Contacts of the helix formed by residues 50 - 64 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B GLY 3.8 1.6 + - - -
49B GLU* 1.3 74.8 - - - +
51B ASP* 1.3 65.2 + - - +
52B LEU* 3.0 24.1 + - - +
53B GLU* 2.9 35.1 + - + +
54B THR* 3.1 12.6 + - - -
50C ASP* 2.3 34.2 - - - +
51C ASP* 3.5 21.1 + - - +
52C LEU* 3.5 10.5 - - - +
77C LYS* 4.0 4.0 - - - +
94C TRP* 4.1 10.1 - - + -
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Residues in contact with ASP 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ARG* 3.1 37.9 + - - -
6B CYS* 3.4 30.9 - - - +
45B VAL* 3.7 17.7 - - - +
49B GLU 4.3 4.3 - - - +
50B ASP* 1.3 77.2 + - - +
52B LEU* 1.3 61.7 + - - +
54B THR* 3.3 3.8 + - - -
55B ALA* 3.2 17.2 + - - +
92B ILE* 4.0 5.5 - - - +
94B TRP* 3.9 11.7 - - + -
50C ASP* 3.5 12.5 + - - +
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Residues in contact with LEU 52 (chain B).
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* 3.0 11.6 + - - +
51B ASP* 1.3 74.3 - - - +
53B GLU* 1.3 63.7 + - - +
55B ALA* 3.7 5.6 - - + -
56B LEU* 3.2 32.2 + - + +
72B ILE* 3.6 35.4 - - + -
74B GLU* 5.3 0.7 - - - +
94B TRP* 3.5 40.0 - - + +
50C ASP* 3.4 7.6 + - - +
52C LEU* 4.1 23.3 - - + -
53C GLU* 3.9 28.5 - - + +
56C LEU* 5.0 8.1 - - + -
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLU* 3.8 17.9 - - + +
50B ASP* 2.9 43.3 + - + +
52B LEU* 1.3 79.4 - - - +
54B THR* 1.3 54.3 - - - +
56B LEU* 4.0 5.7 - - + +
57B ARG* 3.0 29.5 + - - +
52C LEU* 4.1 7.7 - - + +
72C ILE* 6.4 0.7 - - + -
74C GLU* 6.0 0.2 - - - +
75C GLY 5.8 3.7 + - - +
76C PHE 4.5 2.4 + - - +
77C LYS* 3.4 27.7 + - - +
94C TRP* 3.0 31.8 + - + +
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Residues in contact with THR 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B CYS* 3.8 11.0 - - + +
43B GLY 3.5 17.9 - - - +
44B HIS 3.5 27.1 - - - +
45B VAL* 3.5 15.7 - - - +
49B GLU* 2.7 25.3 + - - +
50B ASP 3.1 11.6 + - - -
51B ASP 3.5 7.0 - - - -
53B GLU* 1.3 75.2 - - - +
55B ALA* 1.3 58.0 + - - +
57B ARG* 3.7 6.3 - - - +
58B GLU* 2.7 42.5 + - - +
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B CYS* 4.0 13.0 - - + -
7B GLY* 3.3 30.5 - - - +
8B LEU* 3.8 13.8 - - + +
51B ASP 3.2 10.3 + - - +
52B LEU* 3.7 10.1 - - + +
53B GLU 3.4 0.4 - - - -
54B THR* 1.3 78.5 - - - +
56B LEU* 1.3 54.6 + - - +
58B GLU* 3.9 1.0 - - - +
59B THR* 2.7 36.6 + - - -
94B TRP* 4.2 8.7 - - + -
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 4.1 4.9 - - + -
52B LEU* 3.2 24.2 + - + +
53B GLU* 4.0 6.3 - - + +
55B ALA* 1.3 72.6 - - - +
57B ARG* 1.3 67.7 + - - +
58B GLU 3.0 1.9 + - - -
59B THR* 3.1 11.1 + - - +
60B GLN 3.1 10.6 + - - -
65B ILE 4.8 0.7 - - - +
67B ALA* 4.7 11.2 - - + -
70B LEU* 4.1 23.5 - - + +
72B ILE* 4.0 26.9 - - + -
157B SO4 4.6 8.1 - - - +
52C LEU* 4.8 7.0 - - + -
72C ILE* 4.5 26.7 - - + -
74C GLU* 3.1 26.0 - - + +
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B HIS 3.3 11.9 + - - -
46B GLU* 4.1 18.1 + - - +
49B GLU* 2.3 54.2 + - - +
53B GLU 3.0 20.2 + - - +
54B THR* 3.7 8.8 - - - +
56B LEU* 1.3 77.0 - - - +
58B GLU* 1.3 89.4 + - - +
60B GLN* 3.4 8.0 + - + +
61B GLU* 3.1 52.4 + - - +
158B SO4 3.8 5.7 + - - -
74C GLU* 3.8 13.2 + - + +
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B CYS 4.1 4.0 - - - +
41B PRO* 4.7 2.7 - - - -
42B LYS* 3.1 9.5 - - - +
43B GLY* 3.0 42.2 - - - +
44B HIS 3.7 0.3 - - - +
54B THR* 2.7 21.0 + - + +
55B ALA 4.2 0.7 - - - +
57B ARG* 1.3 107.9 + - - +
59B THR* 1.3 63.3 + - - +
61B GLU* 3.7 13.0 - - - +
62B GLU* 3.0 40.9 + - - +
158B SO4 2.9 27.9 + - - -
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Residues in contact with THR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.3 27.7 + - + +
10B ILE* 4.0 25.1 - - + -
41B PRO* 3.8 21.3 + - + +
55B ALA 2.7 24.5 + - - -
56B LEU* 3.1 4.9 + - - -
58B GLU* 1.3 75.9 - - - +
60B GLN* 1.3 57.5 + - - +
63B ALA* 2.8 29.5 + - - +
64B GLY 3.4 0.5 + - - -
65B ILE* 3.9 21.9 + - + +
70B LEU* 4.5 4.5 - - + -
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Residues in contact with GLN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU 3.1 8.7 + - - +
57B ARG* 3.6 11.4 - - + +
59B THR* 1.3 77.4 - - - +
61B GLU* 1.3 81.6 + - - +
64B GLY* 2.8 25.1 + - - -
65B ILE 3.1 27.7 + - - +
66B GLU* 3.9 22.8 - - - +
74C GLU* 4.1 15.9 - - - +
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Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ARG* 3.1 52.8 + - - +
58B GLU* 3.7 18.0 - - - +
59B THR 3.4 0.2 - - - -
60B GLN* 1.3 94.1 + - - +
62B GLU* 1.3 70.2 + - - +
106B ARG 4.6 2.4 - - - +
108B SER* 3.7 20.6 + - - -
158B SO4 5.0 2.9 + - - -
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 3.9 10.9 - - + +
41B PRO* 4.0 12.1 - - + -
42B LYS 3.8 26.8 - - - +
58B GLU* 3.0 29.4 + - - +
61B GLU* 1.3 85.1 - - - +
63B ALA* 1.3 60.1 + - - +
106B ARG 3.6 8.3 - - - +
107B LEU* 3.8 13.0 - - - +
108B SER* 3.9 10.6 + - - -
110B GLU* 2.7 38.4 - - - +
111B HIS* 3.2 31.8 + - + +
158B SO4 4.0 2.6 + - - -
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 4.5 7.9 - - + -
29B LEU* 4.1 9.4 - - + -
41B PRO* 3.8 23.6 - - + -
59B THR 2.8 15.9 + - - +
62B GLU* 1.3 73.7 - - - +
64B GLY* 1.3 64.1 + - - +
65B ILE* 3.3 18.3 + - + +
105B ILE* 3.4 13.2 - - + -
106B ARG 2.8 25.8 + - - -
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Residues in contact with GLY 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLN* 2.8 24.5 + - - -
63B ALA* 1.3 77.8 - - - +
65B ILE* 1.3 60.3 + - - +
66B GLU* 3.8 9.0 + - - +
69B GLN* 3.7 8.3 + - - +
104B GLU 3.9 8.1 - - - +
106B ARG* 3.3 29.6 + - - +
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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