Contacts of the helix formed by residues 17 - 29 (chain I) in PDB entry 1CSE
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 17 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15I GLY 5.1 2.0 - - - +
16I LYS* 1.3 77.6 - - - +
18I VAL* 1.3 59.5 + - - +
19I ASP* 3.3 8.5 + - - +
20I GLN* 3.1 39.0 + - - +
21I ALA* 2.7 27.5 + - - +
61I ASN* 3.3 14.4 - - - +
62I VAL* 4.4 8.7 - - + +
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Residues in contact with VAL 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I LYS 4.0 0.2 + - - -
17I THR* 1.3 72.5 - - - +
19I ASP* 1.3 59.6 + - - +
21I ALA* 3.1 7.1 + - - +
22I ARG* 2.9 61.1 + - - +
36I PHE* 3.8 17.0 - - + -
56I TYR* 3.5 48.5 - - + -
61I ASN* 3.1 25.0 + - + +
63I VAL* 4.4 6.7 - - + -
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Residues in contact with ASP 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I THR* 3.1 7.5 + - - +
18I VAL* 1.3 78.4 - - - +
20I GLN* 1.4 58.9 - - + +
22I ARG* 3.2 27.0 + - - +
23I GLU* 3.0 29.7 + - - +
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Residues in contact with GLN 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I GLY 4.8 0.5 - - - +
16I LYS* 3.6 25.0 - - + +
17I THR* 3.1 44.0 + - - +
19I ASP* 1.4 77.2 - - + +
21I ALA* 1.4 56.9 + - - +
23I GLU* 3.5 15.5 + - - +
24I TYR* 3.0 27.7 + - - +
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Residues in contact with ALA 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I VAL* 4.1 14.8 - - + -
16I LYS* 4.2 10.7 - - + +
17I THR 2.7 19.9 + - - +
18I VAL 3.5 4.7 - - - +
20I GLN* 1.4 74.5 - - - +
22I ARG* 1.3 64.7 + - - +
24I TYR* 3.2 3.4 + - - +
25I PHE* 3.0 31.7 + - + -
36I PHE* 3.6 20.6 - - + -
63I VAL* 3.7 17.0 - - + -
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Residues in contact with ARG 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I VAL* 2.9 36.2 + - - +
19I ASP* 3.2 29.4 + - - +
21I ALA* 1.3 74.4 - - - +
23I GLU* 1.3 62.3 + - - +
25I PHE* 3.3 2.4 + - - +
26I THR* 3.1 29.6 + - - +
36I PHE* 3.5 43.0 - - - +
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Residues in contact with GLU 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I ASP 3.0 9.9 + - - +
20I GLN* 3.5 18.2 - - - +
22I ARG* 1.3 78.5 - - - +
24I TYR* 1.3 60.7 + - - +
26I THR* 3.4 5.1 + - - -
27I LEU* 2.9 52.0 + - + +
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Residues in contact with TYR 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I PHE* 4.8 2.7 - + - -
12I GLU* 2.6 37.7 + - + +
13I VAL* 3.5 28.7 - - + -
16I LYS* 4.0 25.1 - - - -
20I GLN 3.0 14.3 + - - +
21I ALA* 3.2 8.5 + - - +
23I GLU* 1.3 77.8 + - - +
25I PHE* 1.4 67.4 + + - +
27I LEU* 4.9 3.4 - - - -
28I HIS* 2.9 64.8 + + - +
29I TYR* 3.8 25.1 + + - -
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Residues in contact with PHE 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I PHE* 3.9 39.7 - + + -
13I VAL* 3.8 34.1 - - + -
21I ALA 3.0 27.8 + - - +
22I ARG* 4.1 3.1 - - - +
24I TYR* 1.4 80.8 - + - +
26I THR* 1.3 57.3 + - - +
29I TYR* 2.7 56.4 + + + +
32I TYR* 5.6 1.3 - + + -
34I VAL* 3.9 34.8 - - + -
36I PHE* 4.1 6.7 - + + -
52I VAL* 4.1 14.4 - - + -
54I VAL* 3.6 25.8 - - + -
67I PRO* 4.4 2.9 - - + -
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Residues in contact with THR 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I ARG* 3.1 22.9 + - - +
23I GLU* 3.8 5.8 - - - +
25I PHE* 1.3 76.4 - - - +
27I LEU* 1.4 70.2 + - + +
30I PRO* 3.8 21.0 - - - +
34I VAL* 5.7 3.7 - - - +
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Residues in contact with LEU 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I GLU* 2.9 44.0 + - + +
24I TYR* 5.3 0.7 - - - -
26I THR* 1.4 87.9 - - + +
28I HIS* 1.3 85.2 + - + +
30I PRO* 4.3 5.7 - - - +
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Residues in contact with HIS 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I TYR* 2.9 53.0 + + - +
27I LEU* 1.3 103.4 + - + +
29I TYR* 1.3 82.7 - - + +
30I PRO* 3.3 9.2 - - - +
31I GLN* 4.4 1.9 + - - +
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Residues in contact with TYR 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I LYS* 3.1 35.1 + - - -
10I PHE* 3.6 22.3 - + - -
12I GLU* 4.6 2.1 + - - -
24I TYR* 3.8 26.2 + + - -
25I PHE* 2.7 36.8 + + + +
28I HIS* 1.3 100.7 - - + +
30I PRO* 1.3 59.7 - - - +
31I GLN* 2.9 23.5 + - - -
32I TYR* 3.1 44.1 + + + +
34I VAL* 5.6 1.4 - - - +
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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