Contacts of the helix formed by residues 53 - 65 (chain C) in PDB entry 1LXF
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 53 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C ASN 5.4 0.7 - - - +
52C PRO* 1.3 78.9 - - + +
54C PRO* 1.3 73.2 - - - +
55C GLU* 2.8 33.9 + - - +
56C GLU* 3.3 27.0 + - - +
57C LEU* 3.0 34.3 + - - +
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Residues in contact with PRO 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C THR* 4.3 17.5 + - - +
53C THR* 1.3 96.1 - - - +
55C GLU* 1.3 61.5 + - + +
57C LEU* 4.0 9.6 - - + -
58C GLN* 3.6 19.4 + - - +
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Residues in contact with GLU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C THR* 2.8 21.1 + - - +
54C PRO* 1.3 82.9 - - + +
56C GLU* 1.3 86.3 + - + +
58C GLN* 4.1 11.4 + - - +
59C GLU* 4.4 4.2 + - - +
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Residues in contact with GLU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C PRO* 5.3 7.2 - - + +
53C THR* 3.3 32.1 + - - +
55C GLU* 1.3 98.1 - - + +
57C LEU* 1.3 64.5 + - - +
58C GLN 3.4 0.2 - - - -
59C GLU* 3.4 25.8 - - - +
60C MET* 3.9 7.4 - - - +
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Residues in contact with LEU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C THR* 3.0 38.4 - - - +
41C LEU* 3.5 29.6 - - + -
42C GLY* 3.0 27.1 - - - +
45C MET* 4.6 0.2 - - + -
52C PRO* 4.0 22.9 - - + +
53C THR 3.0 28.0 + - - +
54C PRO* 4.2 1.6 - - + -
55C GLU 3.4 0.2 - - - -
56C GLU* 1.3 75.0 - - - +
58C GLN* 1.3 56.6 + - - +
59C GLU 2.9 2.2 - - - -
60C MET* 2.5 55.0 + - + +
61C ILE* 3.6 3.0 + - - +
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Residues in contact with GLN 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C THR* 3.3 27.4 - - + +
54C PRO 3.6 16.1 + - - +
55C GLU* 4.1 8.1 - - - +
57C LEU* 1.3 77.4 - - - +
59C GLU* 1.3 58.7 + - - +
61C ILE* 2.9 22.2 + - - +
62C ASP* 2.8 36.6 + - + +
65C ASP* 4.9 2.6 - - - +
70C GLY* 4.7 4.9 + - - +
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Residues in contact with GLU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C GLU 4.4 3.5 + - - +
56C GLU* 3.4 23.6 + - - +
57C LEU 2.9 0.6 + - - -
58C GLN* 1.3 80.2 - - - +
60C MET* 1.3 59.9 + - + +
62C ASP* 3.9 12.4 - - + +
63C GLU* 3.0 36.4 + - + +
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Residues in contact with MET 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 4.9 1.1 - - + -
45C MET* 4.4 20.4 - - - -
56C GLU 3.9 5.2 - - - +
57C LEU* 2.5 44.8 + - + +
59C GLU* 1.3 75.9 - - - +
61C ILE* 1.3 63.7 + - + +
63C GLU* 4.0 3.2 - - - +
64C VAL* 3.4 13.7 + - - +
80C MET* 3.6 18.0 - - - +
92C BEP 3.1 86.1 - - + +
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Residues in contact with ILE 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ILE 4.0 7.6 - - - +
37C SER* 4.1 16.8 - - - -
38C THR* 4.2 4.9 - - + +
41C LEU* 3.9 10.8 - - + -
57C LEU 4.0 5.2 - - - +
58C GLN* 2.9 16.0 + - - +
60C MET* 1.3 86.6 - - + +
62C ASP* 1.3 54.5 + - - +
64C VAL* 2.7 9.6 - - - +
65C ASP* 2.4 68.4 + - - +
70C GLY 3.3 18.4 - - - +
71C THR 3.9 3.6 - - - +
72C VAL* 3.3 14.4 - - + -
92C BEP 3.6 22.0 - - + -
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Residues in contact with ASP 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C GLN* 2.8 29.2 + - + +
59C GLU* 3.9 15.4 - - + +
61C ILE* 1.3 71.5 - - - +
63C GLU* 1.3 69.1 + - + +
65C ASP* 2.7 28.7 + - - +
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Residues in contact with GLU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C GLU* 3.0 28.3 - - + +
60C MET* 4.0 7.4 - - - +
61C ILE 3.2 0.2 - - - -
62C ASP* 1.3 81.1 - - + +
64C VAL* 1.3 62.4 + - - +
66C GLU* 3.7 20.3 - - - +
80C MET* 4.3 13.7 - - - -
83C ARG* 4.3 28.1 + - - +
92C BEP 4.2 21.0 - - - +
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Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C MET 3.4 2.2 - - - +
61C ILE* 2.7 37.0 - - + +
63C GLU* 1.3 76.9 - - - +
65C ASP* 1.3 54.4 + - - +
66C GLU* 2.8 13.7 + - - +
67C ASP* 4.7 0.9 + - - +
72C VAL* 3.2 23.8 - - + -
76C GLU* 2.4 57.6 - - + +
80C MET* 3.2 44.9 - - + -
83C ARG* 6.0 0.9 - - - +
92C BEP 4.6 0.4 - - + -
93C CA 3.3 0.7 - - - -
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Residues in contact with ASP 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C GLN* 4.9 2.3 - - - +
61C ILE* 2.4 41.9 + - - +
62C ASP* 2.7 23.6 + - - +
64C VAL* 1.3 65.7 - - - +
66C GLU* 1.3 60.8 - - - +
67C ASP 3.2 2.5 - - - -
68C GLY* 3.4 13.0 + - - +
69C SER* 3.2 4.3 + - - -
70C GLY* 2.6 32.8 + - - -
71C THR 2.5 29.5 - - - +
93C CA 2.8 6.6 - - - -
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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