Contacts of the helix formed by residues 4 - 20 (chain F) in PDB entry 4I6U
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 PHE 4 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E GLU* 3.3 13.8 + - - +
64E ASP* 6.0 0.4 - - - -
3F SER* 1.3 70.9 + - - +
5F LEU* 1.3 62.1 + - + +
7F SER* 2.8 25.0 + - - -
8F LYS* 3.0 50.7 + - + +
75F ILE* 3.9 38.1 - - + -
77F LYS* 4.0 12.3 - - - -
79F ASP* 4.8 9.2 - - - -
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Residues in contact with LEU 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E ILE* 3.8 28.3 - - + +
53E LEU* 4.1 20.9 - - + -
54E GLU* 2.9 37.8 + - + +
57E MET* 4.3 10.8 - - - -
64E ASP* 4.8 5.4 - - - +
68E PHE* 4.5 7.0 - - + -
3F SER* 3.4 1.8 + - - +
4F PHE* 1.3 79.2 - - + +
6F LEU* 1.3 58.3 + - - +
8F LYS* 3.3 3.3 + - - +
9F VAL* 3.0 45.1 + - + +
71F LEU* 4.2 11.0 - - + -
75F ILE* 3.9 27.4 - - + -
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Residues in contact with LEU 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E ILE* 3.7 24.4 - - + +
51E LYS* 3.8 31.0 - - + +
3F SER* 3.1 19.7 + - - +
5F LEU* 1.3 77.4 - - - +
7F SER* 1.3 60.4 + - - +
9F VAL* 3.8 3.8 - - + +
10F SER* 2.9 32.8 + - - +
41F ILE* 5.9 2.5 - - + -
44F ASN* 4.4 12.8 - - - +
46F ARG 3.7 20.4 - - - +
47F ASN* 4.4 4.7 - - - +
48F LEU* 3.9 31.6 - - + +
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Residues in contact with SER 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F SER 3.0 15.2 + - - -
4F PHE* 2.8 21.3 + - - -
6F LEU* 1.3 75.8 - - - +
8F LYS* 1.3 67.2 + - - +
10F SER* 2.5 22.2 + - - -
11F PHE* 3.1 11.8 + - - +
44F ASN* 3.4 21.2 + - - -
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Residues in contact with LYS 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F PHE* 3.0 33.2 + - + +
5F LEU* 3.3 7.1 + - - +
7F SER* 1.3 86.5 + - - +
9F VAL* 1.3 59.7 + - - +
11F PHE* 3.7 8.2 - - + +
12F VAL* 3.0 32.4 + - - +
71F LEU* 3.8 16.4 - - + -
74F GLU* 3.5 40.8 + - + +
75F ILE* 4.2 17.0 - - + -
77F LYS* 3.4 31.9 - - - +
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Residues in contact with VAL 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E ILE* 4.2 18.4 - - + -
5F LEU* 3.0 27.8 + - + +
6F LEU* 3.8 7.2 - - + +
8F LYS* 1.3 73.9 - - - +
10F SER* 1.3 64.2 + - - +
12F VAL* 3.2 4.8 + - - +
13F ILE* 3.0 43.9 + - + +
48F LEU* 4.2 13.2 - - + -
53F LEU* 4.1 22.0 - - + -
67F PHE* 4.3 6.0 - - + -
71F LEU* 3.9 29.2 - - + -
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Residues in contact with SER 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F LEU* 2.9 15.9 + - - +
7F SER* 2.5 31.9 + - - -
9F VAL* 1.3 77.0 - - - +
11F PHE* 1.3 62.3 + - - +
13F ILE* 3.6 4.6 + - - +
14F LYS* 3.2 23.9 + - - +
41F ILE* 3.4 39.7 - - - -
42F GLU* 4.7 8.7 - - - +
44F ASN* 3.4 15.5 + - - -
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Residues in contact with PHE 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F SER 3.1 13.4 + - - +
8F LYS* 3.7 8.7 - - + +
9F VAL 3.2 0.2 - - - -
10F SER* 1.3 81.9 + - - +
12F VAL* 1.3 63.2 + - + +
14F LYS* 3.4 9.7 + - + +
15F LYS* 2.9 52.9 + - + +
74F GLU* 3.4 44.9 - - + -
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Residues in contact with VAL 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LYS 3.0 19.3 + - - +
9F VAL* 3.2 4.9 + - - +
11F PHE* 1.3 79.1 - - + +
13F ILE* 1.3 61.1 + - - +
15F LYS* 3.4 5.1 + - - +
16F ILE* 3.0 37.2 + - + +
67F PHE* 3.5 32.5 - - + +
70F MET* 4.1 21.5 - - + +
71F LEU* 4.0 18.2 - - + -
74F GLU* 3.9 25.6 - - + -
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Residues in contact with ILE 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 3.0 33.4 + - + +
10F SER* 3.7 5.4 - - - +
12F VAL* 1.3 76.6 - - - +
14F LYS* 1.3 63.1 + - - +
16F ILE* 3.9 1.7 - - - +
17F ARG* 3.0 23.4 + - - +
27F LEU* 4.0 16.2 - - + -
38F ILE* 6.0 0.9 - - + -
41F ILE* 4.3 15.3 - - + -
42F GLU* 4.4 10.8 - - + +
48F LEU* 4.2 12.3 - - + -
53F LEU* 4.1 8.7 - - + -
56F ILE* 3.9 35.0 - - + -
60F LEU* 4.3 6.4 - - + +
67F PHE* 3.9 19.7 - - + -
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Residues in contact with LYS 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F SER 3.2 15.3 + - - +
11F PHE* 3.8 8.7 - - + +
13F ILE* 1.3 80.0 - - - +
15F LYS* 1.3 61.8 + - - +
17F ARG* 3.3 14.1 + - - +
18F LEU* 3.0 47.4 + - + +
42F GLU* 3.7 43.4 + - + +
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Residues in contact with LYS 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F PHE* 2.9 46.6 + - + +
12F VAL* 3.8 6.7 - - - +
14F LYS* 1.3 73.2 - - - +
16F ILE* 1.3 57.3 + - - +
18F LEU* 3.9 6.8 - - - +
19F GLU* 2.9 57.6 + - - +
70F MET* 3.8 22.5 - - + +
73F LYS* 6.0 1.8 - - - +
74F GLU* 4.3 13.0 + - + +
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Residues in contact with ILE 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F VAL* 3.0 26.0 + - + +
13F ILE 3.9 2.7 - - - +
15F LYS* 1.3 75.4 - - - +
17F ARG* 1.3 58.5 + - - +
19F GLU* 3.2 7.0 + - - +
20F LYS* 2.8 56.8 + - + +
60F LEU* 3.9 23.8 - - + -
62F VAL* 4.3 18.2 - - + -
67F PHE* 3.7 30.7 - - + -
70F MET* 3.7 28.7 - - + -
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Residues in contact with ARG 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F ILE 3.0 16.8 + - - +
14F LYS* 3.6 16.0 + - - +
16F ILE* 1.3 78.2 - - - +
18F LEU* 1.3 88.1 + - - +
20F LYS* 3.4 1.4 + - - -
21F GLY 3.3 3.5 + - - -
22F MET* 2.9 77.8 + - + +
23F THR* 3.7 16.9 - - - +
24F GLN* 3.6 28.3 - - - +
27F LEU* 4.1 15.5 - - + -
42F GLU* 2.8 40.4 + - - +
60F LEU* 3.8 16.1 - - + +
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Residues in contact with LEU 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F LYS* 3.0 46.1 + - + +
15F LYS* 4.0 5.8 - - - +
17F ARG* 1.3 103.4 - - - +
19F GLU* 1.3 64.1 + - - +
21F GLY* 3.1 13.7 + - - -
22F MET 4.7 2.2 - - - +
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Residues in contact with GLU 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LYS* 2.9 52.7 + - - +
16F ILE* 3.2 7.0 + - + +
18F LEU* 1.3 78.0 - - - +
20F LYS* 1.3 58.7 + - + +
21F GLY* 3.1 4.6 + - - -
70F MET* 4.7 6.8 - - - +
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Residues in contact with LYS 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ILE* 2.8 41.8 + - + +
17F ARG 3.4 1.1 + - - +
18F LEU 3.3 0.2 - - - -
19F GLU* 1.3 71.6 - - + +
21F GLY* 1.3 61.0 + - - +
22F MET* 3.4 24.7 + - + +
60F LEU* 2.7 29.4 + - + +
61F GLU* 3.3 21.8 + - - +
62F VAL* 4.1 6.8 - - - +
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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