Contacts of the strand formed by residues 36 - 41 (chain D) in PDB entry 1E3S
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 36 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D GLY* 4.9 3.7 + - - +
11D LEU 3.0 7.5 + - - +
12D VAL* 3.3 33.9 - - - +
13D ALA* 2.9 29.0 + - - +
34D GLY 5.4 1.6 - - - +
35D ALA* 1.3 76.7 - - - +
37D ALA* 1.3 61.1 + - - +
57D ASN* 3.4 34.3 - - + +
82D PHE* 4.1 26.5 - - + -
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Residues in contact with ALA 37 (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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13D ALA* 3.4 8.1 - - + +
15D ILE* 4.5 9.6 - - + -
27D ALA* 4.4 16.6 - - + -
30D LEU* 5.8 3.4 - - + -
31D VAL* 3.8 21.5 - - + +
35D ALA 4.2 0.2 - - - -
36D THR* 1.3 75.8 - - - +
38D VAL* 1.3 65.3 + - - +
39D LEU* 4.1 1.8 - - + -
57D ASN 3.0 7.7 + - - -
58D CYS* 3.2 14.8 - - - -
59D ILE* 3.1 24.1 + - - +
82D PHE* 4.6 1.9 - - - -
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Residues in contact with VAL 38 (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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12D VAL* 5.2 3.1 - - + -
13D ALA 2.9 13.7 + - - +
14D VAL* 3.6 19.1 - - + +
15D ILE* 3.0 26.5 + - - +
37D ALA* 1.3 75.5 - - - +
39D LEU* 1.3 65.6 + - - +
40D LEU* 3.6 1.6 + - + +
59D ILE* 3.5 17.7 - - + +
61D ALA* 4.0 25.6 - - + -
74D ALA* 5.0 4.0 - - + +
77D LEU* 6.0 0.2 - - + -
78D ALA* 3.7 27.6 - - + +
82D PHE* 3.9 23.8 - - + -
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Residues in contact with LEU 39 (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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15D ILE* 3.8 6.5 - - + -
18D GLY* 3.8 33.7 - - - +
19D ALA* 4.8 1.1 - - - +
24D LEU* 5.0 2.7 - - + -
27D ALA* 3.5 32.1 - - + -
37D ALA* 4.8 2.5 - - + -
38D VAL* 1.3 74.1 - - - +
40D LEU* 1.3 59.8 + - - +
41D ASP 3.9 0.4 - - - -
47D GLY* 4.1 11.4 - - - +
50D GLU* 4.3 8.3 - - + -
51D ALA* 4.0 20.9 - - + +
54D LEU* 5.5 0.4 - - + -
58D CYS* 3.7 25.6 - - - -
59D ILE 2.9 15.0 + - - +
60D PHE* 3.4 11.5 - - + -
61D ALA* 2.9 30.0 + - - +
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Residues in contact with LEU 40 (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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14D VAL* 4.2 22.0 - - + -
15D ILE 3.1 11.4 + - - +
16D THR* 3.4 13.4 - - + -
17D GLY 2.8 27.2 + - - -
18D GLY 3.6 1.1 + - - -
38D VAL* 3.6 2.1 + - + -
39D LEU* 1.3 70.3 - - - +
41D ASP* 1.3 61.3 + - - +
61D ALA* 3.4 8.3 - - + +
63D ALA* 3.7 33.9 - - + +
65D VAL* 3.9 26.0 - - + +
71D VAL* 4.9 17.3 - - + -
74D ALA* 3.7 24.0 - - + -
75D LEU* 5.1 3.8 - - + -
128D VAL* 5.4 2.2 - - + -
301D NAD 4.8 0.7 - - + -
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Residues in contact with ASP 41 (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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17D GLY* 3.3 11.3 - - - -
19D ALA* 3.2 31.4 + - + +
39D LEU* 3.9 2.5 + - + -
40D LEU* 1.3 75.1 - - - +
42D VAL* 1.3 77.3 + - - +
45D SER* 3.7 14.9 - - - +
60D PHE* 3.7 8.6 - - + -
61D ALA 3.6 4.0 + - - -
62D PRO* 3.3 6.2 - - - +
63D ALA 3.0 26.1 + - - -
301D NAD 2.7 56.5 + - - -
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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