Contacts of the helix formed by residues 15 - 30 (chain B) in PDB entry 5A6C
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 ALA 15 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B SER* 1.3 63.6 + - - +
17B CYS* 3.8 9.2 - - + +
18B LEU* 3.6 27.2 + - - +
19B GLU* 3.3 29.2 + - - +
46B VAL* 5.9 2.0 - - + -
47B GLY 5.4 2.4 + - - +
48B THR* 4.4 10.9 + - - -
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Residues in contact with SER 16 (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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15B ALA* 1.3 79.4 - - - +
17B CYS* 1.3 60.8 + - - +
18B LEU 3.3 0.4 - - - -
19B GLU* 3.2 20.3 + - - +
20B LEU* 2.9 48.0 + - - +
46B VAL* 4.8 11.4 - - - +
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Residues in contact with CYS 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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15B ALA* 4.2 7.9 - - + +
16B SER* 1.3 80.2 - - - +
18B LEU* 1.3 56.7 + - - +
20B LEU* 3.6 4.6 - - - +
21B ALA* 2.9 30.5 + - - +
43B ALA* 3.5 22.6 - - - +
44B VAL* 5.4 0.4 - - - -
46B VAL* 3.8 15.7 - - + +
47B GLY 3.1 28.5 - - - +
48B THR* 3.7 18.2 - - - -
53B THR* 5.3 1.6 - - - -
54B LEU* 5.5 1.3 - - - -
57B ILE* 3.6 22.2 - - - -
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LYS* 5.9 5.8 - - - +
15B ALA* 3.6 21.4 - - - +
17B CYS* 1.3 79.0 - - - +
19B GLU* 1.3 61.0 + - + +
21B ALA* 3.3 3.6 + - - +
22B LEU* 2.9 54.8 + - + +
48B THR* 5.5 1.3 + - - +
53B THR* 5.2 13.9 - - + +
386B LEU* 4.3 22.0 - - + +
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Residues in contact with GLU 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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29A LYS* 6.3 0.9 - - - +
15B ALA 3.3 18.4 + - - +
16B SER* 3.2 24.2 + - - +
18B LEU* 1.3 77.7 - - + +
20B LEU* 1.3 58.4 + - + +
22B LEU* 3.1 12.6 + - + +
23B GLU* 3.0 27.4 + - - +
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Residues in contact with LEU 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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16B SER* 2.9 32.4 + - - +
17B CYS 3.6 3.4 - - - +
19B GLU* 1.3 73.8 - - + +
21B ALA* 1.3 65.9 + - - +
23B GLU* 3.1 7.3 + - - +
24B GLY 2.9 18.2 + - - -
39B PHE* 3.6 37.3 - - + +
42B ALA* 3.9 17.5 - - + -
43B ALA* 3.9 26.5 - - + +
46B VAL* 3.9 21.1 - - + -
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B CYS 2.9 18.5 + - - +
18B LEU* 3.3 6.3 + - + +
20B LEU* 1.3 75.9 - - - +
22B LEU* 1.3 57.4 + - - +
24B GLY 3.3 0.7 + - - -
25B GLU* 2.9 27.4 + - - +
40B PHE* 3.3 18.8 - - + -
43B ALA* 3.9 3.2 - - + +
57B ILE* 3.8 26.0 - - + -
386B LEU* 3.5 23.9 - - + +
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Residues in contact with LEU 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 LEU* 2.9 41.1 + - + +
19B GLU* 3.1 11.8 + - + +
21B ALA* 1.3 73.4 - - - +
23B GLU* 1.3 65.9 + - - +
25B GLU* 3.3 7.9 + - - +
26B ARG* 2.9 24.9 + - - +
386B LEU* 3.6 31.0 - - + +
387B ALA* 4.0 17.3 - - + +
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Residues in contact with GLU 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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19B GLU 3.0 12.4 + - - +
20B LEU* 3.4 8.3 - - - +
22B LEU* 1.3 76.3 - - - +
24B GLY* 1.3 57.3 + - - +
26B ARG* 2.6 49.1 + - - +
27B LEU* 2.9 53.4 + - + +
39B PHE* 3.9 26.2 - - + -
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Residues in contact with GLY 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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20B LEU 2.9 11.5 + - - -
21B ALA 3.3 3.8 + - - -
23B GLU* 1.3 76.3 - - - +
25B GLU* 1.3 55.4 + - - +
27B LEU* 3.2 1.3 + - - -
28B CYS* 2.9 29.1 + - - -
36B GLY* 3.4 34.0 - - - -
39B PHE* 3.7 7.6 - - - +
40B PHE* 3.5 9.4 - - - -
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Residues in contact with GLU 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 ALA 2.9 18.2 + - - +
22B LEU* 3.7 7.6 - - - +
24B GLY* 1.3 68.7 - - - +
26B ARG* 1.3 65.9 + - - +
28B CYS* 4.0 2.5 - - - +
29B LYS* 3.0 56.7 + - - +
40B PHE* 3.3 7.9 - - - -
60B GLN* 3.1 29.0 + - - +
385B SER* 3.8 8.2 - - - -
386B LEU* 2.9 34.8 + - - +
387B ALA* 3.4 20.5 + - - +
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Residues in contact with ARG 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 LEU 2.9 13.9 + - - +
23B GLU* 2.6 43.4 + - - +
25B GLU* 1.3 79.1 - - - +
27B LEU* 1.3 71.9 + - - +
29B LYS* 3.3 10.5 + - - +
30B SER* 3.1 34.1 + - - -
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Residues in contact with LEU 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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23B GLU* 2.9 40.7 + - - +
24B GLY 3.6 0.9 - - - +
26B ARG* 1.3 81.7 - - - +
28B CYS* 1.3 65.8 + - - +
30B SER* 2.8 21.5 + - - +
32B ASP* 2.9 31.2 + - + +
35B ALA* 3.9 15.5 - - + -
36B GLY* 3.6 19.7 - - - +
39B PHE* 3.4 36.1 - - + -
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Residues in contact with CYS 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 GLY 2.9 20.2 + - - +
25B GLU* 4.0 4.9 - - - +
27B LEU* 1.3 74.5 - - - +
29B LYS* 1.3 65.2 + - - +
31B GLY* 2.9 15.6 + - - -
32B ASP 3.8 6.6 + - - -
33B CYS* 4.0 33.0 - - - +
36B GLY* 3.9 12.8 - - - -
40B PHE* 3.8 19.7 - - + -
60B GLN* 5.4 2.2 - - - +
64B ALA* 4.4 10.1 - - - -
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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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131A LYS* 5.5 3.6 - - - +
132A VAL* 3.8 32.2 - - + +
188A LEU* 3.9 49.5 - - + +
190A ASP* 3.6 31.7 + - + +
25B GLU* 3.0 53.6 + - - +
26B ARG* 3.5 8.7 - - - +
28B CYS* 1.3 77.5 - - - +
30B SER* 1.3 57.0 + - - +
31B GLY 3.3 3.5 + - - -
387B ALA* 4.2 6.7 - - - +
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Residues in contact with SER 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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132A VAL* 5.4 4.7 - - - -
26B ARG* 3.1 22.5 + - - -
27B LEU* 2.8 25.1 + - - +
28B CYS 3.0 0.4 - - - -
29B LYS* 1.3 76.2 - - - +
31B GLY* 1.3 59.2 + - - +
32B ASP* 4.2 4.7 + - - +
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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