Contacts of the strand formed by residues 16 - 23 (chain S) in PDB entry 1ESV
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 GLY 16 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S GLU 3.5 2.6 + - - -
15S PRO* 1.3 75.2 - - - +
17S LEU* 1.3 60.5 + - - -
18S GLN* 4.4 1.8 - - - -
47S LEU 3.9 0.4 - - - +
48S LYS* 3.0 17.5 - - - +
49S THR* 2.7 37.8 + - - -
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Residues in contact with LEU 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16S GLY* 1.3 73.0 - - - -
18S GLN* 1.3 65.9 + - - +
19S ILE* 3.3 41.1 - - + -
35S TYR* 3.3 29.0 + - + -
46S ILE* 3.6 24.7 - - + -
47S LEU 3.6 4.3 - - - +
48S LYS* 3.5 26.0 - - + -
109S TYR* 4.2 24.7 - - + +
110S PHE* 4.8 6.1 - - + -
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Residues in contact with GLN 18 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S LYS* 3.0 33.7 + - - +
11S ALA* 3.8 3.5 - - - +
12S GLY* 2.9 26.0 + - - -
13S LYS 5.2 0.6 - - - +
14S GLU 5.3 3.7 - - - +
16S GLY 5.6 0.9 - - - -
17S LEU* 1.3 80.1 - - - +
19S ILE* 1.3 63.2 + - - +
20S TRP* 3.6 23.7 - - + -
35S TYR* 3.8 4.9 - - - +
45S VAL 3.9 0.5 - - - +
46S ILE* 3.5 4.2 - - - +
47S LEU* 2.9 46.0 + - - +
49S THR* 4.7 1.7 + - - -
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Residues in contact with ILE 19 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17S LEU* 3.3 26.7 - - + -
18S GLN* 1.3 75.1 - - - +
20S TRP* 1.3 75.5 + - - +
29S PRO* 3.9 1.0 - - - +
30S VAL* 2.9 33.6 + - + +
35S TYR* 3.3 53.2 + - + -
36S GLY 4.3 1.8 - - - +
38S PHE* 4.4 7.2 - - + -
44S TYR* 4.2 17.0 - - + -
45S VAL 3.6 2.5 - - - -
46S ILE* 4.0 21.5 - - + -
110S PHE* 4.1 16.4 - - + -
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Residues in contact with TRP 20 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7S GLU* 2.9 42.4 + - + +
10S LYS* 5.4 0.7 - - + -
11S ALA* 3.8 31.4 - - + -
18S GLN* 3.6 37.7 - - + -
19S ILE* 1.3 74.9 + - - +
21S ARG* 1.3 59.4 + - - +
27S LEU* 3.6 28.5 - - + -
28S VAL 3.4 7.9 - - - +
29S PRO* 3.6 25.9 - - + +
30S VAL* 4.2 1.3 - - - +
44S TYR* 3.2 11.8 - - - +
45S VAL* 2.7 59.6 + - + +
47S LEU* 3.7 26.5 - - + -
84S LEU* 3.9 14.6 - - + -
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Residues in contact with ARG 21 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20S TRP* 1.3 75.1 - - - +
22S VAL* 1.3 76.1 + - - +
23S GLU* 2.7 36.5 + - + +
27S LEU* 4.8 1.1 - - - -
28S VAL* 2.8 34.1 + - - +
30S VAL* 3.9 10.9 - - + +
39S PHE* 3.2 27.5 - - - -
42S ASP* 3.1 30.2 + - + -
43S ALA 3.8 10.1 - - - +
44S TYR* 3.7 27.3 + - + -
120S GLY* 4.7 0.8 - - - -
121S VAL* 4.5 15.7 - - - +
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Residues in contact with VAL 22 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21S ARG* 1.3 77.2 - - - +
23S GLU* 1.3 65.6 + - - +
24S LYS 4.9 0.4 - - - +
25S PHE* 4.4 11.2 - - - +
26S ASP 3.3 9.4 - - - +
27S LEU* 4.6 4.5 - - + +
42S ASP* 5.1 0.3 - - - +
43S ALA 3.0 20.5 + - - +
45S VAL* 4.8 2.9 - - + -
72S ASP* 4.8 0.9 - - - +
73S GLU* 4.0 38.5 - - + +
76S ALA* 3.8 21.3 - - + -
77S ALA* 4.0 13.9 - - + -
80S PHE* 4.0 23.8 - - + -
121S VAL* 3.7 12.0 - - - +
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Residues in contact with GLU 23 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21S ARG* 2.7 52.0 + - - +
22S VAL* 1.3 79.9 - - - +
24S LYS* 1.3 74.2 + - + +
25S PHE 3.3 0.4 - - - -
26S ASP* 2.8 26.8 + - - +
28S VAL* 3.6 36.6 - - + +
30S VAL* 5.9 0.2 - - - +
121S VAL* 4.5 17.2 - - + +
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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