Contacts of the helix formed by residues 16 - 30 (chain D) in PDB entry 6B0Z
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 ASP 16 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLY* 1.3 74.0 - - - +
17D GLU* 1.3 71.7 + - + +
19D THR* 3.0 22.5 - - - +
20D ARG* 3.1 7.1 + - - +
45D GLY* 3.0 9.8 - - - -
46D ILE* 2.8 29.6 + - - +
47D GLU* 4.3 1.0 - - - +
49D ARG* 2.7 15.3 + - - -
73D CYS* 4.5 0.4 - - - -
74D ALA 3.1 5.7 + - - -
75D THR* 3.4 1.1 - - - -
76D ILE* 2.5 57.9 + - + +
311D THR* 3.9 4.3 - - + -
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Residues in contact with GLU 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 ASP* 1.3 72.5 - - - +
18D MET* 1.3 60.6 + - - +
20D ARG* 2.9 33.0 + - - +
21D ILE* 3.3 9.7 + - - +
76D ILE* 3.8 15.3 - - + +
82D ARG* 3.2 27.5 + - - -
85D GLU* 4.6 1.0 - - - +
86D PHE* 5.6 1.5 - - + -
311D THR* 2.4 34.5 + - - +
313D THR* 2.7 27.6 + - - +
316D TYR* 3.3 40.5 - - + -
317D ARG* 3.6 12.4 + - - +
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Residues in contact with MET 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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17D GLU* 1.3 81.0 - - - +
19D THR* 1.3 62.7 + - - +
20D ARG 3.2 1.0 + - - -
21D ILE* 3.2 28.5 + - + +
22D ILE* 3.2 24.2 + - + +
311D THR 3.3 12.9 + - - +
312D VAL* 3.6 14.1 - - + +
315D HIS* 4.0 12.6 - - + +
316D TYR* 3.3 24.9 - - + -
319D TYR* 4.0 10.3 - - + -
325D THR* 3.5 27.6 - - + +
327D THR* 3.5 30.5 - - + +
394D THR* 4.1 15.3 - - + +
395D PHE* 5.5 1.6 - - + -
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Residues in contact with THR 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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16D ASP 3.0 20.0 - - - +
18D MET* 1.3 78.2 - - - +
20D ARG* 1.3 56.9 + - - +
22D ILE* 3.9 11.0 - - - +
23D TRP* 2.9 24.1 + - - +
73D CYS* 3.2 18.0 - - - -
74D ALA* 3.5 30.3 + - + +
309D HIS* 4.6 8.1 - - - -
310D GLY 4.1 10.5 - - - -
311D THR* 3.6 20.4 + - - -
312D VAL* 5.3 1.9 - - - +
327D THR* 6.2 0.2 - - - -
332D SER* 4.0 15.4 + - - -
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Residues in contact with ARG 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D GLN* 5.7 4.9 - - + -
15D GLY 3.3 24.9 + - - +
16D ASP* 3.1 15.1 + - - +
17D GLU 2.9 20.1 + - - +
19D THR* 1.3 75.2 - - - +
21D ILE* 1.3 73.7 + - - +
23D TRP* 3.2 11.3 + - + +
24D GLU* 3.4 19.7 + - + +
43D ASP* 6.1 0.7 - - - -
73D CYS* 3.8 8.3 - - - -
316D TYR* 2.8 37.8 + - - -
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Residues in contact with ILE 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 GLU 3.7 7.9 - - - +
18D MET* 3.2 18.1 + - + +
20D ARG* 1.3 89.0 - - - +
22D ILE* 1.3 63.1 + - + +
24D GLU* 3.5 5.4 + - - +
25D LEU* 3.4 24.2 + - + +
316D TYR* 3.6 20.4 - - + -
319D TYR* 3.4 50.0 - - + +
394D THR* 6.2 0.4 - - + -
395D PHE* 4.5 23.1 - - + -
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Residues in contact with ILE 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 MET* 3.2 19.8 + - + +
19D THR* 3.9 7.2 - - - +
20D ARG 3.2 0.4 - - - -
21D ILE* 1.3 73.9 - - + +
23D TRP* 1.3 68.0 + - - +
25D LEU* 3.1 11.3 + - + +
26D ILE* 3.0 33.9 + - + +
309D HIS* 6.6 0.2 - - + -
327D THR* 3.6 48.2 - - + +
328D ASN 4.5 5.8 - - - +
329D PRO* 3.6 28.7 - - + -
332D SER* 4.5 9.0 - - - +
394D THR* 4.0 18.6 - - + -
398D MET* 5.5 2.7 - - - -
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Residues in contact with TRP 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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12D GLU* 2.8 26.5 + - - -
13D MET 4.2 4.5 + - - -
14D GLN* 4.5 8.0 - - + +
19D THR* 2.9 21.7 + - - +
20D ARG* 3.2 8.4 + - + +
22D ILE* 1.3 78.4 - - - +
24D GLU* 1.3 65.8 + - - +
26D ILE* 3.3 9.1 + - + +
27D LYS* 3.3 35.2 + - - +
71D VAL* 3.9 16.2 - - + -
72D LYS 3.4 35.0 - - - -
73D CYS* 3.5 33.4 - - + -
332D SER* 4.3 24.0 - - - -
335D ALA* 4.8 4.5 - - + -
336D TRP* 3.2 44.7 - + - -
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Residues in contact with GLU 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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14D GLN* 4.1 18.7 + - - +
20D ARG* 3.4 16.4 + - + +
21D ILE* 4.1 6.7 - - - +
22D ILE 3.2 0.6 - - - -
23D TRP* 1.3 77.1 - - + +
25D LEU* 1.3 66.0 + - + +
27D LYS* 2.7 41.8 + - - +
28D GLU* 3.0 31.0 + - - +
32D PHE* 5.7 1.2 - - - -
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Residues in contact with LEU 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 ILE* 3.4 17.6 + - + +
22D ILE* 3.1 14.6 + - + +
24D GLU* 1.3 78.6 - - + +
26D ILE* 1.3 56.6 + - - +
28D GLU* 4.0 15.0 - - - +
29D LYS* 2.9 62.5 + - + +
394D THR* 5.3 6.5 - - + -
395D PHE* 3.9 35.0 - - + -
398D MET* 3.6 26.5 - - + +
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Residues in contact with ILE 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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22D ILE* 3.0 25.0 + - + +
23D TRP* 3.5 10.1 - - - +
24D GLU 3.2 0.2 - - - -
25D LEU* 1.3 77.0 - - - +
27D LYS* 1.3 58.9 + - - +
30D LEU* 3.0 33.9 + - + +
31D ILE* 3.2 20.4 + - + -
329D PRO* 4.2 0.7 - - + +
332D SER* 3.6 33.0 - - - +
333D ILE* 3.7 25.1 - - + +
336D TRP* 4.0 25.4 - - + +
398D MET* 3.5 21.8 - - + -
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Residues in contact with LYS 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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12D GLU* 2.5 48.7 + - - +
14D GLN* 4.0 2.8 - - - +
23D TRP* 3.3 16.0 + - - +
24D GLU* 2.7 44.9 + - - +
26D ILE* 1.3 76.7 - - - +
28D GLU* 1.3 58.8 + - - +
31D ILE* 4.0 7.6 - - + -
32D PHE* 2.8 65.4 + - + -
39D LEU* 5.2 2.1 - - + +
336D TRP* 3.5 30.3 - - + -
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Residues in contact with GLU 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 GLU* 3.0 23.0 + - - +
25D LEU* 3.7 21.7 - - - +
27D LYS* 1.3 79.9 - - + +
29D LYS* 1.3 78.6 + - + +
32D PHE* 4.3 10.4 - - + +
33D PRO* 3.2 21.6 - - - +
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Residues in contact with LYS 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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25D LEU* 2.9 36.5 + - + +
28D GLU* 1.3 95.6 + - + +
30D LEU* 1.3 71.4 + - + +
33D PRO* 3.9 11.2 - - - +
34D TYR* 4.0 10.4 + - - -
398D MET* 4.0 31.6 - - + +
399D ASP* 3.4 28.2 + - - +
402D GLY* 4.5 8.7 - - - -
405D LEU* 4.4 0.5 - - - +
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Residues in contact with LEU 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 ILE* 3.0 13.8 + - + +
29D LYS* 1.3 87.7 - - + +
31D ILE* 1.3 62.4 + - + +
34D TYR* 3.4 20.3 - - - -
333D ILE* 3.6 30.3 - - + -
355D PHE* 3.4 14.6 - - - -
359D LEU* 4.3 20.8 - - + +
398D MET* 3.5 30.5 - - + -
401D LEU* 4.1 9.6 - - + +
402D GLY* 3.8 25.8 - - - +
405D LEU* 3.5 25.6 - - + +
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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
------------------------------------------------------------
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