Contacts of the strand formed by residues 12 - 16 (chain B) 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 VAL 12 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLY 4.4 1.6 - - - +
11B LEU* 1.3 73.7 - - - +
13B ALA* 1.3 66.7 + - - +
14B VAL* 5.6 0.4 - - + -
36B THR* 3.3 24.0 - - - +
38B VAL* 5.1 4.9 - - + -
78B ALA* 5.2 2.2 - - + +
82B PHE* 3.8 34.5 - - + +
84B ARG* 3.4 44.9 - - + +
85B ILE* 3.9 6.8 - - + +
86B ASP* 2.8 39.9 + - - +
87B VAL* 3.0 8.7 + - - +
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Residues in contact with ALA 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 5.4 1.3 - - + +
12B VAL* 1.3 77.5 - - - +
14B VAL* 1.3 64.5 + - - +
15B ILE* 4.0 10.7 + - + +
30B LEU* 4.5 19.3 - - + -
35B ALA* 5.8 2.0 - - + -
36B THR 3.0 14.1 + - - +
37B ALA* 3.3 6.1 - - + +
38B VAL* 2.9 24.4 + - - +
87B VAL* 3.2 27.1 - - + +
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Residues in contact with VAL 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 5.6 1.1 - - + -
13B ALA* 1.3 74.6 - - - +
15B ILE* 1.3 62.0 + - - +
16B THR* 4.1 5.6 + - + +
38B VAL* 3.7 17.7 - - + +
40B LEU* 4.3 24.5 - - + -
74B ALA* 6.2 1.1 - - + -
75B LEU* 4.3 17.3 - - + -
78B ALA* 4.2 18.2 - - + -
85B ILE* 4.1 32.8 - - + -
87B VAL 3.0 10.4 + - - +
88B ALA* 3.4 8.3 - - + +
89B VAL* 2.9 26.2 + - - +
128B VAL* 5.8 3.8 - - + -
132B VAL* 5.7 0.7 - - + -
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Residues in contact with ILE 15 (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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13B ALA* 4.5 10.1 - - + +
14B VAL* 1.3 77.4 - - - +
16B THR* 1.4 65.7 + - - +
18B GLY* 3.3 12.8 + - - -
23B GLY* 3.6 32.1 - - - +
26B THR* 4.1 13.0 - - + +
27B ALA* 3.7 38.1 - - + +
30B LEU* 4.6 8.1 - - + -
37B ALA* 4.6 10.5 - - + -
38B VAL 3.0 11.9 + - - +
39B LEU* 3.9 2.6 - - + -
40B LEU* 3.1 23.1 + - - -
89B VAL* 3.6 23.6 - - + +
91B CYS* 4.8 1.8 - - - -
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Residues in contact with THR 16 (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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14B VAL* 5.1 4.9 - - + +
15B ILE* 1.4 73.4 - - - +
17B GLY* 1.3 64.8 + - - +
18B GLY 3.3 0.5 + - - -
40B LEU* 3.3 22.2 - - + -
65B VAL* 4.1 9.5 - - + +
89B VAL 2.9 8.9 + - - +
90B ASN* 3.5 21.8 + - - +
91B CYS* 3.1 31.4 + - - +
92B ALA* 3.0 26.4 + - - +
128B VAL* 4.0 26.5 - - + -
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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
------------------------------------------------------------
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