Contacts of the helix formed by residues 21 - 30 (chain S) in PDB entry 3SDI
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 LEU 21 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S THR* 3.9 9.2 - - + +
14S THR 3.6 17.9 - - - +
15S PHE* 3.5 30.7 - - + -
19S GLY 5.3 0.4 - - - +
20S ARG* 1.3 73.5 - - - +
22S PHE* 1.3 64.4 + - - +
23S GLN 3.4 2.0 - - - -
24S VAL* 3.2 31.3 + - + +
25S GLU* 3.1 24.3 + - - +
124S THR* 4.5 5.2 - - - +
81T LEU* 4.0 24.9 - - + -
130T ARG* 3.8 32.5 - - - +
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Residues in contact with PHE 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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8S TYR* 4.7 17.4 + + + +
9S ASP* 3.7 25.1 - - + -
11S ASP 5.8 0.8 + - - -
14S THR 4.9 3.0 + - - -
16S SER* 3.6 32.8 - - - -
18S THR* 5.5 0.4 - - - -
20S ARG* 3.3 49.1 + - + -
21S LEU* 1.3 72.1 - - - +
23S GLN* 1.3 53.6 + - - +
25S GLU* 2.9 12.7 + - - -
26S TYR* 2.7 68.4 + + + -
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Residues in contact with GLN 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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13R SER 4.5 2.3 - - - +
14R THR* 3.5 14.3 - - - +
15R PHE* 2.9 60.5 + - - +
9S ASP* 3.0 29.0 + - - +
10S GLY 4.5 0.4 - - - -
11S ASP* 3.8 24.1 + - - +
12S THR* 3.9 24.7 - - + +
21S LEU 3.4 0.4 - - - -
22S PHE* 1.3 77.2 - - - +
24S VAL* 1.3 56.0 + - - +
26S TYR* 3.6 12.0 + - - +
27S ALA* 3.0 26.9 + - - +
130S ARG* 5.6 0.3 - - - +
131S PRO* 3.9 8.8 - - + +
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Residues in contact with VAL 24 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S THR* 3.7 25.4 - - + -
21S LEU* 3.2 30.6 + - + +
22S PHE 3.1 0.8 - - - -
23S GLN* 1.3 72.6 - - - +
25S GLU* 1.3 68.3 + - + +
27S ALA* 3.1 4.9 + - + +
28S LEU* 2.9 28.1 + - + +
124S THR* 4.2 10.5 - - + -
131S PRO* 4.0 12.3 - - + -
153S PRO 4.9 2.2 - - - +
154S SER* 3.8 36.1 - - - +
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Residues in contact with GLU 25 (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 ARG* 2.9 62.9 + - - +
21S LEU 3.1 10.9 + - - +
22S PHE* 2.9 18.9 + - + +
24S VAL* 1.3 79.2 - - + +
26S TYR* 1.3 67.3 + - + +
28S LEU* 3.3 18.6 - - + +
29S GLU* 3.3 22.0 + - - +
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Residues in contact with TYR 26 (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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15R PHE* 3.6 21.8 - - + -
16R SER 3.3 26.2 - - - +
17R PRO* 3.7 34.3 - - + +
19R GLY* 3.3 14.2 - - - -
9S ASP* 2.9 40.9 + - + +
22S PHE* 2.7 49.0 + + + +
23S GLN* 3.8 11.0 - - - +
25S GLU* 1.3 73.9 - - + +
27S ALA* 1.3 61.6 + - - +
29S GLU* 3.0 27.7 + - - +
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Residues in contact with ALA 27 (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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15R PHE* 3.6 28.2 - - + -
23S GLN 3.0 15.6 + - - +
24S VAL* 3.1 8.7 + - + +
26S TYR* 1.3 76.8 - - - +
28S LEU* 1.3 61.7 + - - +
29S GLU 3.2 1.0 + - - -
30S ALA* 3.2 18.7 + - - +
31S ILE* 4.1 4.3 + - - +
131S PRO* 3.8 9.6 - - + -
132S TYR 3.4 22.7 - - - +
133S GLY* 4.0 8.7 - - - -
153S PRO* 4.8 3.1 - - + -
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Residues in contact with LEU 28 (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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24S VAL* 2.9 18.2 + - + +
25S GLU* 3.3 21.8 - - + +
27S ALA* 1.3 75.7 - - - +
29S GLU* 1.3 61.0 + - - +
31S ILE* 3.3 28.0 - - + +
32S LYS* 3.6 16.2 - - - -
152S GLN* 4.5 14.8 - - + +
153S PRO* 4.1 13.7 - - + -
154S SER* 3.8 38.6 - - - +
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Residues in contact with GLU 29 (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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17R PRO 3.4 23.6 - - - +
18R GLU* 4.0 15.4 - - - +
25S GLU 3.3 9.9 + - - +
26S TYR* 3.0 18.9 + - - +
28S LEU* 1.3 73.6 - - - +
30S ALA* 1.3 60.8 + - - +
31S ILE 3.0 6.8 + - - -
32S LYS* 3.1 50.1 + - - +
33S GLN* 3.7 4.0 + - - +
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Residues in contact with ALA 30 (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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15R PHE* 4.9 5.2 - - + -
18R GLU 4.7 2.0 - - - -
19R GLY* 3.2 28.8 - - - +
26S TYR 3.6 2.0 + - - -
27S ALA 3.2 14.1 + - - +
29S GLU* 1.3 77.3 - - - +
31S ILE* 1.3 62.3 + - - +
33S GLN* 3.5 17.0 + - - +
34S GLY 3.7 2.9 + - - -
80S GLY* 3.6 15.3 - - - -
81S LEU* 5.0 7.0 - - + +
133S GLY* 3.9 17.9 - - - +
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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