Contacts of the helix formed by residues 53 - 65 (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 GLU 53 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51X THR* 2.6 16.2 - - + +
52X GLU* 1.3 84.3 - - - +
54X ASN* 1.3 70.1 + - - +
55X ARG 3.1 1.3 - - - -
56X ARG* 2.7 43.4 + - - +
57X GLN* 2.7 60.5 + - - +
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Residues in contact with ASN 54 (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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43X LEU* 4.1 11.9 - - + -
48X VAL* 4.2 14.7 - - + +
49X GLU* 2.4 38.0 + - - +
51X THR* 2.4 33.5 + - - +
53X GLU* 1.3 78.7 - - - +
55X ARG* 1.3 64.3 + - - +
57X GLN* 3.1 8.5 + - - +
58X PHE* 2.9 24.1 + - - +
313X TRP* 3.7 16.1 - - + -
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Residues in contact with ARG 55 (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 5.6 0.2 - - - -
36X VAL* 4.0 25.1 - - - +
39X MET* 3.7 33.9 - - + -
43X LEU* 4.4 4.2 - - + +
50X ASN* 2.4 50.1 + - - +
51X THR* 3.2 18.2 + - - +
52X GLU* 3.6 21.1 - - - +
53X GLU 3.1 0.6 - - - -
54X ASN* 1.3 78.5 - - - +
56X ARG* 1.3 63.5 + - - +
58X PHE* 3.4 2.8 + - - +
59X ARG* 3.0 44.6 + - - +
79X PHE* 6.0 1.1 - - - -
81X GLU* 2.7 46.0 + - - +
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Residues in contact with ARG 56 (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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52X GLU* 3.8 5.4 - - - +
53X GLU* 2.7 45.9 + - - +
55X ARG* 1.3 76.4 - - - +
57X GLN* 1.3 69.1 + - - +
59X ARG* 3.3 1.0 + - - -
60X GLU* 2.6 64.8 + - - +
85X GLN* 3.0 37.4 + - + +
86X LYS 2.5 41.9 + - - +
87X ASP* 3.0 12.7 - - - +
88X SER* 4.2 9.8 + - - +
93X PHE* 2.9 21.1 - - + -
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Residues in contact with GLN 57 (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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53X GLU* 2.7 56.7 + - - +
54X ASN* 3.5 10.3 - - - +
56X ARG* 1.3 83.0 - - - +
58X PHE* 1.3 69.4 + - - +
59X ARG 2.9 1.1 - - - -
60X GLU* 2.6 21.9 + - - +
61X ILE* 3.0 16.3 + - + +
313X TRP* 4.0 13.6 - - + -
317X ALA* 4.2 19.4 - - - +
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Residues in contact with PHE 58 (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* 5.1 9.0 - - + -
43X LEU* 5.7 2.7 - - + -
54X ASN 2.9 15.8 + - - +
55X ARG* 4.0 3.4 - - - +
57X GLN* 1.3 70.8 - - - +
59X ARG* 1.3 65.0 + - + +
61X ILE* 3.0 36.9 - - + +
62X LEU* 3.3 34.4 + - + +
306X GLN* 3.5 30.7 - - + -
309X ALA* 3.3 25.8 - - + -
310X LEU* 3.3 46.7 - - + -
313X TRP* 3.5 32.2 - + + -
323X THR* 4.0 7.4 - - + -
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Residues in contact with ARG 59 (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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32X ALA* 2.8 36.8 + - + +
34X GLU* 3.4 27.4 + - - +
39X MET* 3.0 39.7 - - - +
55X ARG* 3.0 31.8 + - - +
56X ARG 3.6 4.3 - - - +
57X GLN 2.9 0.8 - - - -
58X PHE* 1.3 83.3 - - + +
60X GLU* 1.3 64.0 + - - +
61X ILE 3.1 1.6 - - - -
62X LEU* 3.5 12.6 + - + +
63X PHE* 3.1 45.1 + - + -
79X PHE* 3.8 11.1 - - - +
82X THR* 2.9 36.1 + - - -
93X PHE* 3.8 6.1 - - + -
306X GLN* 5.8 1.4 + - - +
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Residues in contact with GLU 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56X ARG* 2.6 44.3 + - - +
57X GLN* 2.6 14.0 + - - +
59X ARG* 1.3 73.8 - - - +
61X ILE* 1.3 52.6 + - + +
63X PHE* 4.0 1.2 - - - +
64X SER* 2.7 37.9 + - - +
87X ASP* 3.1 29.8 - - + +
88X SER* 3.0 27.3 + - - -
89X GLN* 5.8 0.5 - - - +
93X PHE* 3.1 17.9 - - + -
96X ILE* 5.7 0.7 - - - +
320X LYS* 5.1 8.1 + - - +
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Residues in contact with ILE 61 (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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57X GLN* 3.0 10.3 + - + +
58X PHE* 3.0 19.5 - - + +
60X GLU* 1.3 76.4 - - + +
62X LEU* 1.3 62.9 + - + +
64X SER* 2.8 10.6 + - - -
313X TRP* 3.1 49.4 - - + +
320X LYS* 3.8 26.0 - - + +
323X THR* 3.8 12.8 - - + -
324X GLN* 2.7 55.5 + - + +
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Residues in contact with LEU 62 (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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30X LEU* 4.8 11.9 - - + -
32X ALA* 5.3 2.7 - - + -
58X PHE* 3.3 54.2 + - + +
59X ARG* 3.9 14.1 - - + +
60X GLU 3.4 0.2 - - - -
61X ILE* 1.3 85.8 - - + +
63X PHE* 1.3 73.1 + - + +
64X SER 3.3 1.0 + - - -
65X VAL* 3.3 22.2 - - - +
69X ILE* 5.6 0.7 - - - +
306X GLN* 4.0 14.8 - - + +
309X ALA* 4.6 2.7 - - + -
323X THR* 5.2 1.1 - - + -
324X GLN* 5.4 2.2 - - - -
327X PHE* 3.7 50.3 - - + -
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Residues in contact with PHE 63 (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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30X LEU* 4.3 9.4 - - + -
32X ALA* 3.9 17.9 - - + -
59X ARG* 3.1 33.4 + - + +
60X GLU 4.2 2.5 - - - +
62X LEU* 1.3 83.3 - - + +
64X SER* 1.3 56.6 + - - +
65X VAL* 5.3 0.2 - - - -
69X ILE* 6.4 0.2 - - - -
76X VAL* 3.9 23.3 - - + -
78X LEU* 3.6 34.1 - - + -
82X THR* 4.3 0.2 - - + -
93X PHE* 3.7 35.7 - + + -
96X ILE* 3.2 24.7 - - + +
97X LEU* 3.6 31.3 - - + +
100X LYS* 3.3 15.3 - - - +
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Residues in contact with SER 64 (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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60X GLU* 2.7 27.1 + - - -
61X ILE 2.8 12.8 + - - -
63X PHE* 1.3 76.7 - - - +
65X VAL* 1.3 70.4 + - - +
66X ASP* 4.5 0.3 - - - -
96X ILE* 4.5 7.4 - - - -
100X LYS* 3.2 14.8 + - - +
320X LYS* 3.5 18.9 + - - -
324X GLN* 3.4 7.0 + - - -
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Residues in contact with VAL 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61X ILE 4.2 0.2 - - - +
62X LEU 3.3 16.8 + - - +
63X PHE 3.4 0.9 - - - -
64X SER* 1.3 83.6 - - - +
66X ASP* 1.3 75.0 + - - +
69X ILE* 3.4 41.1 - - + -
100X LYS* 2.8 15.8 - - - -
324X GLN* 3.2 49.5 - - + +
327X PHE* 4.5 5.2 - - + -
328X MET* 3.6 22.0 - - + -
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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