Contacts of the helix formed by residues 11 - 25 (chain E) in PDB entry 3HYW
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 GLY 11 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E GLY 3.4 5.7 + - - -
10E GLY* 1.3 78.0 - - - +
12E VAL* 1.3 67.3 + - - -
13E GLY 3.4 2.2 - - - -
14E GLY 4.1 1.0 - - - +
15E ILE* 3.0 26.9 + - - +
39E PHE* 3.7 12.3 - - - -
40E GLY 5.5 2.0 - - - -
441E FAD 3.2 26.5 + - - -
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Residues in contact with VAL 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E GLY* 1.3 71.8 - - - -
13E GLY* 1.3 58.9 + - - +
15E ILE* 4.4 0.8 - - - +
16E ALA* 3.1 33.1 + - + +
39E PHE* 4.0 21.8 - - + -
41E PHE* 5.9 1.3 - - + -
42E THR* 4.6 4.9 - - - +
43E PRO* 5.5 6.1 - - + -
314E GLY* 4.4 13.9 - - - +
317E ILE* 3.9 22.4 - - + -
318E GLU* 4.7 6.5 - - + -
389E PHE* 4.3 22.0 - - + -
441E FAD 3.3 40.1 + - - +
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Residues in contact with GLY 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E VAL* 1.3 72.8 - - - +
14E GLY* 1.3 54.7 + - - +
16E ALA* 3.9 2.1 - - - +
17E THR* 2.7 38.6 + - - -
104E ALA* 4.0 4.7 - - - -
292E VAL* 3.6 13.1 - - - +
317E ILE* 3.4 22.8 - - - +
441E FAD 2.7 19.8 + - - -
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Residues in contact with GLY 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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7E VAL* 3.4 21.3 - - - +
9E GLY 3.2 23.4 + - - -
11E GLY 3.6 3.2 + - - +
12E VAL 3.5 0.4 - - - -
13E GLY* 1.3 73.0 - - - +
15E ILE* 1.3 59.8 + - - +
17E THR* 3.4 0.4 + - - -
18E ALA* 2.9 31.9 + - - +
32E LEU* 4.0 2.7 - - - -
104E ALA* 3.5 12.3 - - - +
441E FAD 4.2 0.6 + - - -
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Residues in contact with ILE 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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9E GLY 4.2 0.6 + - - -
10E GLY* 3.9 13.7 - - - +
11E GLY 3.0 21.6 + - - +
12E VAL 4.4 0.9 - - - +
14E GLY* 1.3 74.2 - - - +
16E ALA* 1.3 57.5 + - - +
18E ALA* 3.4 1.2 + - - -
19E TYR* 2.9 59.0 + - + +
32E LEU* 4.2 17.7 - - + -
39E PHE* 4.1 11.9 - - + -
62E LEU* 3.8 32.1 - - + -
66E LEU* 4.2 14.6 - - + -
389E PHE* 5.9 1.1 - - + -
393E VAL* 4.5 11.0 - - + -
398E ILE* 4.0 14.4 - - + -
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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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12E VAL* 3.1 22.6 + - + +
13E GLY* 3.9 0.4 - - - +
15E ILE* 1.3 77.6 - - - +
17E THR* 1.3 55.2 + - - +
19E TYR* 4.0 0.9 - - - +
20E ASN* 2.7 41.7 + - - +
318E GLU* 4.8 10.5 - - + -
321E ALA* 3.5 19.3 - - + -
389E PHE* 5.7 0.2 - - + -
398E ILE* 4.0 31.3 - - + +
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Residues in contact with THR 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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7E VAL* 5.1 2.0 - - + -
13E GLY 2.7 23.9 + - - -
14E GLY 4.0 2.9 - - - -
16E ALA* 1.3 75.1 - - - +
18E ALA* 1.3 58.1 + - - +
20E ASN* 3.4 1.9 + - - +
21E LEU* 3.0 45.2 + - + +
102E VAL* 3.9 22.2 - - + -
292E VAL* 3.5 13.7 - - - +
321E ALA* 3.4 25.7 - - - +
324E VAL* 3.9 27.4 - - + -
325E ALA 4.4 2.9 - - - +
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Residues in contact with ALA 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E VAL* 4.2 7.7 - - + +
14E GLY 2.9 18.8 + - - +
15E ILE 3.9 2.5 - - - +
17E THR* 1.3 76.1 - - - +
19E TYR* 1.3 59.3 + - + +
21E LEU* 3.5 2.6 + - - -
22E ARG* 3.0 27.9 + - - +
30E ILE* 3.6 29.8 - - + +
32E LEU* 4.0 19.1 - - + -
71E ILE* 4.2 12.9 - - + +
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Residues in contact with TYR 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 ILE* 2.9 38.0 + - + +
16E ALA 4.1 2.2 - - - +
18E ALA* 1.3 73.0 - - + +
20E ASN* 1.3 61.0 + - - +
22E ARG* 3.3 5.5 + - - +
23E ASN* 2.7 37.1 + - - +
65E LEU* 3.7 5.5 - - - +
66E LEU* 3.6 30.9 - - + +
69E PHE* 3.4 18.8 - + + -
71E ILE* 3.7 15.7 - - + -
392E LYS 3.7 5.4 - - - -
393E VAL* 2.6 34.3 + - - +
396E GLY* 3.4 32.1 - - - +
397E ASN 3.6 0.4 - - - -
398E ILE* 3.4 28.5 - - + +
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Residues in contact with ASN 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* 2.7 34.1 + - - +
17E THR 3.7 1.1 - - - +
19E TYR* 1.3 75.9 - - - +
21E LEU* 1.3 58.0 + - - +
23E ASN* 3.4 4.9 + - - +
24E LEU* 2.9 39.2 + - + +
318E GLU 4.8 0.6 + - - -
321E ALA* 4.0 17.4 - - - +
322E MET* 4.0 19.5 - - - +
325E ALA* 3.5 20.4 - - + -
326E HIS* 5.8 2.8 - - - -
397E ASN* 5.6 1.0 - - - +
398E ILE* 5.2 3.6 - - - +
399E ALA* 3.7 26.1 - - - +
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Residues in contact with LEU 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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5E VAL* 3.7 33.2 - - + -
7E VAL* 4.9 2.9 - - + -
17E THR* 3.0 34.7 + - + +
18E ALA* 3.7 8.5 - - - +
20E ASN* 1.3 75.8 - - - +
22E ARG* 1.3 57.7 + - - +
24E LEU* 3.7 3.8 - - - +
25E MET* 2.8 35.2 + - - +
28E LEU* 3.9 16.9 - - + +
30E ILE* 3.9 13.5 - - + -
325E ALA* 3.6 33.7 - - + +
328E ILE* 4.0 20.0 - - + -
329E VAL* 4.0 5.2 - - + -
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Residues in contact with ARG 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 ALA 3.0 18.1 + - - +
19E TYR* 3.6 9.0 - - - +
20E ASN 3.3 0.2 - - - -
21E LEU* 1.3 77.4 - - - +
23E ASN* 1.3 65.2 + - - +
25E MET 2.9 22.4 + - - -
26E PRO* 3.3 38.2 + - - +
28E LEU 2.8 31.7 + - - -
29E LYS* 4.5 0.2 - - - +
30E ILE* 3.5 32.7 - - + +
69E PHE* 2.8 36.0 + - + +
70E ASN* 2.8 34.0 + - - +
71E ILE* 4.6 4.2 - - + +
396E GLY 5.7 2.0 - - - +
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Residues in contact with ASN 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 TYR 2.7 26.7 + - - +
20E ASN* 3.9 5.1 - - - +
22E ARG* 1.3 79.5 - - - +
24E LEU* 1.3 67.6 + - + +
26E PRO* 4.5 6.8 - - - +
396E GLY 3.1 23.1 + - - +
397E ASN* 3.8 27.8 - - - +
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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 ASN* 2.9 25.6 + - + +
21E LEU 3.7 4.3 - - - +
23E ASN* 1.3 82.0 - - + +
25E MET* 1.3 58.0 + - - +
26E PRO* 3.9 5.2 - - - +
325E ALA* 4.0 35.2 - - + +
326E HIS* 4.0 36.8 - - + +
329E VAL* 4.0 19.3 - - + -
333E ARG* 3.8 19.9 + - - +
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Residues in contact with MET 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 LEU 2.8 13.2 + - - +
22E ARG* 2.9 21.5 + - - -
23E ASN 3.4 0.2 - - - -
24E LEU* 1.3 80.4 - - - +
26E PRO* 1.3 64.5 - - - +
27E ASP* 3.1 27.1 - - - +
28E LEU* 3.1 35.7 + - + +
329E VAL* 3.6 23.6 - - + -
332E ILE* 3.9 37.9 - - + -
333E ARG* 3.5 38.1 - - + +
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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