Contacts of the helix formed by residues 51 - 65 (chain Z) 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 Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Z GLU* 3.6 23.2 + - - -
50Z ASN* 1.3 81.7 + - - +
52Z GLU* 1.3 74.4 + - + +
53Z GLU* 3.9 12.1 - - + +
54Z ASN* 2.5 45.8 + - - +
55Z ARG* 3.3 11.8 + - - +
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Residues in contact with GLU 52 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Z THR* 1.3 74.4 - - + +
53Z GLU* 1.3 70.5 + - - +
55Z ARG* 2.8 49.9 + - - +
56Z ARG* 3.4 4.5 + - - +
81Z GLU* 2.8 37.9 - - - +
85Z GLN* 3.1 17.7 + - - +
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Residues in contact with GLU 53 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Z THR* 3.0 8.5 + - + +
52Z GLU* 1.3 84.2 + - - +
54Z ASN* 1.3 59.4 + - - +
55Z ARG 2.6 12.6 + - - -
56Z ARG* 3.0 40.1 + - - +
57Z GLN* 3.0 44.8 + - - +
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Residues in contact with ASN 54 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Z LEU* 4.5 8.0 - - + +
48Z VAL* 5.3 4.9 - - + -
49Z GLU* 2.8 20.9 + - - +
50Z ASN* 3.9 0.2 - - - +
51Z THR* 2.5 57.1 + - - +
53Z GLU* 1.3 72.4 - - - +
55Z ARG* 1.3 59.8 + - - +
57Z GLN* 3.1 20.8 + - - +
58Z PHE* 3.7 2.3 + - - +
313Z TRP* 2.9 39.2 - - + -
315Z GLY* 6.1 0.7 - - - -
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Residues in contact with ARG 55 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Z GLU 6.0 0.2 - - - -
35Z SER 6.2 0.2 - - - -
36Z VAL* 3.8 34.1 + - - +
39Z MET* 3.6 33.3 - - + +
43Z LEU* 4.2 6.1 - - + -
50Z ASN* 2.5 36.8 - - - +
51Z THR* 3.3 4.9 + - - +
52Z GLU* 2.8 51.1 + - - +
53Z GLU 2.6 5.7 + - - -
54Z ASN* 1.3 72.1 - - - +
56Z ARG* 1.3 53.2 + - - +
57Z GLN 2.5 16.1 + - - -
58Z PHE* 2.7 16.8 + - - +
59Z ARG* 3.0 28.2 + - - +
81Z GLU* 3.1 33.0 + - - +
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Residues in contact with ARG 56 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52Z GLU* 3.4 3.2 + - - +
53Z GLU* 3.0 31.1 + - - +
55Z ARG* 1.3 77.8 - - - +
57Z GLN* 1.3 58.1 + - - +
59Z ARG* 4.4 0.4 - - - -
60Z GLU* 2.8 55.7 + - - +
85Z GLN* 2.9 46.7 + - - +
86Z LYS 2.6 33.7 + - - +
87Z ASP* 3.1 9.1 - - - +
88Z SER* 3.6 15.4 + - - +
93Z PHE* 3.0 25.5 - - + -
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Residues in contact with GLN 57 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53Z GLU* 3.0 38.9 - - - +
54Z ASN* 3.1 31.2 + - - +
55Z ARG 2.5 7.3 + - - -
56Z ARG* 1.3 73.5 - - + +
58Z PHE* 1.3 58.2 + - - +
59Z ARG 3.1 4.0 - - - -
60Z GLU* 3.5 5.9 + - - +
61Z ILE* 3.0 32.4 + - - +
313Z TRP* 3.5 22.6 - - + +
315Z GLY 5.2 2.2 + - - +
317Z ALA* 4.7 15.3 - - + +
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Residues in contact with PHE 58 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39Z MET* 5.3 9.9 - - + -
43Z LEU* 4.9 3.8 - - + -
54Z ASN 3.7 9.3 + - - +
55Z ARG* 2.7 11.1 + - - +
57Z GLN* 1.3 75.1 - - - +
59Z ARG* 1.3 62.3 + - + +
61Z ILE* 4.0 4.9 - - - +
62Z LEU* 3.0 50.6 + - + +
306Z GLN* 4.3 17.5 - - + -
309Z ALA* 2.8 32.3 - - + -
310Z LEU* 3.1 49.8 - - + -
313Z TRP* 3.8 36.3 - + + -
323Z THR* 3.9 11.4 - - + -
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Residues in contact with ARG 59 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Z ALA* 4.7 13.9 + - + +
33Z ASP 4.4 0.2 - - - +
34Z GLU* 3.6 33.9 + - - +
39Z MET* 3.3 35.1 - - - +
55Z ARG* 3.0 24.2 + - - +
56Z ARG 4.3 0.4 - - - -
58Z PHE* 1.3 84.4 - - + +
60Z GLU* 1.3 63.4 + - - +
61Z ILE 3.2 0.9 - - - -
62Z LEU* 4.4 4.3 - - + -
63Z PHE* 3.0 46.7 + - + -
79Z PHE* 4.4 12.3 - - - +
81Z GLU* 4.0 14.6 + - - -
82Z THR* 2.5 41.8 + - - +
85Z GLN* 4.2 5.2 - - - -
93Z PHE* 3.2 20.6 - - + -
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Residues in contact with GLU 60 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Z ARG* 2.8 38.0 + - - +
57Z GLN* 4.0 5.8 - - - +
59Z ARG* 1.3 75.9 - - - +
61Z ILE* 1.3 64.1 + - + +
63Z PHE* 3.6 3.1 + - - +
64Z SER* 3.1 30.6 + - - -
87Z ASP* 3.1 24.6 - - + +
88Z SER* 2.7 47.7 + - - -
89Z GLN* 5.0 0.9 - - - +
93Z PHE* 3.2 13.4 - - + -
96Z ILE* 5.1 3.7 - - + +
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Residues in contact with ILE 61 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57Z GLN 3.0 17.7 - - - +
58Z PHE* 4.0 6.3 - - - +
59Z ARG 3.2 0.2 - - - -
60Z GLU* 1.3 78.8 - - + +
62Z LEU* 1.3 62.5 + - - +
64Z SER* 2.5 24.0 + - - -
65Z VAL 3.4 1.7 + - - -
313Z TRP* 3.3 39.3 - - + +
317Z ALA* 4.8 9.0 - - + -
320Z LYS* 4.3 25.1 - - + -
323Z THR* 3.4 32.3 - - + +
324Z GLN* 2.8 29.3 - - + +
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Residues in contact with LEU 62 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Z LEU* 5.0 5.8 - - + -
32Z ALA* 5.3 1.1 - - + -
58Z PHE* 3.0 46.4 - - + +
59Z ARG* 3.5 3.7 + - + -
60Z GLU 3.4 0.4 - - - -
61Z ILE* 1.3 72.5 - - + +
63Z PHE* 1.3 79.4 + - + +
64Z SER 2.9 10.5 + - - -
65Z VAL* 3.0 26.4 + - - +
69Z ILE* 5.0 0.9 - - - +
306Z GLN* 4.5 19.3 - - + +
309Z ALA* 4.4 11.7 - - + -
323Z THR* 4.4 11.0 - - + -
324Z GLN* 5.5 1.1 - - - -
327Z PHE* 3.6 49.3 - - + -
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Residues in contact with PHE 63 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Z LEU* 4.5 8.3 - - + -
32Z ALA* 4.0 21.3 - - + -
59Z ARG* 3.0 29.0 + - + +
60Z GLU 3.8 2.7 - - - +
62Z LEU* 1.3 86.1 - - + +
64Z SER* 1.3 57.0 + - - +
65Z VAL* 5.4 0.4 - - - -
69Z ILE* 6.4 0.4 - - - -
76Z VAL* 4.7 1.1 - - + -
78Z LEU* 3.7 32.1 - - + -
82Z THR* 4.0 2.0 - - + -
93Z PHE* 3.4 37.2 - + + -
96Z ILE* 2.9 27.7 - - + +
97Z LEU* 3.3 42.3 - - + +
100Z LYS* 2.8 20.1 + - - +
327Z PHE* 6.4 0.2 - + - -
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Residues in contact with SER 64 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60Z GLU* 3.1 18.7 + - - -
61Z ILE* 2.5 23.6 + - - -
62Z LEU 2.9 0.8 + - - -
63Z PHE* 1.3 77.1 - - - +
65Z VAL* 1.3 63.6 - - - +
66Z ASP* 3.6 1.0 + - - -
87Z ASP* 6.2 0.4 - - - -
96Z ILE* 4.5 5.6 - - - -
100Z LYS* 2.7 15.7 + - - +
324Z GLN* 2.9 12.6 + - - -
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Residues in contact with VAL 65 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61Z ILE 3.4 0.6 + - - +
62Z LEU 3.0 17.4 + - - +
63Z PHE 3.5 0.6 - - - -
64Z SER* 1.3 87.9 + - - +
66Z ASP* 1.3 80.0 + - + +
69Z ILE* 3.8 30.1 - - + -
100Z LYS* 2.7 15.1 + - - +
324Z GLN* 3.1 53.8 - - + +
327Z PHE* 4.1 7.0 - - + -
328Z MET* 3.9 15.0 - - + -
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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