Contacts of the helix formed by residues 16 - 31 (chain D) in PDB entry 1H69
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 16 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B PHE 6.0 0.4 - - - -
11D HIS* 3.2 43.2 + - - -
13D GLU* 2.8 20.6 + - - +
14D ARG 3.4 0.5 - - - +
15D THR* 1.3 83.2 + - - +
17D PHE* 1.3 65.0 + - - +
19D TYR* 3.2 16.8 + - - +
20D ALA 3.2 15.1 + - - -
1274D FAD 3.6 23.3 + - - -
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Residues in contact with PHE 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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16D SER* 1.3 70.4 - - - +
18D ASN* 1.3 58.8 + - - +
20D ALA* 3.0 4.1 + - + +
21D MET* 2.8 66.0 + - + +
147D THR* 4.2 9.6 - - + -
189D THR* 4.5 3.1 - - - -
192D ILE* 3.4 28.5 - - + -
200D ARG* 3.8 27.1 - - + -
203D ILE* 3.8 25.4 - - + -
204D LEU* 3.8 29.2 - - + -
1274D FAD 2.8 64.4 + + - +
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Residues in contact with ASN 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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9D LEU* 3.7 5.3 - - + +
11D HIS* 3.8 21.5 - - + -
16D SER* 3.1 0.6 - - - +
17D PHE* 1.3 77.2 - - - +
19D TYR* 1.3 60.4 + - - +
21D MET* 3.4 1.1 + - - -
22D LYS* 3.0 19.1 + - - +
100D GLN* 2.9 40.5 + - - +
101D PHE* 3.1 20.3 + - - -
102D PRO* 3.5 17.2 - - - +
147D THR* 2.9 25.3 + - - +
1274D FAD 2.9 30.5 + - - -
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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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9D LEU* 3.7 19.0 - - + +
11D HIS* 5.9 0.9 - - + -
13D GLU 3.7 12.1 - - - +
14D ARG* 3.4 56.8 + - + +
16D SER* 3.2 11.5 + - - +
17D PHE 3.2 0.4 - - - -
18D ASN* 1.3 76.9 - - - +
20D ALA* 1.3 67.7 + - - +
22D LYS* 3.1 34.7 + - - +
23D GLU* 2.9 51.2 + - + +
40D ASP* 3.9 14.4 - - - -
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Residues in contact with ALA 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 SER 3.2 8.8 + - - +
17D PHE* 3.0 11.1 + - + +
19D TYR* 1.3 81.7 - - - +
21D MET* 1.3 56.5 + - - +
23D GLU* 3.1 9.1 + - - +
24D ALA* 2.8 29.5 + - - +
204D LEU* 3.9 14.4 - - + +
1274D FAD 3.2 39.3 - - + +
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Residues in contact with MET 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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17D PHE* 2.8 52.5 + - + +
18D ASN 3.6 0.7 - - - +
20D ALA* 1.3 73.5 - - - +
22D LYS* 1.3 61.4 + - - +
24D ALA* 4.3 0.4 - - - -
25D ALA* 3.2 17.8 + - - +
100D GLN* 3.5 28.6 - - - +
145D SER* 4.4 11.0 - - - -
147D THR* 5.0 2.0 - - + -
187D GLN* 5.7 0.7 - - + -
189D THR* 4.4 10.8 - - - -
203D ILE* 4.2 9.6 - - + +
204D LEU* 3.6 24.0 - - + -
207D TRP* 3.2 55.1 + - + -
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Residues in contact with LYS 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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7D ILE* 3.6 27.7 - - + +
9D LEU* 3.9 26.7 - - + -
18D ASN 3.0 14.0 + - - +
19D TYR* 3.1 45.7 + - - +
21D MET* 1.3 74.2 - - - +
23D GLU* 1.3 83.4 + - - +
25D ALA* 3.5 4.6 + - - +
26D ALA* 3.0 25.3 + - - +
38D GLU* 2.9 40.3 + - + +
40D ASP* 4.9 2.1 + - - -
100D GLN* 4.4 6.3 - - + +
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Residues in contact with GLU 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* 2.9 41.0 + - + +
20D ALA* 3.1 11.0 + - - +
22D LYS* 1.3 103.7 + - - +
24D ALA* 1.3 65.0 + - - +
26D ALA* 3.4 6.1 + - - +
27D ALA* 3.0 26.3 + - - +
38D GLU* 4.3 4.0 - - - +
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Residues in contact with ALA 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 ALA 2.8 16.9 + - - +
21D MET* 3.8 6.1 - - - +
23D GLU* 1.3 77.1 - - - +
25D ALA* 1.3 57.1 + - - +
27D ALA* 4.6 1.3 - - - -
28D ALA* 2.9 31.9 + - - +
204D LEU* 4.1 22.9 - - + +
207D TRP* 4.4 4.3 - - + -
208D LYS* 3.6 31.3 - - + +
211D LEU* 5.0 0.2 - - - -
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Residues in contact with ALA 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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7D ILE* 3.9 15.7 - - + -
21D MET 3.2 15.3 + - - +
22D LYS* 3.8 5.2 - - - +
24D ALA* 1.3 75.1 - - - +
26D ALA* 1.3 67.7 + - - +
29D LEU* 2.7 31.2 + - - +
98D ILE* 4.3 12.3 - - + -
207D TRP* 3.6 8.9 - - + +
211D LEU* 3.4 28.0 - - + -
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Residues in contact with ALA 26 (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 ILE* 3.7 14.7 - - + +
22D LYS 3.0 18.1 + - - +
23D GLU* 3.7 9.6 - - - +
24D ALA 3.3 0.2 - - - -
25D ALA* 1.3 76.8 - - - +
27D ALA* 1.3 64.1 + - - +
29D LEU* 4.0 0.7 - - - +
30D LYS* 3.0 41.3 + - - +
36D VAL* 4.3 15.0 - - + -
38D GLU* 4.4 12.8 - - - +
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Residues in contact with ALA 27 (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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23D GLU 3.0 18.1 + - - +
24D ALA* 3.8 3.6 - - - +
26D ALA* 1.3 76.4 - - - +
28D ALA* 1.3 55.0 + - - +
30D LYS* 3.7 7.1 - - - +
31D LYS* 2.8 47.1 + - + +
208D LYS* 3.8 17.0 - - - +
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Residues in contact with ALA 28 (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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24D ALA 2.9 18.7 + - - +
25D ALA 3.8 2.5 - - - +
27D ALA* 1.3 76.4 - - - +
29D LEU* 1.3 68.2 + - + +
31D LYS* 3.4 9.6 + - - +
32D LYS* 3.2 22.1 + - - +
208D LYS* 3.7 44.6 - - + +
211D LEU* 4.4 5.6 - - + -
212D GLU* 5.7 4.5 - - + +
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Residues in contact with LEU 29 (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 ALA* 3.4 32.3 - - + -
7D ILE* 5.0 3.1 - - + -
25D ALA* 2.7 36.1 + - + +
28D ALA* 1.3 72.4 - - - +
30D LYS* 1.3 58.8 + - - +
32D LYS* 2.9 20.9 + - - +
33D GLY 3.2 0.3 + - - -
34D TRP* 3.0 42.2 + - + +
36D VAL* 3.8 11.0 - - + -
96D LEU* 4.2 7.6 - - + -
98D ILE* 4.2 15.0 - - + -
211D LEU* 3.4 45.1 - - + +
214D ILE* 5.8 0.4 - - + -
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Residues in contact with LYS 30 (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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26D ALA* 3.0 33.8 + - + +
27D ALA* 3.7 5.6 - - - +
29D LEU* 1.3 69.8 - - - +
31D LYS* 1.3 57.7 + - + +
32D LYS 2.9 4.7 - - - -
33D GLY* 2.6 26.2 + - - -
34D TRP 3.6 15.6 + - - +
36D VAL* 3.8 37.7 + - + +
38D GLU* 5.6 2.6 + - - -
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Residues in contact with LYS 31 (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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27D ALA* 2.8 36.4 + - + +
28D ALA* 3.6 7.6 - - - +
29D LEU 3.3 0.2 - - - -
30D LYS* 1.3 75.3 - - + +
32D LYS* 1.3 62.7 + - + +
33D GLY 3.3 1.1 - - - -
208D LYS* 2.6 39.0 - - - +
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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