Contacts of the helix formed by residues 15 - 27 (chain E) in PDB entry 3PTZ
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 VAL 15 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14E TYR* 1.3 79.8 - - + +
16E GLY* 1.3 64.6 + - - +
17E GLY 3.6 0.2 - - - -
18E PRO* 4.3 0.5 - - - +
19E THR* 2.9 29.2 + - - -
88E SER* 3.9 22.2 - - - +
129E LYS* 4.1 17.0 - - + +
130E SER* 4.7 0.4 - - - -
131E THR* 3.8 29.8 - - + +
161E GLU* 4.1 22.4 - - + -
163E LEU* 4.8 6.2 - - + +
500E NAD 2.8 37.5 + - - +
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Residues in contact with GLY 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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9E CYS* 4.0 12.8 - - - -
11E GLY 3.6 20.4 + - - -
13E GLY 3.4 6.0 + - - +
15E VAL* 1.3 75.5 - - - +
17E GLY* 1.3 68.8 + - - +
19E THR* 4.6 3.4 - - - -
20E CYS* 2.9 29.5 + - - +
34E VAL* 4.5 2.5 - - - -
88E SER* 4.3 8.3 + - - -
500E NAD 4.4 0.8 + - - -
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Residues in contact with GLY 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ALA 4.0 6.0 - - - -
13E GLY 2.9 13.7 + - - -
16E GLY* 1.3 71.5 - - - +
18E PRO* 1.4 58.9 - - - +
20E CYS* 4.0 0.7 - - - +
21E SER* 2.8 35.9 + - - -
34E VAL* 4.5 9.4 - - - -
45E TRP* 3.5 28.5 - - - -
71E PHE* 4.6 3.4 - - - -
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Residues in contact with PRO 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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13E GLY 3.1 10.1 - - - +
14E TYR* 3.1 29.4 - - - +
15E VAL 3.7 2.5 - - - +
17E GLY* 1.4 84.5 - - - +
19E THR* 1.3 62.1 + - - +
21E SER* 3.3 1.2 + - - -
22E VAL* 2.9 21.7 + - - +
45E TRP* 4.2 4.2 - - + -
52E ILE* 3.9 17.9 - - + -
54E GLU* 5.1 2.5 - - + +
57E LEU* 4.0 21.1 - - + -
163E LEU* 4.6 1.3 - - + -
168E ALA* 4.3 16.4 - - + -
169E ILE* 4.8 2.8 - - + +
172E LEU* 3.4 23.8 - - + +
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Residues in contact with THR 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 VAL 2.9 23.1 + - - -
16E GLY* 4.0 3.1 - - - -
18E PRO* 1.3 76.5 - - - +
20E CYS* 1.3 63.2 + - - +
22E VAL* 3.2 4.5 + - - +
23E ILE* 2.9 43.4 + - + +
86E PHE* 5.3 3.4 - - + -
129E LYS* 3.8 32.1 - - + +
161E GLU* 3.6 20.0 + - - +
163E LEU* 4.3 1.7 - - - +
172E LEU* 3.8 18.4 - - + +
199E TYR* 4.9 2.5 - - + +
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Residues in contact with CYS 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E ILE* 5.1 0.7 - - - -
9E CYS* 3.2 38.8 - - - -
16E GLY* 2.9 19.7 + - - +
19E THR* 1.3 78.1 - - - +
21E SER* 1.3 61.5 + - - +
23E ILE* 3.2 6.3 + - - +
24E ALA* 2.8 30.5 + - - +
32E VAL* 3.4 26.2 - - + +
34E VAL* 3.5 16.6 - - + -
69E LEU* 4.1 2.7 - - - -
86E PHE* 4.5 13.7 - - - -
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Residues in contact with SER 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E GLY 2.8 22.9 + - - -
18E PRO 3.7 3.6 - - - -
20E CYS* 1.3 79.4 - - - +
22E VAL* 1.3 61.6 + - - +
24E ALA* 3.4 3.1 + - - +
25E HIS 3.0 17.0 + - - -
57E LEU* 4.1 8.3 - - - -
60E VAL* 3.6 17.0 - - - +
61E VAL* 3.3 31.2 - - - +
64E CYS* 4.5 1.7 - - - -
69E LEU* 3.4 20.9 - - - +
71E PHE* 3.7 7.1 - - - -
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Residues in contact with VAL 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E PRO 2.9 20.4 + - - +
19E THR 3.7 4.0 - - - +
21E SER* 1.3 75.7 - - - +
23E ILE* 1.3 65.2 + - - +
25E HIS* 3.0 7.4 + - - +
26E MET* 3.0 23.0 + - + +
60E VAL* 4.5 2.5 - - + -
169E ILE* 3.7 26.2 - - + -
172E LEU* 3.7 31.2 - - + +
173E LYS* 4.0 28.7 - - + -
202E TRP* 4.1 22.2 - - + -
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Residues in contact with ILE 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E ILE* 4.2 10.8 - - + -
19E THR* 2.9 36.8 + - + +
20E CYS* 3.7 9.6 - - - +
22E VAL* 1.3 75.0 - - + +
24E ALA* 1.3 67.4 + - - +
25E HIS 3.1 0.2 + - - -
26E MET 3.1 1.0 + - - -
27E CYS* 2.9 31.1 + - + +
30E ILE* 5.1 1.3 - - + -
32E VAL* 4.1 15.7 - - + -
86E PHE* 4.0 27.6 - - + -
198E VAL* 4.1 23.6 - - + -
199E TYR* 4.8 7.0 - - + +
202E TRP* 3.7 26.7 - - + -
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Residues in contact with ALA 24 (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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20E CYS 2.8 17.0 + - - +
21E SER 3.6 4.9 - - - +
23E ILE* 1.3 78.0 - - - +
25E HIS* 1.3 61.0 + - - +
27E CYS 3.3 8.2 + - - -
28E PRO* 3.8 2.1 - - - +
32E VAL* 3.9 13.6 - - + +
64E CYS* 4.0 6.5 - - + -
68E ASN* 3.0 42.5 + - - +
69E LEU* 3.9 23.8 - - + -
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Residues in contact with HIS 25 (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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21E SER 3.0 12.7 + - - +
22E VAL* 3.0 11.2 + - - +
24E ALA* 1.3 76.6 - - - +
26E MET* 1.3 66.8 + - - +
27E CYS 3.7 0.2 + - - -
28E PRO* 4.4 6.6 - - - +
59E GLU 5.4 0.4 - - - -
60E VAL* 3.7 24.9 - - + +
63E SER* 3.2 24.9 + - - -
64E CYS* 3.3 22.9 - - - -
173E LYS* 2.9 31.3 + - - +
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Residues in contact with MET 26 (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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22E VAL* 3.0 22.5 + - + +
23E ILE 4.0 1.3 - - - +
25E HIS* 1.3 83.5 - - + +
27E CYS* 1.3 62.9 + - - +
28E PRO* 3.6 8.2 - - - +
173E LYS* 4.2 26.5 - - + -
201E HIS* 3.7 16.6 - - - +
202E TRP* 3.3 66.0 - - + -
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Residues in contact with CYS 27 (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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23E ILE* 2.9 24.8 + - + +
24E ALA* 3.3 4.4 + - - -
26E MET* 1.3 83.2 - - - +
28E PRO* 1.4 60.3 - - - +
29E GLU* 2.9 18.5 + - - +
30E ILE* 3.0 36.1 + - + +
68E ASN* 3.1 10.6 + - - -
198E VAL* 3.9 8.5 - - - -
201E HIS* 3.6 29.6 - - + -
202E TRP* 4.0 10.5 - - - -
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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