Contacts of the helix formed by residues 14 - 25 (chain E) in PDB entry 3O65
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 LEU 14 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E GLN* 4.2 1.4 - - - +
11E GLU 4.4 5.8 + - - +
12E GLY 3.8 2.0 + - - -
13E PHE* 1.3 84.3 - - - +
15E CYS* 1.3 62.9 + - - +
16E ALA* 3.3 3.1 - - - -
17E GLN* 3.3 33.3 + - + +
18E HIS* 3.1 42.1 + - + +
31E PRO* 5.1 10.1 - - + -
70E MSE 6.6 0.2 - - + -
74E GLY* 5.0 8.3 - - - +
76E PHE* 5.0 13.9 - - + -
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Residues in contact with CYS 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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10E GLN* 4.0 9.6 - - - +
13E PHE 3.2 5.5 + - - -
14E LEU* 1.3 76.6 - - - +
16E ALA* 1.3 57.4 + - - +
18E HIS* 3.3 4.8 + - - +
19E CYS* 2.8 32.1 + - - +
120E HIS* 3.7 21.8 - - + +
121E TRP* 3.4 27.4 - - - +
136E SER* 4.5 0.4 - - - +
75F GLY 3.2 9.4 - - - -
76F NEH 1.8 54.1 - - + -
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Residues in contact with ALA 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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14E LEU 3.3 0.6 - - - -
15E CYS* 1.3 80.6 - - - +
17E GLN* 1.3 63.4 + - - +
19E CYS* 3.3 5.8 - - - +
20E LEU* 3.0 30.9 + - + +
34E LEU* 4.5 4.9 - - + -
76E PHE* 3.9 34.9 - - + -
80E VAL* 6.2 0.9 - - + -
81E ILE* 4.1 13.0 - - + -
121E TRP* 3.9 22.7 - - + -
75F GLY 4.8 1.3 + - - +
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Residues in contact with GLN 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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8E GLU* 3.8 14.5 - - - +
14E LEU* 3.3 30.9 + - + +
16E ALA* 1.3 78.4 - - - +
18E HIS* 1.3 63.8 + - - +
20E LEU* 3.3 4.0 + - - -
21E ASN* 2.8 40.3 + - - +
29E PHE* 3.4 26.9 - - - +
30E SER* 4.0 0.6 - - - -
31E PRO* 3.2 44.3 - - - +
34E LEU* 3.7 18.6 - - + +
76E PHE* 5.5 1.0 - - + -
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Residues in contact with HIS 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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8E GLU* 2.8 43.0 - - + +
9E LYS 3.8 5.8 + - - -
10E GLN* 3.6 34.7 + - + -
11E GLU 4.3 5.6 - - - -
14E LEU* 3.1 35.5 + - + +
15E CYS 3.8 4.7 - - - +
17E GLN* 1.3 83.2 + - - +
19E CYS* 1.3 55.1 + - - +
22E ASN* 2.8 41.1 + - - +
136E SER* 3.5 35.3 + - - -
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Residues in contact with CYS 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 CYS 2.8 21.6 + - - +
16E ALA* 3.3 6.7 - - - +
18E HIS* 1.3 73.4 - - - +
20E LEU* 1.3 59.0 + - - +
22E ASN* 4.7 1.6 - - - +
23E LEU* 2.9 19.2 + - - +
81E ILE* 5.2 2.9 - - - -
114E ILE* 3.8 36.8 - - - -
121E TRP* 3.9 18.2 - - + -
122E PHE* 3.9 16.6 - - - +
123E THR* 2.7 34.0 + - - +
134E LEU 5.9 0.7 - - - -
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Residues in contact with LEU 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 ALA* 3.0 21.7 + - + +
17E GLN* 3.9 3.1 - - - +
19E CYS* 1.3 74.2 - - + +
21E ASN* 1.3 62.1 + - - +
23E LEU* 3.8 3.0 - - - +
24E LEU* 2.9 36.5 + - + +
29E PHE* 3.9 24.7 - - + -
34E LEU* 4.1 15.9 - - + -
80E VAL* 5.3 0.9 - - + +
81E ILE* 4.0 31.9 - - + +
84E ALA* 3.7 26.9 - - + -
85E LEU* 3.8 31.0 - - + +
114E ILE* 4.5 6.5 - - + -
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Residues in contact with ASN 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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6E PHE* 3.7 5.0 - - + -
8E GLU* 2.7 38.1 + - - +
17E GLN* 2.8 26.2 + - - +
20E LEU* 1.3 73.7 - - - +
22E ASN* 1.3 53.5 + - - +
24E LEU* 4.8 1.8 - - - -
25E GLN* 2.7 29.6 + - - -
26E GLY 3.0 30.0 + - - +
27E GLU* 3.9 5.9 - - - +
28E TYR* 3.2 4.4 + - - +
29E PHE* 2.7 47.4 + - - +
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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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6E PHE* 3.6 9.3 - - - -
7E HIS* 3.1 26.1 - - - -
8E GLU* 2.8 36.4 + - - +
18E HIS 2.8 28.6 + - - +
19E CYS* 3.9 3.1 - - - +
21E ASN* 1.3 70.7 - - - +
23E LEU* 1.3 63.1 + - - +
25E GLN* 2.8 25.5 + - - +
123E THR* 4.7 2.2 - - - +
134E LEU* 2.8 48.4 + - + +
136E SER 4.7 1.4 - - - +
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Residues in contact with LEU 23 (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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19E CYS 2.9 18.6 + - - +
20E LEU* 3.8 3.8 - - + +
22E ASN* 1.3 77.5 - - - +
24E LEU* 1.3 66.7 + - + +
25E GLN 3.4 0.2 + - - -
85E LEU* 3.7 30.3 - - + -
112E SER* 3.4 35.4 - - - +
114E ILE* 4.1 15.9 - - + -
123E THR* 3.5 22.6 + - + +
125E ARG* 2.9 33.2 + - + +
166E VAL* 4.4 11.0 - - + -
170E LEU* 3.9 21.3 - - + +
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Residues in contact with LEU 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 LEU* 2.9 23.5 + - + +
23E LEU* 1.3 79.0 - - + +
25E GLN* 1.3 65.6 + - - +
26E GLY 3.5 0.2 - - - -
28E TYR* 3.0 44.7 + - + -
29E PHE* 3.5 30.7 - - + -
85E LEU* 5.2 7.6 - - + -
88E TRP* 4.0 17.5 - - + -
90E LEU* 4.1 20.4 - - + -
125E ARG* 5.4 1.3 + - - -
170E LEU* 4.4 3.8 - - + -
171E PRO* 3.7 38.4 - - + +
172E ASP 5.5 0.2 - - - +
173E CYS* 5.0 2.1 - - - +
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Residues in contact with GLN 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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4E PHE 4.4 1.6 - - - +
5E ILE* 4.0 3.6 - - - -
6E PHE* 3.1 56.3 + - - +
21E ASN 2.7 14.6 + - - -
22E ASN 2.8 22.2 + - - -
23E LEU 3.2 0.8 - - - -
24E LEU* 1.3 79.2 - - - +
26E GLY* 1.3 54.5 + - - +
28E TYR* 3.9 2.2 - - - -
125E ARG* 4.0 9.9 - - - +
127E PHE* 3.5 31.6 - - + -
134E LEU* 3.8 2.4 - - - +
173E CYS* 3.5 37.2 - - + +
175E ALA* 4.1 5.4 + - - +
32G VAL* 4.6 5.4 - - - +
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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