Contacts of the helix formed by residues 17 - 38 (chain B) in PDB entry 3OVS
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 17 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE 3.8 2.2 + - - -
16B PRO* 1.3 75.3 - - - +
18B GLU* 1.3 66.4 + - - +
19B GLU* 3.0 32.3 - - - +
20B GLU* 3.1 32.8 + - - +
21B VAL* 3.2 9.6 + - - +
55B LYS* 4.0 21.0 - - - +
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Residues in contact with GLU 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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16B PRO 3.9 0.8 + - - -
17B ASP* 1.3 71.8 - - - +
19B GLU* 1.3 58.8 + - - +
21B VAL* 3.2 13.4 + - + +
22B ARG* 2.5 43.2 + - - +
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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
----------------------------------------------------------
17B ASP* 3.0 30.6 - - - +
18B GLU* 1.3 84.8 + - - +
20B GLU* 1.3 58.9 + - - +
22B ARG* 3.7 17.4 - - + +
23B LYS* 3.3 29.8 + - - +
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Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PRO* 3.3 23.0 - - + +
17B ASP* 3.1 22.8 + - - +
19B GLU* 1.3 77.9 - - - +
21B VAL* 1.3 65.4 + - - +
22B ARG 3.2 0.4 - - - -
23B LYS* 3.4 9.2 + - + +
24B GLY* 3.2 18.4 + - - -
53B TRP* 3.9 7.7 + - - +
55B LYS* 3.8 5.9 - - - +
56B GLY* 3.0 35.6 + - - -
58B LEU* 3.6 35.1 - - + +
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Residues in contact with VAL 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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16B PRO* 3.9 18.8 - - + +
17B ASP 3.2 14.3 + - - +
18B GLU* 3.3 14.6 - - + +
20B GLU* 1.3 76.1 - - - +
22B ARG* 1.3 56.3 + - - +
24B GLY* 3.2 3.1 + - - -
25B ARG* 2.9 56.5 + - + +
48B TYR* 5.5 1.3 - - + -
53B TRP* 4.1 27.6 - - + -
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Residues in contact with ARG 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 GLU* 2.5 26.3 + - - +
19B GLU* 3.8 14.9 - - - +
20B GLU 3.2 0.2 - - - -
21B VAL* 1.3 73.1 - - - +
23B LYS* 1.3 63.6 + - - +
25B ARG* 4.2 5.7 - - + +
26B GLU* 3.4 50.9 + - + +
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Residues in contact with LYS 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 3.3 17.7 + - - +
20B GLU* 3.6 9.4 - - + +
22B ARG* 1.3 78.2 - - - +
24B GLY* 1.3 59.6 + - - +
26B GLU* 3.8 5.1 + - - +
27B ALA* 3.4 21.1 + - - +
58B LEU* 5.0 3.8 - - + -
105B LYS* 4.5 18.9 + - - +
106B GLY* 4.0 20.5 + - - -
107B VAL* 3.6 11.2 - - + +
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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 GLU 3.2 12.9 + - - -
21B VAL* 3.2 4.0 + - - -
23B LYS* 1.3 77.1 - - - +
25B ARG* 1.3 59.2 + - - +
27B ALA* 3.4 7.6 + - - +
28B GLU* 2.9 21.7 + - - +
48B TYR* 3.2 18.2 + - - -
58B LEU* 4.3 19.3 - - - -
60B ILE* 4.1 3.3 - - - +
107B VAL* 4.3 4.7 - - - -
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Residues in contact with ARG 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 VAL* 2.9 40.7 + - + +
22B ARG* 3.7 7.4 + - + +
24B GLY* 1.3 72.5 - - - +
26B GLU* 1.3 59.6 + - + +
27B ALA 3.0 4.3 - - - -
28B GLU* 3.0 27.6 + - - +
29B GLU* 3.1 17.2 + - - +
48B TYR* 3.3 27.8 + - - -
51B ASN* 4.3 19.0 + - - +
53B TRP* 4.7 1.8 - - - -
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Residues in contact with GLU 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 ARG* 3.4 45.3 + - + +
23B LYS* 4.1 6.1 - - - +
24B GLY 3.4 0.2 - - - -
25B ARG* 1.3 77.3 - - + +
27B ALA* 1.3 57.4 + - - +
29B GLU* 4.4 6.9 - - - +
30B GLU* 3.8 16.8 + - - +
105B LYS* 3.8 16.6 - - + +
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Residues in contact with ALA 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 LYS 3.4 16.7 + - - +
24B GLY 3.6 6.1 - - - +
25B ARG 3.0 0.2 - - - -
26B GLU* 1.3 78.7 - - - +
28B GLU* 1.3 62.5 + - - +
29B GLU 3.4 0.4 - - - -
30B GLU* 3.7 3.2 + - - +
31B LEU* 3.4 22.2 + - - +
60B ILE* 4.4 5.3 - - + +
104B VAL* 3.6 30.8 - - + +
105B LYS* 4.4 9.6 - - + -
107B VAL* 3.7 18.6 - - + -
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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 GLY 2.9 7.1 + - - +
25B ARG* 3.0 23.0 + - - +
27B ALA* 1.3 74.5 - - - +
29B GLU* 1.3 69.8 + - - +
31B LEU* 3.3 14.2 + - - +
32B ARG* 2.8 48.5 + - - +
44B PHE* 4.7 10.5 - - + -
48B TYR* 2.5 52.2 + - + +
60B ILE* 4.6 6.3 - - + -
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Residues in contact with GLU 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 ARG 3.1 14.5 + - - +
26B GLU* 4.7 6.3 - - - +
28B GLU* 1.3 78.7 - - - +
30B GLU* 1.3 66.2 + - - +
32B ARG* 2.9 33.5 + - - +
33B ARG* 3.2 48.8 + - + +
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLU 3.8 17.0 + - - +
27B ALA 3.7 6.3 + - - +
29B GLU* 1.3 77.8 - - - +
31B LEU* 1.3 60.1 + - - +
33B ARG* 3.6 26.4 + - - +
34B ARG* 2.8 68.8 + - - +
104B VAL* 3.8 13.0 - - + -
105B LYS* 4.2 17.8 + - + +
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Residues in contact with LEU 31 (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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27B ALA 3.4 10.6 + - - +
28B GLU* 3.3 11.2 + - - +
29B GLU 2.9 0.6 + - - -
30B GLU* 1.3 78.4 - - - +
32B ARG* 1.3 64.7 + - - +
34B ARG* 3.5 5.4 + - - +
35B LEU* 3.2 33.7 + - + +
44B PHE* 4.2 12.6 - - + -
60B ILE* 4.6 5.6 - - + -
62B VAL* 3.5 30.7 - - + -
86B VAL* 3.8 32.3 - - + +
87B LEU* 4.4 3.6 - - + -
104B VAL* 3.8 23.3 - - + +
109B VAL* 3.8 19.7 - - + -
111B VAL* 6.1 0.2 - - + -
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Residues in contact with ARG 32 (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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28B GLU* 2.8 46.7 + - - +
29B GLU* 2.9 25.1 + - - +
31B LEU* 1.3 76.0 - - - +
33B ARG* 1.3 58.1 + - + +
35B LEU* 3.4 1.2 + - - +
36B ASP* 3.0 40.3 + - - +
42B TYR* 3.8 32.2 + - - +
44B PHE* 3.4 40.7 - - + +
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Residues in contact with ARG 33 (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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29B GLU* 3.2 45.2 + - + +
30B GLU* 3.7 27.1 + - - +
32B ARG* 1.3 78.5 - - + +
34B ARG* 1.3 59.3 + - + +
36B ASP* 4.6 3.0 - - - +
37B GLU* 3.3 25.5 + - - +
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Residues in contact with ARG 34 (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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30B GLU* 2.8 52.9 + - - +
31B LEU* 3.9 6.3 - - - +
32B ARG 3.3 0.2 - - - -
33B ARG* 1.3 76.4 - - + +
35B LEU* 1.3 63.9 + - - +
37B GLU* 3.4 8.7 - - - +
38B LEU* 3.4 25.6 + - - +
85B ALA 5.3 0.7 - - - +
86B VAL* 2.9 48.2 + - + +
87B LEU* 4.1 0.8 - - - +
88B ASP* 2.8 37.9 + - - +
104B VAL* 4.2 10.4 - - - +
105B LYS* 5.4 4.0 - - - +
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Residues in contact with LEU 35 (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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31B LEU* 3.2 28.0 + - + +
32B ARG* 3.8 3.8 - - - +
34B ARG* 1.3 78.4 - - - +
36B ASP* 1.3 60.0 + - - +
38B LEU* 3.1 8.3 + - + +
39B GLY 3.1 28.6 + - - +
40B VAL* 4.2 15.0 - - + +
42B TYR* 3.7 37.7 - - + -
44B PHE* 5.2 0.9 - - + -
62B VAL* 4.0 18.2 - - + -
64B LEU* 4.1 22.7 - - + -
82B ILE* 4.1 17.9 - - + -
86B VAL* 4.2 18.2 - - + -
111B VAL* 5.7 1.1 - - + -
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Residues in contact with ASP 36 (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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32B ARG* 3.0 24.7 + - - +
33B ARG* 4.6 3.8 - - - +
35B LEU* 1.3 72.3 - - - +
37B GLU* 1.3 61.3 + - - +
38B LEU 3.1 1.3 - - - -
39B GLY* 2.9 26.6 + - - +
42B TYR* 3.2 37.3 + - - -
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Residues in contact with GLU 37 (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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33B ARG 3.3 20.0 + - - +
34B ARG* 3.4 10.1 - - - +
36B ASP* 1.3 78.7 - - - +
38B LEU* 1.3 66.8 + - + +
39B GLY 3.7 0.3 + - - -
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Residues in contact with LEU 38 (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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34B ARG 3.4 13.0 + - - +
35B LEU* 3.1 9.5 + - + +
36B ASP 3.1 0.6 - - - -
37B GLU* 1.3 86.6 - - + +
39B GLY* 1.3 58.6 + - - +
40B VAL* 3.4 19.7 + - + +
82B ILE* 4.7 19.1 - - + +
85B ALA* 3.6 33.0 - - + +
86B VAL* 4.2 8.5 - - + -
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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