Contacts of the helix formed by residues 50 - 64 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48D GLY 4.3 0.4 + - - -
49D GLU* 1.3 71.8 - - - +
51D ASP* 1.3 75.0 + - - +
52D LEU* 3.4 20.6 + - - +
53D GLU* 2.7 35.1 + - + +
54D THR* 2.9 23.1 + - - -
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Residues in contact with ASP 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ARG* 2.8 40.3 + - - -
6D CYS* 3.3 22.1 - - - +
45D VAL* 3.8 18.4 - - - +
49D GLU 4.7 1.4 - - - +
50D ASP* 1.3 75.6 + - - +
52D LEU* 1.3 57.6 + - - +
54D THR* 3.0 7.8 + - - -
55D ALA* 2.9 23.6 + - - +
92D ILE* 4.6 4.2 - - - +
94D TRP* 3.6 20.6 - - + -
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 4.2 4.3 - - + -
50D ASP* 3.2 14.0 + - - +
51D ASP* 1.3 75.0 - - - +
53D GLU* 1.3 65.7 + - + +
55D ALA* 3.2 3.5 + - - +
56D LEU* 3.0 32.7 + - + +
72D ILE* 3.9 32.8 - - + -
94D TRP* 3.3 55.2 - - + +
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D GLY 4.9 1.8 - - - +
49D GLU* 3.9 14.8 - - + +
50D ASP* 2.7 46.0 + - + +
52D LEU* 1.3 78.5 - - + +
54D THR* 1.3 62.6 + - - +
56D LEU* 3.1 10.4 + - + +
57D ARG* 2.9 26.8 + - - +
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Residues in contact with THR 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D CYS* 3.9 11.7 - - + +
43D GLY 3.7 15.9 - - - +
44D HIS 3.7 23.6 - - - +
45D VAL* 3.5 21.0 - - - +
49D GLU* 2.8 20.5 + - - -
50D ASP 2.9 12.5 + - - -
51D ASP* 3.0 9.4 + - - -
53D GLU* 1.3 76.4 - - - +
55D ALA* 1.3 66.4 + - - +
57D ARG* 3.9 10.2 - - - +
58D GLU* 2.9 29.4 + - - +
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D CYS* 3.8 14.3 - - + +
7D GLY* 3.4 29.8 - - - +
8D LEU* 3.6 17.8 - - + +
51D ASP 2.9 11.9 + - - +
52D LEU 3.5 8.3 - - - +
54D THR* 1.3 79.2 - - - +
56D LEU* 1.3 53.3 + - - +
58D GLU* 4.1 1.0 - - - +
59D THR* 2.7 37.2 + - - -
94D TRP* 4.1 7.4 - - + -
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Residues in contact with LEU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 3.7 23.6 - - + -
52D LEU* 3.0 25.9 + - + +
53D GLU* 3.7 8.7 - - + +
55D ALA* 1.3 76.2 - - - +
57D ARG* 1.3 66.1 + - - +
59D THR* 3.3 3.6 + - - +
60D GLN* 3.2 21.3 + - - +
65D ILE 4.5 1.6 - - - +
67D ALA* 4.3 29.0 + - + +
70D LEU* 3.9 19.2 - - + +
72D ILE* 4.5 18.8 - - + -
158D SO4 4.6 14.4 - - - +
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Residues in contact with ARG 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D HIS* 3.4 15.2 + - - -
46D GLU* 3.2 31.4 + - - -
49D GLU* 2.6 51.9 + - - +
53D GLU 2.9 16.6 + - - +
54D THR* 3.9 14.9 - - - +
56D LEU* 1.3 76.3 - - - +
58D GLU* 1.3 83.3 + - - +
60D GLN* 3.3 10.3 + - + +
61D GLU* 2.7 62.4 + - - +
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Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D CYS 4.4 1.8 - - - +
41D PRO* 4.4 1.7 - - - +
42D LYS* 3.4 3.6 - - - -
43D GLY* 3.2 42.9 - - - +
44D HIS* 3.8 12.3 + - - -
54D THR* 2.9 18.7 + - + +
55D ALA 4.1 2.0 - - - +
57D ARG* 1.3 107.1 + - - +
59D THR* 1.3 60.7 + - - +
61D GLU* 3.7 17.4 - - - +
62D GLU* 2.8 60.7 + - - +
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Residues in contact with THR 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 3.6 22.1 + - - +
10D ILE* 3.9 24.0 - - + -
41D PRO* 3.8 21.5 + - + +
55D ALA 2.7 23.4 + - - -
56D LEU 3.5 6.1 - - - -
57D ARG 3.2 0.2 - - - -
58D GLU* 1.3 75.6 - - - +
60D GLN* 1.3 56.3 + - - +
63D ALA* 2.8 33.2 + - + +
64D GLY 3.5 0.2 + - - -
65D ILE* 4.0 12.1 - - + +
70D LEU* 3.9 16.4 - - + -
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Residues in contact with GLN 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LEU 3.2 7.1 + - - +
57D ARG* 3.6 11.7 - - + +
59D THR* 1.3 75.4 - - - +
61D GLU* 1.3 78.6 + - + +
64D GLY* 2.8 34.8 + - - +
65D ILE 3.0 26.4 + - - +
66D GLU* 4.3 23.3 - - - +
67D ALA 5.1 0.7 - - - +
106D ARG* 4.0 18.8 + - - +
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Residues in contact with GLU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D HIS* 6.0 0.5 - - - -
46D GLU* 4.7 2.9 - - - +
57D ARG* 2.7 63.1 + - - +
58D GLU* 3.3 21.7 + - - +
60D GLN* 1.3 88.8 + - - +
62D GLU* 1.3 62.3 + - - +
64D GLY* 4.3 1.0 + - - -
106D ARG* 4.9 1.2 + - - +
108D SER* 3.9 16.0 + - - -
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Residues in contact with GLU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D LEU* 3.9 18.4 - - + +
41D PRO* 4.4 5.2 - - + -
42D LYS 3.0 28.7 + - - +
44D HIS* 5.5 2.9 + - - -
58D GLU* 2.8 42.1 + - - +
59D THR 4.4 0.2 - - - +
61D GLU* 1.3 76.2 - - - +
63D ALA* 1.3 58.9 + - - +
64D GLY 3.5 0.2 - - - -
106D ARG 3.5 9.1 - - - +
107D LEU* 3.6 14.2 - - - +
108D SER* 3.6 8.3 + - - -
110D GLU* 3.8 23.0 - - + +
111D HIS* 3.5 33.0 - - + +
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Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D LEU* 4.4 15.7 - - + -
29D LEU* 4.6 8.3 - - + -
41D PRO* 4.5 13.7 - - + -
59D THR* 2.8 15.4 + - + +
62D GLU* 1.3 72.6 - - - +
64D GLY* 1.3 62.7 + - - +
65D ILE* 3.3 20.7 + - + +
105D ILE* 3.4 14.1 - - + -
106D ARG 2.9 28.4 + - - -
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Residues in contact with GLY 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D GLN* 2.8 26.5 + - - +
61D GLU 4.9 0.2 - - - -
62D GLU 3.5 0.2 - - - -
63D ALA* 1.3 79.4 - - - +
65D ILE* 1.3 61.0 + - - +
66D GLU* 3.8 3.1 + - - +
69D GLN* 4.1 6.1 + - - -
104D GLU 4.2 7.0 - - - +
106D ARG* 3.3 38.0 + - - -
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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