Contacts of the helix formed by residues 7 - 22 (chain E) in PDB entry 4P9U
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 SER 7 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E LYS* 1.3 80.9 - - - +
8E PRO* 1.3 69.4 - - - +
9E ALA 3.6 1.8 + - - -
10E GLY* 3.8 8.7 + - - -
11E PHE* 2.8 32.4 + - - +
13G G 4.9 0.2 + - - -
14G T 3.2 12.6 + - - -
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Residues in contact with PRO 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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6E LYS 4.3 2.7 - - - +
7E SER* 1.3 90.5 - - - +
9E ALA* 1.3 56.8 + - - +
11E PHE* 3.2 4.0 + - + +
12E ALA* 2.9 28.2 + - - +
43E VAL* 3.6 25.8 - - + +
47E THR* 4.3 2.2 - - + -
14G T 3.6 39.5 - - - +
15G C 4.0 14.8 - - - +
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Residues in contact with ALA 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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7E SER* 4.9 0.2 - - - +
8E PRO* 1.3 78.3 - - - +
10E GLY* 1.3 57.2 + - - +
12E ALA* 3.2 0.7 + - - -
13E GLU* 2.9 27.7 + - - +
47E THR* 3.7 16.1 - - + +
50E GLU* 6.0 1.8 - - + +
51E VAL* 3.3 16.0 - - + +
54E ARG* 3.6 22.8 + - - +
14G T 3.2 27.7 + - - +
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Residues in contact with GLY 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 LYS* 4.6 12.1 + - - -
7E SER* 3.4 12.6 + - - -
8E PRO 3.3 0.6 - - - -
9E ALA* 1.3 77.8 - - - +
11E PHE* 1.3 58.5 + - - +
13E GLU* 3.4 6.4 + - - +
14E LYS* 3.0 28.8 + - - +
54E ARG* 4.6 2.7 - - - +
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Residues in contact with PHE 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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6E LYS* 4.5 27.3 - - + +
7E SER 2.8 20.0 + - - +
8E PRO* 3.6 4.9 - - + +
10E GLY* 1.3 73.5 - - - +
12E ALA* 1.3 62.0 + - - +
14E LYS* 4.5 9.9 - - + +
15E TYR* 2.9 53.6 + + + +
41E ILE* 3.9 35.0 - - + -
43E VAL* 5.4 2.7 - - + -
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Residues in contact with ALA 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 PRO 2.9 13.2 + - - +
9E ALA* 3.5 9.0 - - - +
11E PHE* 1.3 78.1 - - - +
13E GLU* 1.3 55.5 + - - +
15E TYR* 3.4 2.0 + - - +
16E ILE* 2.9 34.7 + - - +
41E ILE* 4.3 13.5 - - + -
43E VAL* 4.2 22.4 - - + -
47E THR* 5.6 0.2 - - + -
48E LEU* 4.5 8.7 - - + -
51E VAL* 3.7 20.9 - - + -
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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 ALA 2.9 15.8 + - - +
10E GLY* 3.8 5.7 - - - +
11E PHE 3.3 0.2 - - - -
12E ALA* 1.3 76.4 - - - +
14E LYS* 1.3 63.7 + - - +
16E ILE* 3.4 0.9 + - - +
17E ILE* 2.9 41.4 + - + +
51E VAL* 3.6 14.1 - - + +
54E ARG* 2.9 30.9 + - - -
55E LEU* 3.6 28.3 - - + +
57F ARG* 2.9 32.7 + - - -
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Residues in contact with LYS 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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6E LYS* 4.7 23.1 - - - +
10E GLY 3.0 17.1 + - - +
11E PHE* 4.0 10.8 - - + +
13E GLU* 1.3 77.1 - - - +
15E TYR* 1.3 58.7 + - - +
17E ILE* 4.0 4.7 - - - +
18E GLU* 2.9 68.1 + - + +
277E ASP* 5.8 6.3 - - + +
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Residues in contact with TYR 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 PHE* 2.9 46.6 + + + +
12E ALA* 3.6 4.7 - - - +
14E LYS* 1.3 79.0 - - - +
16E ILE* 1.3 58.1 + - + +
18E GLU* 3.8 5.3 - - - +
19E SER* 2.6 52.7 + - - -
24E ARG* 3.4 24.6 + - - -
25E PHE* 4.4 14.8 - + - -
40E LEU* 4.1 21.1 + - + +
41E ILE* 3.6 34.3 - - + -
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Residues in contact with ILE 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 ALA 2.9 19.8 + - - +
15E TYR* 1.3 77.8 - - + +
17E ILE* 1.3 65.5 + - - +
19E SER* 3.1 5.5 + - - -
20E ILE* 2.9 44.8 + - + +
25E PHE* 4.7 3.8 - - + -
31E LEU* 4.6 16.4 - - + -
37E LEU* 4.4 11.4 - - + -
41E ILE* 4.1 13.0 - - + -
48E LEU* 3.8 20.6 - - + -
51E VAL* 4.2 4.5 - - + -
52E LEU* 3.7 27.8 - - + -
55E LEU* 3.7 24.7 - - + -
61E LEU* 5.1 2.0 - - + -
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Residues in contact with ILE 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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13E GLU* 2.9 32.9 + - + +
14E LYS* 4.0 4.5 - - - +
16E ILE* 1.3 75.4 - - - +
18E GLU* 1.3 60.1 + - + +
20E ILE* 3.2 11.4 + - + +
21E TRP* 2.9 25.5 + - - +
55E LEU* 3.6 31.6 - - + -
58E ASP* 6.1 0.2 - - - +
60E TRP* 3.9 32.4 - - + +
85E THR* 4.3 12.1 - - + +
89E LEU* 3.7 28.9 - - + -
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Residues in contact with GLU 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 LYS* 2.9 57.3 + - + +
15E TYR* 4.0 4.9 - - - +
17E ILE* 1.3 77.6 - - + +
19E SER* 1.3 56.5 + - - +
21E TRP* 3.2 7.6 + - - +
22E ASN* 2.9 41.8 + - - +
88E THR 5.7 0.7 - - - +
89E LEU* 3.8 20.9 - - + +
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Residues in contact with SER 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 TYR* 2.6 44.6 + - - -
16E ILE 3.1 1.1 + - - -
18E GLU* 1.3 76.3 - - - +
20E ILE* 1.3 60.1 + - - +
22E ASN* 3.0 12.3 + - - +
24E ARG* 2.7 43.9 + - - -
25E PHE* 2.8 31.4 + - - -
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Residues in contact with ILE 20 (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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16E ILE* 2.9 36.1 + - + +
17E ILE* 3.2 9.2 + - + +
19E SER* 1.3 79.3 - - - +
21E TRP* 1.3 62.2 + - - +
23E GLY* 3.8 5.0 + - - -
25E PHE* 3.3 31.0 - - + +
27E PRO* 3.8 19.9 - - + +
55E LEU* 5.9 0.2 - - + -
60E TRP* 4.2 28.5 - - + +
61E LEU* 4.2 14.4 - - + -
71E VAL* 4.0 21.8 - - + -
74E PHE* 4.2 22.9 - - + -
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Residues in contact with TRP 21 (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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17E ILE 2.9 15.5 + - - +
18E GLU* 3.2 4.7 + - + +
20E ILE* 1.3 80.4 - - - +
22E ASN* 1.3 70.8 - - + +
23E GLY* 3.4 0.9 + - - -
60E TRP* 5.6 1.5 - - + -
74E PHE* 4.0 26.9 - + + -
86E LEU* 3.6 23.8 - - + -
89E LEU* 3.1 51.3 + - + -
90E ASP* 3.4 44.2 - - + -
92E GLU* 5.2 2.4 + - - -
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Residues in contact with ASN 22 (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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18E GLU* 2.9 26.7 + - - +
19E SER* 3.0 19.4 + - - +
21E TRP* 1.3 85.9 - - + +
23E GLY* 1.3 73.9 + - - +
24E ARG* 3.2 11.5 + - - +
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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