Contacts of the helix formed by residues 53 - 64 (chain B) in PDB entry 3EUS
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 53 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 5.9 0.2 - - - +
10A HIS* 4.2 15.9 + - - -
51A ARG* 4.0 28.6 - - + +
52A LEU 3.5 17.5 - - - +
53A ASP* 4.3 0.2 - - - +
54A VAL* 4.1 3.4 - - - -
51B ARG 3.9 0.8 + - - -
52B LEU* 1.3 75.8 - - - +
54B VAL* 1.3 58.9 + - - +
55B ILE* 2.9 12.9 + - - +
56B GLU* 2.8 56.3 + - - +
57B PHE* 2.9 27.7 + - - +
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Residues in contact with VAL 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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13A LEU* 3.7 30.9 - - + +
52A LEU* 3.7 8.2 + - + +
53A ASP 4.0 10.3 - - - +
54A VAL* 4.4 4.3 - - + -
57A PHE* 3.5 51.6 - - + -
74A VAL* 4.9 7.6 - - + -
77A ILE* 4.1 17.7 - - + -
53B ASP* 1.3 73.8 - - - +
55B ILE* 1.3 60.8 + - - +
57B PHE* 3.5 9.9 + - + +
58B ALA* 2.9 26.7 + - - +
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Residues in contact with ILE 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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7A THR* 5.8 0.2 - - - +
9A GLU* 3.7 30.5 - - + +
10A HIS* 4.5 21.3 - - + +
13A LEU* 3.5 35.0 - - + -
77A ILE* 3.8 24.0 - - + -
53B ASP* 2.9 11.8 + - - +
54B VAL* 1.3 77.9 - - + +
56B GLU* 1.3 65.8 + - + +
58B ALA* 3.2 4.2 + - - +
59B LYS* 3.0 50.6 + - - +
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Residues in contact with GLU 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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51A ARG* 5.2 0.3 + - - -
35B LEU* 5.3 0.9 - - - +
37B LYS* 5.0 4.1 + - + +
41B PHE* 4.2 12.9 - - + -
50B ARG* 2.7 45.9 + - - -
52B LEU* 3.5 17.3 - - + +
53B ASP* 2.8 40.8 + - - +
55B ILE* 1.3 80.3 - - + +
57B PHE* 1.3 51.9 + - - +
59B LYS* 3.3 9.9 + - + +
60B TRP* 2.8 36.6 + - - +
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Residues in contact with PHE 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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54A VAL* 3.4 28.5 - - + -
57A PHE* 5.7 1.8 - + - -
74A VAL* 4.4 12.8 - - + -
13B LEU* 3.8 21.3 - - + -
17B LEU* 3.9 17.3 - - + -
52B LEU* 3.8 11.5 - - + +
53B ASP 2.9 16.9 + - - +
54B VAL* 3.5 9.9 - - + +
56B GLU* 1.3 74.5 - - - +
58B ALA* 1.3 58.8 + - - +
60B TRP* 3.3 1.4 + - - +
61B MET* 2.9 56.1 + - + +
70B VAL* 4.1 24.0 - - + -
73B ILE* 4.2 15.0 - - + -
74B VAL* 4.0 28.3 - - + -
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Residues in contact with ALA 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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74A VAL* 3.5 41.7 - - + +
77A ILE* 3.8 17.9 - - + -
78A ALA* 3.5 8.4 - - - +
54B VAL 2.9 17.7 + - - +
55B ILE 3.4 9.0 - - - +
57B PHE* 1.3 73.1 - - - +
59B LYS* 1.3 57.5 + - - +
61B MET* 4.0 1.1 - - - +
62B ALA* 2.9 32.1 + - - +
67B LEU* 4.2 1.2 - - - +
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Residues in contact with LYS 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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9A GLU* 4.6 16.9 + - - -
77A ILE* 5.5 3.4 - - + +
78A ALA* 4.8 15.5 - - - +
35B LEU* 3.5 19.4 - - + +
55B ILE* 3.0 41.3 + - + +
56B GLU* 3.8 8.3 - - + +
58B ALA* 1.3 74.6 - - + +
60B TRP* 1.3 57.5 + - - +
62B ALA* 3.3 4.8 + - - +
63B ALA* 2.9 31.9 + - - +
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Residues in contact with TRP 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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17B LEU* 3.1 54.0 + - + +
31B LEU* 3.5 20.8 - - + +
35B LEU* 3.8 26.6 - - + +
41B PHE* 4.0 15.9 - + - -
42B VAL* 3.7 29.4 - - + -
45B VAL* 3.5 40.2 - - + -
46B GLU* 3.6 18.2 - - + -
52B LEU* 4.3 6.3 - - + -
56B GLU 2.8 18.1 + - - +
57B PHE* 3.3 7.4 + - - +
59B LYS* 1.3 75.3 - - - +
61B MET* 1.3 68.7 + - - +
63B ALA* 3.3 2.8 + - - +
64B CYS* 2.9 37.2 + - - -
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Residues in contact with MET 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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17B LEU* 4.0 22.4 - - - -
20B ALA* 3.8 26.7 - - + -
57B PHE* 2.9 44.8 + - + +
58B ALA* 4.1 2.9 - - - +
60B TRP* 1.3 78.3 - - + +
62B ALA* 1.3 61.5 + - - +
64B CYS* 3.2 2.7 + - - -
65B GLU 3.1 4.0 + - - -
66B GLY* 2.9 37.7 + - - +
67B LEU* 4.5 4.5 - - + -
69B VAL* 3.6 30.7 - - + -
70B VAL* 4.0 17.5 - - + -
73B ILE* 3.8 16.2 - - + -
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Residues in contact with ALA 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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78A ALA* 3.5 23.8 - - + +
58B ALA 2.9 18.8 + - - +
59B LYS* 3.8 4.5 - - - +
61B MET* 1.3 75.9 - - - +
63B ALA* 1.3 59.2 + - - +
65B GLU* 3.0 20.7 + - - +
66B GLY 4.9 0.2 - - - +
67B LEU* 3.8 21.5 - - + +
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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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26B LEU* 3.7 2.3 - - - +
31B LEU* 3.6 22.7 - - + -
34B ARG* 2.8 51.9 + - + +
35B LEU* 3.7 12.3 - - + -
59B LYS 2.9 18.2 + - - +
60B TRP 3.3 1.1 + - - +
62B ALA* 1.3 75.5 - - - +
64B CYS* 1.3 57.7 + - - +
65B GLU* 3.3 1.0 + - - +
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Residues in contact with CYS 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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20B ALA* 3.6 25.1 - - + +
21B ARG* 3.6 29.2 - - - -
24B ALA* 3.5 20.3 + - - +
26B LEU* 4.4 1.8 - - - -
31B LEU* 3.8 18.8 - - - -
60B TRP* 2.9 35.3 + - - +
61B MET 3.8 4.9 - - - +
62B ALA 3.2 0.4 - - - -
63B ALA* 1.3 73.5 - - - +
65B GLU* 1.3 72.6 + - - +
66B GLY* 3.2 1.9 + - - +
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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