25.3 + - - -
61W ILE 3.5 0.2 + - - -
62W LEU 3.2 0.2 - - - -
63W PHE* 1.3 73.7 - - - +
65W VAL* 1.3 65.7 + - - +
66W ASP 3.8 0.3 + - - -
87W ASP* 6.4 0.2 - - - -
96W ILE* 4.5 11.0 - - - +
100W LYS* 4.3 6.8 - - - +
320W LYS* 3.5 18.3 + - - -
324W GLN* 3.0 18.2 + - - -
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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