Contacts of the helix formed by residues 11 - 25 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D GLY 3.4 4.9 + - - -
10D GLY* 1.3 77.3 - - - +
12D VAL* 1.3 60.7 + - - -
13D GLY 3.4 2.0 - - - -
14D GLY 4.0 1.2 - - - +
15D ILE* 2.9 32.4 + - - +
39D PHE* 3.8 12.8 - - - -
40D GLY 5.6 1.6 - - - -
441D FAD 3.3 27.4 + - - -
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Residues in contact with VAL 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLY* 1.3 70.5 - - - -
13D GLY* 1.3 62.9 + - - +
15D ILE* 4.5 1.1 - - - +
16D ALA* 3.1 29.1 + - - +
39D PHE* 3.9 23.3 - - + -
41D PHE* 5.7 1.6 - - + -
42D THR* 4.7 4.7 - - - +
43D PRO* 5.6 6.3 - - + -
314D GLY* 4.5 16.8 - - - +
317D ILE* 3.9 20.0 - - + -
318D GLU* 4.6 6.5 - - + -
389D PHE* 4.2 23.5 - - + -
441D FAD 3.2 37.4 + - - +
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Residues in contact with GLY 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 1.3 75.1 - - - +
14D GLY* 1.3 54.7 + - - +
16D ALA* 4.0 1.8 - - - +
17D THR* 2.6 37.4 + - - -
104D ALA* 4.3 1.1 - - - -
292D VAL* 3.6 18.8 - - - -
317D ILE* 3.5 21.0 - - - +
441D FAD 2.7 19.8 + - - -
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Residues in contact with GLY 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D VAL* 3.5 21.6 - - - +
9D GLY 3.3 23.1 + - - -
11D GLY 3.5 3.8 + - - +
12D VAL 3.4 0.2 - - - -
13D GLY* 1.3 77.5 - - - +
15D ILE* 1.3 57.5 + - - +
17D THR 3.8 0.2 - - - -
18D ALA* 2.9 30.7 + - - +
32D LEU* 4.0 2.2 - - - -
104D ALA* 3.5 11.3 - - - +
441D FAD 4.2 0.4 + - - -
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Residues in contact with ILE 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D GLY* 4.1 12.8 - - - +
11D GLY 2.9 20.9 + - - +
12D VAL* 4.5 1.1 - - - +
14D GLY* 1.3 71.9 - - - +
16D ALA* 1.3 60.3 + - - +
18D ALA* 4.5 1.1 - - - -
19D TYR* 2.8 67.4 + - + +
32D LEU* 3.8 20.8 - - + +
39D PHE* 4.4 9.2 - - + -
62D LEU* 4.0 22.4 - - + -
66D LEU* 3.9 23.8 - - + -
389D PHE* 6.2 0.2 - - + -
393D VAL* 4.5 10.1 - - + -
398D ILE* 4.0 12.6 - - + -
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Residues in contact with ALA 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 3.1 22.5 + - + +
13D GLY* 4.7 0.2 - - - -
15D ILE* 1.3 77.9 - - - +
17D THR* 1.3 53.3 + - - +
19D TYR* 4.0 0.9 - - - +
20D ASN* 2.8 41.6 + - - +
318D GLU* 4.7 11.0 - - + -
321D ALA* 3.5 18.2 - - + -
398D ILE* 3.8 32.0 - - + +
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Residues in contact with THR 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D VAL* 5.1 1.6 - - + -
13D GLY 2.6 23.4 + - - -
14D GLY 3.9 2.2 - - - -
16D ALA* 1.3 72.3 - - - +
18D ALA* 1.3 61.1 + - - +
20D ASN* 3.3 1.7 + - - +
21D LEU* 2.9 44.1 + - + +
102D VAL* 3.9 24.0 - - + -
292D VAL* 3.5 13.9 - - - +
321D ALA* 3.4 25.5 - - - +
324D VAL* 3.8 27.6 - - + -
325D ALA 4.4 2.5 - - - +
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Residues in contact with ALA 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D VAL* 4.2 8.4 - - + +
14D GLY 2.9 17.9 + - - +
15D ILE* 3.9 3.6 - - - +
17D THR* 1.3 75.8 - - - +
19D TYR* 1.3 61.7 + - + +
21D LEU* 4.5 2.7 - - - -
22D ARG* 3.0 30.3 + - - +
30D ILE* 3.7 27.9 - - + +
32D LEU* 4.2 16.6 - - + -
66D LEU* 6.1 0.2 - - + -
71D ILE* 4.0 11.8 - - + +
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Residues in contact with TYR 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ILE* 2.8 40.5 + - + +
16D ALA 4.0 2.9 - - - +
18D ALA* 1.3 71.4 - - + +
20D ASN* 1.3 61.5 + - - +
22D ARG* 3.5 4.3 + - + +
23D ASN* 2.8 37.3 + - - +
65D LEU* 3.5 11.3 - - - +
66D LEU* 3.6 25.4 - - + +
69D PHE* 3.3 25.8 - + + -
71D ILE* 3.9 12.1 - - + -
392D LYS 3.7 4.9 - - - -
393D VAL* 2.6 32.7 + - - +
396D GLY* 3.4 32.3 - - - +
397D ASN 3.7 0.4 - - - -
398D ILE* 3.4 29.8 - - + +
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Residues in contact with ASN 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ALA* 2.8 34.0 + - - +
17D THR 3.7 0.7 - - - +
19D TYR* 1.3 73.2 - - - +
21D LEU* 1.3 58.9 + - - +
23D ASN* 3.4 5.0 + - - +
24D LEU* 2.9 36.0 + - + +
318D GLU 4.5 0.6 + - - -
321D ALA* 3.7 22.8 - - - +
322D MET* 3.7 16.5 - - - +
325D ALA* 3.5 20.6 - - + -
326D HIS* 6.3 0.4 - - + -
397D ASN* 5.5 0.7 - - - +
398D ILE* 5.4 4.0 + - - +
399D ALA* 3.7 26.2 + - - +
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Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D VAL* 3.8 30.7 - - + -
7D VAL* 4.7 2.7 - - + -
17D THR* 2.9 37.2 + - + +
18D ALA* 3.8 4.3 - - - +
20D ASN* 1.3 75.0 - - - +
22D ARG* 1.3 58.4 + - - +
24D LEU* 3.5 4.0 + - - +
25D MET* 2.9 34.1 + - - +
28D LEU* 3.8 13.6 - - + +
30D ILE* 3.8 15.3 - - + -
102D VAL* 4.6 1.3 - - + -
325D ALA* 3.7 26.7 - - + +
328D ILE* 3.7 33.4 - - + -
329D VAL* 4.2 4.9 - - + -
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Residues in contact with ARG 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ALA 3.0 18.6 + - - +
19D TYR* 3.8 5.6 - - + +
21D LEU* 1.3 76.4 - - - +
23D ASN* 1.3 66.7 + - - +
25D MET 2.9 43.8 + - - -
26D PRO* 3.3 24.0 + - - +
28D LEU* 2.8 28.6 + - - +
30D ILE* 3.5 26.7 - - + +
69D PHE* 2.8 37.3 + - + +
70D ASN* 2.9 34.2 + - - +
71D ILE* 4.4 6.2 - - + +
396D GLY 6.0 1.1 - - - +
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Residues in contact with ASN 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D TYR 2.8 24.5 + - - +
20D ASN* 4.1 4.4 - - - +
22D ARG* 1.3 82.2 - - - +
24D LEU* 1.3 62.8 + - + +
26D PRO* 4.6 6.5 - - - +
396D GLY 3.0 25.5 + - - +
397D ASN* 3.8 21.4 - - - +
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Residues in contact with LEU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ASN* 2.9 22.1 + - + +
21D LEU 3.7 4.0 - - - +
23D ASN* 1.3 79.6 - - - +
25D MET* 1.3 57.5 + - - +
26D PRO* 3.8 5.6 - - - +
325D ALA* 4.1 14.4 - - + -
326D HIS* 3.9 47.3 - - + +
329D VAL* 4.0 30.1 - - + -
333D ARG* 3.1 25.5 + - - +
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Residues in contact with MET 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU 2.9 12.3 + - - +
22D ARG* 2.9 24.3 + - - +
24D LEU* 1.3 79.3 - - - +
26D PRO* 1.3 64.0 - - + +
27D ASP* 3.2 4.7 - - + +
28D LEU* 3.1 36.3 + - + +
329D VAL* 3.6 31.6 - - + +
332D ILE* 3.8 26.0 - - + -
333D ARG* 3.3 42.2 - - + +
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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