Contacts of the helix formed by residues 50 - 64 (chain C) in PDB entry 3U53
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 ASP 50 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B ASP* 2.3 41.8 - - - +
51B ASP* 3.5 15.6 + - - +
52B LEU* 3.4 20.0 + - - -
77B LYS* 4.4 5.0 + - - +
94B TRP* 3.8 7.6 - - + -
48C GLY 4.4 0.4 + - - -
49C GLU* 1.3 71.7 - - - +
51C ASP* 1.3 65.8 + - - +
52C LEU* 3.0 7.7 + - - +
53C GLU* 2.5 33.3 + - + +
54C THR* 2.9 29.6 + - - -
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Residues in contact with ASP 51 (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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50B ASP* 3.5 13.1 + - - +
4C ARG* 2.5 40.7 + - - -
6C CYS* 3.4 25.0 - - - +
45C VAL* 3.8 13.3 - - - +
49C GLU 3.9 1.8 + - - +
50C ASP* 1.3 76.7 + - - +
52C LEU* 1.3 58.5 + - - +
54C THR* 2.9 7.6 + - - -
55C ALA* 2.9 23.9 + - - +
92C ILE* 3.9 8.8 - - - +
94C TRP* 3.8 13.0 - - + -
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Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ASP* 3.5 21.0 + - - +
52B LEU* 4.1 18.6 - - + +
53B GLU* 4.1 19.7 - - + +
56B LEU* 4.8 4.5 - - + -
8C LEU* 4.3 5.4 - - + -
50C ASP* 3.0 3.9 + - - +
51C ASP* 1.3 74.7 - - - +
53C GLU* 1.3 65.7 - - - +
55C ALA 3.2 1.1 + - - +
56C LEU* 3.0 28.7 + - + +
72C ILE* 4.2 31.4 - - + -
94C TRP* 3.5 50.6 - - + +
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Residues in contact with GLU 53 (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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52B LEU* 3.9 17.3 - - + -
74B GLU* 4.0 18.4 - - - +
75B GLY 5.5 3.6 + - - -
76B PHE 5.2 0.5 - - - +
77B LYS* 3.4 20.2 + - - +
94B TRP* 3.2 23.4 + - - +
49C GLU* 4.1 14.9 - - + +
50C ASP* 2.5 44.1 + - - +
52C LEU* 1.3 79.2 - - - +
54C THR* 1.3 63.3 + - - +
56C LEU* 3.9 6.3 - - - +
57C ARG* 3.0 26.7 + - - +
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Residues in contact with THR 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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6C CYS* 3.9 11.0 - - + +
43C GLY 3.7 17.5 - - - +
44C HIS 3.6 23.8 - - - +
45C VAL* 3.5 20.9 - - - +
49C GLU* 2.7 22.2 + - - +
50C ASP 2.9 14.3 + - - -
51C ASP* 2.9 10.7 + - - -
53C GLU* 1.3 77.0 - - - +
55C ALA* 1.3 64.2 + - - +
57C ARG* 3.8 8.5 + - - +
58C GLU* 3.0 24.6 + - - +
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Residues in contact with ALA 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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6C CYS* 3.9 13.0 - - + -
7C GLY* 3.5 32.1 - - - +
8C LEU* 3.6 15.8 - - + +
41C PRO 5.4 0.2 - - - +
51C ASP 2.9 12.2 + - - +
52C LEU* 3.7 6.5 - - - +
53C GLU 3.2 0.2 - - - -
54C THR* 1.3 79.3 - - - +
56C LEU* 1.3 59.6 + - - +
58C GLU* 4.2 0.9 - - - +
59C THR* 2.9 29.8 + - - -
94C TRP* 4.2 7.4 - - + -
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Residues in contact with LEU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 5.0 9.9 - - + -
72B ILE* 5.6 0.4 - - + -
74B GLU* 3.6 31.4 - - + +
157B SO4 4.5 21.1 - - - +
8C LEU* 3.9 11.2 - - + -
52C LEU* 3.0 24.8 + - + +
53C GLU* 3.9 5.8 - - - +
54C THR 3.2 0.2 - - - -
55C ALA* 1.3 75.0 - - - +
57C ARG* 1.3 65.8 + - - +
59C THR* 3.3 4.3 + - - +
60C GLN* 3.2 20.3 + - - +
65C ILE 4.5 1.6 - - - +
67C ALA* 4.3 20.4 + - + -
70C LEU* 3.7 28.6 - - + +
72C ILE* 4.5 14.1 - - + -
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Residues in contact with ARG 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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44C HIS* 3.8 7.9 + - - -
46C GLU* 3.2 32.3 + - - -
49C GLU* 2.8 41.3 + - - +
53C GLU 3.0 17.8 + - - +
54C THR* 3.8 12.9 - - - +
56C LEU* 1.3 78.8 - - - +
58C GLU* 1.3 85.0 + - - +
60C GLN* 3.3 11.9 + - + +
61C GLU* 2.6 55.0 + - + +
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Residues in contact with GLU 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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6C CYS 4.6 1.8 - - - +
41C PRO* 4.3 1.5 - - - +
42C LYS* 3.5 9.6 - - - +
43C GLY* 2.9 45.7 - - - +
44C HIS* 3.7 8.4 + - - +
54C THR 3.0 16.0 + - - +
55C ALA 4.3 1.6 - - - +
57C ARG* 1.3 100.1 + - - +
59C THR* 1.3 59.0 + - - +
61C GLU* 3.3 23.0 - - - +
62C GLU* 2.7 52.5 + - + +
110C GLU* 4.6 4.0 - - - +
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Residues in contact with THR 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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8C LEU* 3.5 22.5 + - - +
10C ILE* 3.9 22.2 - - + -
41C PRO* 3.8 21.3 - - + +
55C ALA 2.9 22.4 + - - -
56C LEU 3.5 5.4 - - - -
58C GLU* 1.3 77.6 - - - +
60C GLN* 1.3 57.1 + - - +
63C ALA* 2.9 27.9 + - + +
64C GLY 3.3 4.0 + - - -
65C ILE* 3.7 20.8 + - + +
70C LEU* 3.9 12.3 - - + -
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Residues in contact with GLN 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU 3.2 8.3 + - - +
57C ARG* 3.5 12.8 - - + +
59C THR* 1.3 73.4 - - - +
61C GLU* 1.3 78.1 + - + +
64C GLY* 2.8 33.3 + - - +
65C ILE 3.0 23.3 + - - +
66C GLU* 4.1 27.2 - - + +
67C ALA 5.6 0.2 - - - +
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Residues in contact with GLU 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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46C GLU* 4.8 2.1 - - - +
57C ARG* 2.6 60.8 + - + +
58C GLU* 3.3 23.1 - - - +
60C GLN* 1.3 85.8 - - + +
62C GLU* 1.3 66.3 + - - +
64C GLY* 4.2 1.0 + - - -
106C ARG 4.8 0.9 - - - +
107C LEU 5.2 0.2 - - - -
108C SER* 3.6 15.5 + - - -
110C GLU* 5.1 5.2 - - - +
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Residues in contact with GLU 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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29C LEU* 4.0 19.3 - - + +
41C PRO* 4.0 10.8 - - + -
42C LYS 3.9 16.1 - - - +
44C HIS* 6.1 0.9 - - - -
58C GLU* 2.7 45.3 + - + +
61C GLU* 1.3 75.2 - - - +
63C ALA* 1.3 57.2 + - - +
64C GLY 3.6 0.2 - - - -
106C ARG 4.2 0.2 - - - -
107C LEU* 3.6 9.0 - - - +
108C SER* 3.3 31.2 + - - -
110C GLU* 3.0 39.4 - - - +
111C HIS* 3.4 20.2 + - - +
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Residues in contact with ALA 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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27C LEU* 4.4 22.2 - - + -
29C LEU* 4.5 14.1 - - + -
41C PRO* 4.6 8.7 - - + -
59C THR* 2.9 13.1 + - + +
62C GLU* 1.3 73.9 - - - +
64C GLY* 1.3 63.4 + - - +
65C ILE* 3.2 13.5 + - + +
105C ILE* 3.6 12.0 - - + -
106C ARG 3.0 28.0 + - - -
107C LEU* 4.7 1.1 - - - -
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Residues in contact with GLY 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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59C THR 3.3 0.2 + - - -
60C GLN* 2.8 32.1 + - - +
61C GLU 4.2 0.4 + - - -
62C GLU 3.6 0.2 - - - -
63C ALA* 1.3 78.0 - - - +
65C ILE* 1.3 61.6 + - - +
66C GLU* 4.0 6.6 + - - +
69C GLN* 4.2 4.2 + - - -
104C GLU 4.1 4.5 - - - +
106C ARG* 3.4 35.0 + - - -
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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