Contacts of the helix formed by residues 16 - 30 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B GLY* 1.3 74.1 - - - +
17B GLU* 1.3 69.8 + - + +
19B THR* 2.9 23.4 + - - -
20B ARG* 3.1 7.7 + - - +
44B LEU 3.8 0.3 - - - +
45B GLY* 3.2 7.3 - - - -
46B ILE* 2.8 30.7 + - - +
49B ARG* 2.9 16.6 + - - -
73B CYS* 4.4 0.4 - - - -
74B ALA 3.0 5.7 + - - -
75B THR* 3.4 4.5 - - - -
76B ILE* 2.8 54.3 + - + +
311B THR* 3.6 4.4 - - + -
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ASP* 1.3 73.6 - - + +
18B MET* 1.3 67.1 + - - +
20B ARG* 3.0 28.8 + - - +
21B ILE* 3.3 5.9 + - - +
76B ILE* 3.5 23.0 - - + +
82B ARG* 3.1 27.4 + - - -
85B GLU* 4.6 1.2 - - - +
86B PHE* 5.0 1.7 - - + -
311B THR* 2.6 29.4 + - - +
313B THR* 2.8 26.6 + - - +
316B TYR* 3.6 39.8 - - + -
317B ARG* 3.9 9.0 + - - -
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Residues in contact with MET 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLU* 1.3 79.8 - - - +
19B THR* 1.3 62.9 + - - +
21B ILE* 3.2 27.0 + - + +
22B ILE* 3.1 22.1 + - + +
311B THR 3.2 12.9 + - - +
312B VAL* 3.6 14.1 - - + +
315B HIS* 4.0 10.3 - - + +
316B TYR* 3.6 29.5 - - + -
319B TYR* 4.2 14.6 - - + -
325B THR* 3.5 25.6 - - + +
327B THR* 3.6 29.4 - - + +
394B THR* 4.4 14.1 - - + +
395B PHE* 5.3 2.2 - - + -
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Residues in contact with THR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ASP 2.9 16.1 + - - -
18B MET* 1.3 75.9 - - - +
20B ARG* 1.3 50.0 + - - +
22B ILE* 3.2 11.2 + - + +
23B TRP* 2.6 37.4 + - - +
73B CYS* 3.6 12.5 - - - -
74B ALA* 3.5 16.6 + - + +
309B HIS* 3.5 21.1 - - + -
310B GLY 3.3 23.3 - - - +
311B THR* 3.3 15.4 + - - -
312B VAL* 4.3 4.5 - - + -
332B SER* 4.5 9.4 + - - +
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Residues in contact with ARG 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLN* 5.7 4.3 - - + -
15B GLY 3.5 22.7 - - - +
16B ASP* 3.1 15.5 + - - +
17B GLU* 3.0 18.6 + - - +
19B THR* 1.3 77.0 + - - +
21B ILE* 1.3 81.5 + - - +
23B TRP* 3.2 4.5 + - + +
24B GLU* 3.2 30.5 + - + +
73B CYS* 3.7 9.6 - - - -
316B TYR* 3.5 36.6 + - - -
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLU 3.3 2.0 + - - +
18B MET* 3.2 22.1 + - + +
20B ARG* 1.3 99.5 - - - +
22B ILE* 1.3 64.9 + - + +
24B GLU* 3.4 5.9 + - - +
25B LEU* 3.2 36.3 + - + +
316B TYR* 4.0 20.2 - - + -
319B TYR* 3.5 40.6 - - + +
394B THR* 5.9 0.2 - - + -
395B PHE* 4.4 17.3 - - + -
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B MET* 3.1 19.1 + - + +
19B THR* 3.6 12.1 - - + +
21B ILE* 1.3 75.2 - - + +
23B TRP* 1.3 67.9 + - - +
25B LEU* 3.1 10.6 + - + +
26B ILE* 2.9 34.6 + - + +
309B HIS* 6.5 0.7 - - + -
327B THR* 3.6 46.7 - - + +
328B ASN 4.6 5.8 - - - +
329B PRO* 3.6 27.6 - - + -
332B SER* 4.4 9.9 - - - +
394B THR* 4.1 17.7 - - + -
398B MET* 5.1 2.7 - - + -
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Residues in contact with TRP 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLU* 2.9 31.6 + - + +
13B MET 4.0 4.0 + - - -
14B GLN* 4.5 9.0 - - + -
19B THR* 2.6 22.7 + - - +
20B ARG* 3.4 7.0 - - + +
22B ILE* 1.3 73.3 - - - +
24B GLU* 1.3 72.1 + - - +
26B ILE* 3.3 6.7 + - + +
27B LYS* 3.1 27.9 + - + +
71B VAL* 3.7 22.7 - - + -
72B LYS 3.4 30.7 - - - -
73B CYS* 3.6 31.6 - - + -
307B ALA 6.0 0.4 - - - -
332B SER* 4.1 26.7 - - - -
335B ALA* 4.4 5.4 - - + -
336B TRP* 3.2 44.4 - + - -
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLN* 4.0 11.9 + - - +
20B ARG* 3.2 19.1 + - + +
21B ILE* 3.9 8.5 - - - +
23B TRP* 1.3 81.3 - - - +
25B LEU* 1.3 61.9 + - + +
27B LYS* 2.9 38.6 + - - +
28B GLU* 3.0 44.4 + - + +
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 3.2 23.3 + - + +
22B ILE* 3.1 11.7 + - - +
24B GLU* 1.3 75.0 - - + +
26B ILE* 1.3 64.7 + - - +
28B GLU* 4.5 4.0 - - + +
29B LYS* 2.9 53.9 + - + +
394B THR* 4.9 5.6 - - + -
395B PHE* 3.8 38.4 - - + -
398B MET* 3.9 30.0 - - + +
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Residues in contact with ILE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ILE* 2.9 28.4 + - + +
23B TRP* 3.3 10.7 + - + +
25B LEU* 1.3 76.3 - - - +
27B LYS* 1.3 56.5 + - - +
30B LEU* 2.9 30.1 + - + +
31B ILE* 3.2 21.9 + - + -
329B PRO 4.1 0.4 - - - +
332B SER* 3.6 33.7 - - - +
333B ILE* 3.6 33.9 - - + +
336B TRP* 3.8 25.6 - - + +
398B MET* 4.0 15.5 - - + -
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLU* 2.5 43.6 + - - +
14B GLN* 3.5 10.3 - - - +
23B TRP* 3.1 14.3 + - + +
24B GLU* 2.9 39.9 + - - +
25B LEU 3.2 0.2 - - - -
26B ILE* 1.3 78.1 - - - +
28B GLU* 1.3 61.1 + - - +
31B ILE* 3.5 8.7 + - + -
32B PHE* 2.8 65.0 + - + +
39B LEU* 5.1 2.5 - - + +
336B TRP* 3.6 30.3 - - + -
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLU* 3.0 33.9 + - + +
25B LEU* 4.2 3.8 - - + +
27B LYS* 1.3 76.9 - - - +
29B LYS* 1.3 65.1 + - + +
32B PHE* 3.6 29.9 - - - +
33B PRO* 3.3 20.5 - - - +
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Residues in contact with LYS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU* 2.9 40.8 + - + +
28B GLU* 1.3 86.4 - - + +
30B LEU* 1.3 74.1 + - + +
31B ILE 3.9 0.2 - - - -
33B PRO* 3.9 12.3 - - - +
34B TYR* 4.1 9.0 + - - -
395B PHE* 5.5 1.6 - - - +
398B MET* 4.2 28.3 - - + +
399B ASP* 3.0 28.0 + - - +
402B GLY* 4.6 9.2 - - - +
405B LEU* 4.6 0.3 - - - +
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ILE* 2.9 15.7 + - + +
29B LYS* 1.3 88.8 - - + +
31B ILE* 1.3 63.9 + - + +
33B PRO* 4.3 0.2 - - - -
34B TYR* 3.5 12.6 - - - -
333B ILE* 3.6 36.3 - - + -
355B PHE* 3.2 22.0 - - - -
359B LEU* 4.2 20.6 - - + -
398B MET* 3.8 20.4 - - + -
401B LEU* 4.1 10.5 - - + +
402B GLY* 3.8 25.4 - - - +
405B LEU* 3.5 22.9 - - + +
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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