Contacts of the helix formed by residues 4 - 17 (chain E) in PDB entry 2CFX
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 ASP 4 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2E LYS 3.8 2.2 + - - +
3E LEU* 1.3 74.7 - - - +
5E GLN* 1.3 63.7 + - - +
6E ILE* 3.1 14.1 + - - +
7E ASP* 3.1 21.5 + - - +
8E LEU* 3.2 15.1 + - - +
39E ARG* 3.0 42.3 + - - -
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Residues in contact with GLN 5 (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 ASP* 1.3 77.5 - - - +
6E ILE* 1.3 63.9 + - + +
8E LEU* 3.1 33.6 + - - +
9E ASN* 3.1 40.6 + - - +
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Residues in contact with ILE 6 (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 ASP* 3.1 6.7 + - - +
5E GLN* 1.3 78.0 - - + +
7E ASP* 1.3 56.8 + - - +
9E ASN* 3.2 15.6 + - - +
10E ILE* 3.0 28.3 + - + +
29E ILE* 4.3 13.9 - - + +
30E LYS 6.0 0.2 - - - +
31E LEU* 3.8 35.9 - - + -
39E ARG* 3.5 37.5 - - - +
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Residues in contact with ASP 7 (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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1E MET* 4.9 5.5 - - - +
2E LYS 4.2 3.8 - - - +
3E LEU* 3.7 19.8 - - + +
4E ASP* 3.1 29.1 + - - +
6E ILE* 1.3 77.7 - - - +
8E LEU* 1.3 63.8 + - - +
10E ILE* 3.4 8.5 + - - +
11E ILE* 3.2 29.3 + - - +
39E ARG* 2.9 38.5 + - - +
43E LEU* 4.2 21.7 - - + +
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Residues in contact with LEU 8 (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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3E LEU* 3.7 30.1 - - + -
4E ASP 3.2 12.3 + - - +
5E GLN* 3.1 31.5 + - - +
7E ASP* 1.3 77.2 - - - +
9E ASN* 1.3 57.7 + - - +
11E ILE* 3.5 5.7 + - + +
12E GLU* 2.9 45.8 + - + +
61F LEU* 4.3 13.0 - - + -
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Residues in contact with ASN 9 (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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5E GLN* 3.1 38.7 + - - +
6E ILE* 3.2 17.1 + - - +
8E LEU* 1.3 74.2 - - - +
10E ILE* 1.3 57.3 + - - +
12E GLU* 3.3 9.3 + - - +
13E GLU* 2.9 38.3 + - - +
29E ILE* 3.9 22.1 + - + +
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Residues in contact with ILE 10 (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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6E ILE* 3.0 18.1 + - + +
7E ASP* 3.6 12.6 - - - +
8E LEU 3.3 0.2 - - - -
9E ASN* 1.3 72.9 - - - +
11E ILE* 1.3 55.2 + - - +
13E GLU* 3.1 5.1 + - - +
14E LEU* 2.8 56.6 + - + +
25E LEU* 4.0 9.6 - - + +
29E ILE* 3.9 29.6 - - + -
31E LEU* 4.8 0.2 - - + -
36E VAL* 4.6 4.9 - - + -
39E ARG* 3.7 42.0 - - + -
40E VAL* 3.9 18.8 - - + +
43E LEU* 4.1 10.8 - - + -
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Residues in contact with ILE 11 (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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3E LEU* 4.3 6.5 - - + -
7E ASP 3.2 18.5 + - - +
8E LEU* 3.7 9.9 - - + +
10E ILE* 1.3 72.2 - - + +
12E GLU* 1.3 63.4 + - - +
14E LEU* 3.3 1.0 + - - +
15E LYS* 2.7 52.3 + - + +
43E LEU* 3.8 19.5 - - + -
48E ILE* 3.8 16.6 - - + -
49E ILE* 4.8 8.5 - - + -
54F LEU* 4.2 8.9 - - + +
56F VAL* 3.9 22.2 - - + -
61F LEU* 3.8 28.5 - - + -
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Residues in contact with GLU 12 (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 LEU* 2.9 42.7 + - + +
9E ASN* 3.3 10.0 + - - +
11E ILE* 1.3 75.1 - - - +
13E GLU* 1.3 68.2 + - - +
15E LYS* 3.5 32.2 + - - +
16E LYS* 3.1 23.6 + - - +
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Residues in contact with GLU 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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9E ASN* 2.9 13.5 + - - +
10E ILE 3.1 4.7 + - - +
12E GLU* 1.3 83.6 - - - +
14E LEU* 1.3 57.8 + - - +
16E LYS* 3.3 11.2 + - - +
17E ASP* 3.0 26.2 + - - +
20E LEU* 4.0 7.9 - - + +
25E LEU* 3.7 15.9 - - + -
28E LYS* 3.6 34.3 - - + -
29E ILE* 3.3 29.5 - - + +
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Residues in contact with LEU 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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10E ILE* 2.8 41.1 + - + +
11E ILE 4.9 0.2 - - - +
13E GLU* 1.3 70.4 - - - +
15E LYS* 1.4 65.4 + - - +
17E ASP 3.6 7.9 - - - +
18E SER* 3.1 50.2 + - - +
20E LEU* 4.3 21.8 - - + +
22E MET* 5.2 3.1 - - + -
25E LEU* 4.2 16.8 - - + -
40E VAL* 4.6 8.1 - - + -
49E ILE* 4.1 22.9 - - + -
52E TYR* 4.5 13.0 - - + -
52F TYR 3.9 0.2 - - - +
54F LEU* 3.9 19.5 - - + +
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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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11E ILE* 2.7 42.8 + - + +
12E GLU* 3.5 32.4 + - - +
14E LEU* 1.4 73.8 - - - +
16E LYS* 1.3 52.4 + - - +
51F GLN* 2.8 26.6 + - - -
52F TYR 3.5 2.1 - - - +
53F THR* 3.3 12.5 + - - +
54F LEU* 4.0 25.2 - - + +
56F VAL* 4.4 21.0 - - + +
58F GLN* 5.2 6.3 + - - +
61F LEU* 4.5 7.7 - - - +
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Residues in contact with LYS 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 GLU 3.1 14.5 + - - +
13E GLU* 3.8 14.6 - - - +
15E LYS* 1.3 74.2 - - - +
17E ASP* 1.3 63.7 + - + +
51F GLN* 3.3 27.6 + - - +
52F TYR 4.8 0.3 + - - -
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Residues in contact with ASP 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E GLU 3.0 14.4 + - - +
14E LEU* 3.2 4.6 - - - +
15E LYS 3.3 0.8 - - - -
16E LYS* 1.3 80.1 - - + +
18E SER* 1.3 58.7 + - - +
19E ARG* 2.8 59.6 + - - +
20E LEU* 3.3 37.9 + - + +
52F TYR* 3.3 9.4 - - - +
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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