Contacts of the helix formed by residues 12 - 19 (chain E) 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 LYS 12 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8E ILE 3.3 0.4 + - - -
9E PRO 2.9 12.4 + - - +
10E LEU 4.3 11.2 - - - +
11E ILE* 1.3 80.0 - - - +
13E ALA* 1.3 64.0 + - - +
14E ASP* 3.3 14.8 - - - -
15E LYS* 3.4 35.9 + - + +
16E VAL* 3.5 5.7 + - - +
255E THR* 5.2 4.8 + - - -
267E LEU* 6.2 1.6 - - - -
269E ASN* 3.2 44.1 - - + +
270E VAL* 4.4 1.6 - - - -
271E GLU* 4.0 17.4 + - + +
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Residues in contact with ALA 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ILE* 3.0 24.1 + - + +
11E ILE* 3.1 22.9 - - + -
12E LYS* 1.3 77.2 - - - +
14E ASP* 1.3 67.7 + - - +
16E VAL* 3.2 4.7 + - - +
17E GLN* 3.0 27.6 + - - +
84E VAL* 4.2 20.6 - - + +
233E LEU* 3.9 10.8 - - + +
270E VAL* 4.5 5.6 - - + -
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Residues in contact with ASP 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 6.1 0.7 - - + -
8E ILE* 3.7 18.5 + - + +
9E PRO* 3.5 28.3 - - + +
12E LYS* 3.5 17.0 - - - -
13E ALA* 1.3 80.9 - - - +
15E LYS* 1.3 83.7 + - - +
17E GLN* 3.3 9.8 + - - +
18E ALA* 2.9 30.0 + - - +
82E LEU* 6.4 0.4 - - + -
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Residues in contact with LYS 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E LYS* 3.4 36.1 - - + +
13E ALA 3.2 0.4 - - - -
14E ASP* 1.3 96.8 + - - +
16E VAL* 1.3 64.7 + - - +
18E ALA* 3.3 9.5 + - - +
19E GLN* 3.0 25.5 + - - +
271E GLU* 3.9 31.4 - - + +
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Residues in contact with VAL 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E LYS 3.5 3.5 + - - +
13E ALA 3.2 8.7 + - - +
15E LYS* 1.3 75.6 - - - +
17E GLN* 1.3 63.5 + - - +
19E GLN* 3.1 34.9 + - - +
21E PHE* 3.3 32.1 + - + +
233E LEU* 4.0 25.8 - - + +
237E LYS* 5.4 0.7 - - + -
270E VAL* 3.7 14.4 - - + +
271E GLU* 3.7 32.5 - - - +
274E ALA* 4.3 11.7 - - + -
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Residues in contact with GLN 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ILE* 4.6 5.0 - - - +
13E ALA 3.0 22.7 + - - +
14E ASP* 3.5 8.6 - - - +
16E VAL* 1.3 73.1 - - - +
18E ALA* 1.3 55.6 + - - +
20E GLY* 2.8 26.9 + - - -
21E PHE 3.3 17.5 + - - +
22E LYS* 3.6 28.2 - - + -
76E ASP* 4.9 4.2 - - - +
82E LEU* 3.7 22.0 - - - +
83E GLY 3.2 19.0 + - - -
84E VAL* 2.9 30.4 + - - +
86E PRO* 3.6 14.6 - - + +
233E LEU* 4.3 1.6 - - + -
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Residues in contact with ALA 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E ASP 2.9 18.3 + - - +
15E LYS* 3.4 9.0 - - - +
16E VAL 3.2 0.2 - - - -
17E GLN* 1.3 77.3 - - - +
19E GLN* 1.3 60.1 + - - +
20E GLY* 3.4 0.9 + - - -
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Residues in contact with GLN 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E LYS* 3.0 16.6 + - - +
16E VAL* 3.2 31.4 - - - +
18E ALA* 1.3 76.0 - - - +
20E GLY* 1.3 57.6 + - - +
21E PHE* 3.6 26.0 - - + -
237E LYS* 3.0 31.8 + - - +
271E GLU* 4.3 22.2 + - - +
274E ALA* 5.8 0.2 - - - +
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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