Contacts of the strand formed by residues 36 - 41 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLY* 4.9 4.6 + - - +
11A LEU 3.0 7.5 + - - +
12A VAL* 3.3 33.6 - - + +
13A ALA* 2.9 28.5 + - - +
34A GLY 5.3 1.6 - - - +
35A ALA* 1.3 78.4 - - - +
37A ALA* 1.3 61.0 + - - +
57A ASN* 3.4 33.9 - - + +
82A PHE* 4.1 27.7 - - + -
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Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA* 3.4 7.4 - - + +
15A ILE* 4.6 9.4 - - + -
27A ALA* 4.4 16.6 - - + -
30A LEU* 5.8 3.6 - - + -
31A VAL* 3.7 22.4 - - + +
36A THR* 1.3 75.6 - - - +
38A VAL* 1.3 63.8 + - - +
39A LEU* 4.1 2.0 - - + -
57A ASN 3.0 7.7 + - - +
58A CYS* 3.3 14.2 - - - -
59A ILE* 3.1 23.4 + - - +
82A PHE* 4.7 1.5 - - - -
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 5.1 3.6 - - + -
13A ALA 2.9 15.2 + - - +
14A VAL* 3.7 15.1 - - + +
15A ILE* 3.0 26.2 + - - +
37A ALA* 1.3 75.4 - - - +
39A LEU* 1.3 64.7 + - - +
40A LEU* 3.6 1.6 + - + +
59A ILE* 3.5 17.5 - - + +
61A ALA* 4.1 25.8 - - + -
74A ALA* 4.9 3.8 - - + +
77A LEU* 5.9 0.2 - - + -
78A ALA* 3.7 30.1 - - + +
82A PHE* 3.9 24.0 - - + -
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 3.8 7.4 - - + -
18A GLY* 3.7 32.3 - - - +
19A ALA* 4.8 3.1 - - - +
24A LEU* 4.9 2.7 - - + -
27A ALA* 3.6 31.4 - - + -
37A ALA* 4.7 2.7 - - + -
38A VAL* 1.3 74.4 - - - +
40A LEU* 1.3 59.5 + - - +
41A ASP* 4.0 0.4 - - + -
47A GLY 4.0 19.5 - - - +
50A GLU* 4.3 10.1 - - + -
51A ALA* 4.1 10.1 - - + +
54A LEU* 5.4 0.7 - - + -
58A CYS* 3.8 26.7 - - - -
59A ILE 2.9 13.5 + - - +
60A PHE* 3.2 13.6 - - + -
61A ALA 3.0 26.6 + - - -
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 4.4 22.4 - - + -
15A ILE 3.0 13.0 + - - +
16A THR* 3.4 14.8 - - + -
17A GLY 2.9 27.7 + - - -
18A GLY 3.7 0.3 + - - -
38A VAL* 3.6 1.9 + - + -
39A LEU* 1.3 69.9 - - - +
41A ASP* 1.3 61.3 + - - +
61A ALA* 3.5 8.5 - - + +
63A ALA* 3.7 34.8 - - + +
65A VAL* 3.8 26.7 - - + +
71A VAL* 4.9 17.0 - - + +
74A ALA* 3.7 24.0 - - + -
75A LEU* 5.2 3.1 - - + -
128A VAL* 5.3 2.2 - - + -
301A NAD 4.6 1.0 + - + -
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Residues in contact with ASP 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLY* 3.3 10.9 - - - -
19A ALA* 3.2 30.6 + - + +
39A LEU* 3.9 2.5 + - + -
40A LEU* 1.3 74.0 - - - +
42A VAL* 1.3 76.3 + - - +
45A SER* 3.5 14.1 - - - +
60A PHE* 3.8 8.7 - - + -
61A ALA 3.6 3.4 + - - -
62A PRO* 3.2 6.6 - - - +
63A ALA 2.9 26.0 + - - -
301A NAD 2.5 59.6 + - - -
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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