Contacts of the helix formed by residues 8 - 20 (chain A) in PDB entry 2ETK
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 GLU 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A SER* 3.2 5.8 - - - -
7A PHE* 1.3 111.9 + - - +
9A THR* 1.3 55.3 + - - +
10A ARG 3.2 1.3 - - - -
11A PHE* 3.1 8.7 + - + +
12A GLU* 2.8 48.8 + - + +
98B THR* 5.2 2.3 - - - +
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Residues in contact with THR 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A SER* 3.4 26.9 + - - -
8A GLU* 1.3 76.8 - - - +
10A ARG* 1.3 53.1 + - + +
12A GLU* 3.2 12.1 + - + +
13A LYS* 2.7 60.2 + - + +
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Residues in contact with ARG 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A SER 3.3 26.9 + - - +
7A PHE* 4.9 13.2 - - + +
8A GLU 3.2 0.2 - - - -
9A THR* 1.3 76.0 - - + +
11A PHE* 1.3 59.5 + - - +
13A LYS* 4.0 2.3 - - + +
14A MET* 3.0 31.5 + - - +
68B ASP 3.4 1.4 + - - -
69B LEU* 3.0 52.8 + - + +
70B ARG 3.0 27.9 + - - -
71B MET* 4.4 0.6 - - - +
72B LYS* 3.2 19.8 - - - +
75B ASP* 3.1 32.7 + - - -
95B HIS* 6.1 1.4 - - - -
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Residues in contact with PHE 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.8 21.6 + + - +
8A GLU* 3.1 12.8 + - + +
10A ARG* 1.3 78.2 - - - +
12A GLU* 1.3 61.3 + - + +
14A MET* 3.8 5.9 + - - +
15A ASP* 3.2 37.5 + - - +
400B TYR* 5.0 21.3 - + + -
401B SER 5.2 7.0 - - - -
402B ASN* 4.5 19.3 - - - -
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Residues in contact with GLU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLU* 2.8 30.8 + - + +
9A THR* 3.5 9.2 + - - +
11A PHE* 1.3 78.7 - - + +
13A LYS* 1.3 59.9 + - + +
15A ASP* 3.0 9.3 + - - +
16A ASN* 2.8 38.7 + - - +
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Residues in contact with LYS 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A THR* 2.7 42.1 + - + +
10A ARG* 4.0 5.6 - - + +
12A GLU* 1.3 73.6 - - + +
14A MET* 1.3 61.4 + - - +
16A ASN* 3.6 12.2 + - - +
17A LEU* 3.3 32.3 + - + +
65B LYS* 3.3 33.9 - - - +
69B LEU* 4.2 24.0 - - + +
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Residues in contact with MET 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG 3.0 18.2 + - - +
11A PHE* 3.8 7.4 - - - +
13A LYS* 1.3 77.1 - - - +
15A ASP* 1.3 58.2 + - - +
17A LEU* 3.2 6.4 + - - +
18A LEU* 3.1 45.1 + - + +
31B LEU* 4.2 19.3 - - + -
66B ILE* 3.7 34.5 - - + +
69B LEU* 3.6 32.4 - - + +
70B ARG* 3.6 25.8 - - + +
400B TYR* 6.3 2.9 - - + -
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Residues in contact with ASP 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 3.2 28.8 + - - +
12A GLU* 3.0 12.4 + - - +
14A MET* 1.3 75.8 - - - +
16A ASN* 1.3 66.0 + - - +
17A LEU 3.2 0.4 - - - -
18A LEU* 4.2 18.1 - - - +
19A ARG* 3.0 66.4 + - - +
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Residues in contact with ASN 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLU* 2.8 24.9 + - - +
13A LYS* 3.6 19.8 - - - +
14A MET 3.3 0.2 - - - -
15A ASP* 1.3 78.9 - - - +
17A LEU* 1.3 64.1 + - + +
18A LEU 3.4 0.2 - - - -
19A ARG* 4.1 9.5 - - - +
20A ASP* 3.1 33.2 + - - +
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 3.3 16.4 - - + +
14A MET* 3.2 11.3 + - - +
15A ASP 3.2 0.4 - - - -
16A ASN* 1.3 85.6 - - + +
18A LEU* 1.3 59.4 + - - +
19A ARG 3.4 0.9 - - - -
20A ASP* 6.3 0.2 - - + -
23A SER* 2.8 34.2 + - - +
25A VAL* 3.1 27.7 - - + +
26A ASN* 3.3 1.0 + - - -
62B THR* 5.2 5.2 - - + -
65B LYS* 4.8 26.9 - - + -
66B ILE* 3.7 27.8 - - + -
69B LEU* 4.8 6.7 - - + -
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Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A MET* 3.1 37.3 + - + +
15A ASP* 3.4 19.9 + - - +
16A ASN 3.4 0.2 - - - -
17A LEU* 1.3 77.6 - - - +
19A ARG* 1.3 61.9 + - + +
25A VAL 4.0 4.0 - - - +
26A ASN* 4.0 4.5 - - - +
27A SER* 3.3 17.6 + - - +
30A LEU* 3.6 30.1 - - + -
402A ASN* 3.0 17.4 + - - -
27B SER* 4.1 29.4 - - - +
28B ASP* 6.0 0.9 - - - +
31B LEU* 4.2 15.7 - - + -
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Residues in contact with ARG 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ASP* 3.0 57.5 + - - +
16A ASN* 4.7 9.1 - - - +
18A LEU* 1.3 83.5 - - + +
20A ASP* 1.3 68.6 + - - +
21A PRO* 3.1 8.3 - - - +
402A ASN* 3.3 20.5 + - - +
19B ARG* 5.7 9.0 - - - +
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Residues in contact with ASP 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ASN 3.1 21.5 + - - +
17A LEU 4.6 0.4 - - - -
19A ARG* 1.3 75.7 - - - +
21A PRO* 1.3 63.6 - - - +
22A LYS* 2.8 41.3 + - - +
23A SER* 3.0 20.9 + - - -
26A ASN* 2.8 28.4 + - - +
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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