Contacts of the helix formed by residues 13 - 34 (chain F) in PDB entry 1VZJ
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 GLU 13 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F GLN 3.5 13.4 - - - +
10F TRP 3.2 9.8 + - - +
11F LYS 3.0 1.0 - - - -
12F ALA* 1.3 80.7 - - - +
14F PHE* 1.3 62.2 + - - +
15F HIS 3.5 0.8 + - - -
16F ARG* 3.7 19.1 + - - +
17F TRP* 3.5 18.7 + - - +
14G PHE* 3.7 29.1 - - + -
17G TRP* 3.7 30.9 - - + -
18G SER* 4.8 4.7 + - - -
21G MSE 5.9 0.3 - - - +
9J LEU* 4.3 6.3 - - + -
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Residues in contact with PHE 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E GLU* 3.4 33.2 - - + -
10F TRP 4.0 2.3 + - - +
11F LYS* 3.1 19.3 + - - +
13F GLU* 1.3 74.8 - - - +
15F HIS* 1.3 72.1 + - + +
16F ARG 3.2 2.2 - - - -
17F TRP* 3.3 15.4 + + - -
18F SER* 2.9 45.4 + - - -
8J PRO* 6.5 0.4 - - + -
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Residues in contact with HIS 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F LYS 4.5 1.4 + - - -
12F ALA 4.4 7.2 + - - +
13F GLU 3.5 0.6 - - - -
14F PHE* 1.3 88.6 - - + +
16F ARG* 1.3 68.0 + - + +
18F SER* 4.0 3.1 - - - -
19F SER* 3.1 31.2 + - - -
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Residues in contact with ARG 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F ALA 5.1 1.7 + - - +
13F GLU* 3.7 22.7 + - - +
14F PHE 3.2 0.2 - - - -
15F HIS* 1.3 82.2 - - + +
17F TRP* 1.3 66.5 + - - +
19F SER* 3.0 9.7 + - - -
20F TYR* 2.9 62.2 + - + -
17G TRP* 6.2 0.9 - - + -
21G MSE 5.0 9.2 - - + -
25G LYS* 4.6 11.1 - - - +
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Residues in contact with TRP 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E GLU* 3.3 53.4 - - + -
16E ARG* 5.0 0.7 - - - -
17E TRP* 4.2 4.3 - - + -
13F GLU 3.5 11.2 + - - +
14F PHE* 3.3 19.4 + + - +
16F ARG* 1.3 79.8 - - - +
18F SER* 1.3 77.0 + - - +
20F TYR* 3.0 10.9 + - - +
21F MSE 2.8 60.3 + - + +
17G TRP* 3.8 28.7 - + + -
21G MSE 4.0 11.0 - - - -
5J PRO* 4.3 7.4 - - + +
6J PRO 2.9 24.1 + - - -
8J PRO* 3.5 37.5 - - + +
9J LEU 5.3 0.2 - - - -
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Residues in contact with SER 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E GLU* 4.6 2.5 + - - -
16E ARG* 4.5 10.4 + - - +
14F PHE* 2.9 43.7 + - - -
15F HIS* 4.0 4.5 - - - -
17F TRP* 1.3 87.4 - - - +
19F SER* 1.3 56.2 + - - +
21F MSE 3.2 6.2 + - - +
22F VAL* 2.9 31.9 + - - +
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Residues in contact with SER 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F HIS* 3.1 25.5 + - - -
16F ARG* 3.0 13.6 + - - -
18F SER* 1.3 73.8 - - - +
20F TYR* 1.3 66.4 + - - +
22F VAL* 2.8 26.6 - - - +
23F HIS* 2.8 35.8 + - - -
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Residues in contact with TYR 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ARG* 2.9 52.9 + - + -
17F TRP* 3.6 5.6 - - - +
19F SER* 1.3 82.1 - - - +
21F MSE 1.3 57.3 + - - +
23F HIS* 3.8 7.9 - + + +
24F TRP* 2.9 34.0 + - - +
21G MSE 3.1 50.9 + - + +
24G TRP* 3.3 26.2 - + + -
25G LYS* 3.0 55.1 - - + +
28G PHE* 6.1 1.1 - + - -
5J PRO* 4.0 9.0 - - + -
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Residues in contact with MSE 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ARG* 3.7 16.8 - - - +
17E TRP* 4.0 15.3 - - + -
20E TYR* 3.2 54.3 + - + -
17F TRP* 2.8 48.0 + - + +
18F SER* 3.3 14.4 - - - +
19F SER 3.1 0.2 - - - -
20F TYR* 1.3 78.8 - - - +
22F VAL* 1.3 60.1 + - - +
24F TRP* 4.2 2.5 - - + -
25F LYS* 3.5 8.3 + - - +
4J PRO* 3.4 14.8 - - + -
5J PRO* 3.1 38.5 - - + +
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Residues in contact with VAL 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ARG* 4.6 8.9 - - - +
20E TYR* 5.5 0.4 - - - -
18F SER* 2.9 15.7 + - - +
19F SER* 2.8 30.7 - - - +
21F MSE 1.3 73.5 - - - +
23F HIS* 1.3 72.3 + - + +
24F TRP 3.0 2.0 + - - -
25F LYS* 3.1 5.0 + - - +
26F ASN* 3.1 39.7 + - - +
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Residues in contact with HIS 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F SER* 2.8 44.5 + - - +
20F TYR* 3.8 9.6 - + + +
22F VAL* 1.3 80.7 - - + +
24F TRP* 1.3 64.9 + - - +
26F ASN* 3.6 8.0 + - - +
27F GLN* 3.3 16.1 + - - +
28G PHE* 3.9 26.1 - + + -
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Residues in contact with TRP 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E TYR* 3.6 54.5 - + + -
23E HIS* 6.0 0.4 - - + -
24E TRP* 4.0 13.0 - + + -
20F TYR 2.9 18.2 + - - +
21F MSE 4.0 3.1 - - - +
23F HIS* 1.3 73.5 - - - +
25F LYS* 1.3 80.8 + - + +
27F GLN* 2.5 30.5 + - - +
28F PHE* 2.9 42.5 + + + -
24G TRP* 4.1 12.3 - + + -
28G PHE* 4.2 14.8 - + - -
1J LEU* 4.5 10.1 - - + +
2J LEU* 3.0 30.4 + - + +
3J THR 3.3 11.9 + - - -
4J PRO* 3.5 28.9 - - + -
5J PRO* 4.2 7.6 - - + -
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Residues in contact with LYS 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E TYR* 3.8 39.2 + - + +
23E HIS* 5.2 10.8 - - - -
21F MSE 3.5 12.1 + - - +
22F VAL* 3.1 9.1 + - - +
24F TRP* 1.3 90.7 - - + +
26F ASN* 1.3 61.0 + - - +
28F PHE* 2.7 37.4 + - + +
29F ASP* 3.0 41.5 + - - +
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Residues in contact with ASN 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F VAL* 3.1 28.9 + - - +
23F HIS* 3.7 9.7 - - - +
24F TRP 2.9 1.2 + - - -
25F LYS* 1.3 81.8 - - - +
27F GLN* 1.3 58.0 + - - +
29F ASP* 3.4 9.0 + - - +
30F HIS* 3.0 44.8 + - + +
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Residues in contact with GLN 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F HIS 3.3 8.9 + - - +
24F TRP* 2.5 15.6 + - - +
26F ASN* 1.3 74.7 - - - +
28F PHE* 1.3 62.1 + - - +
30F HIS* 4.0 5.8 - - + +
31F TYR* 3.6 38.3 + - + +
28G PHE* 4.3 6.3 - - + -
32G SER* 3.8 14.1 - - - +
1J LEU* 3.2 37.3 - - + +
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Residues in contact with PHE 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E HIS* 3.7 47.6 - - + -
24E TRP* 4.2 7.6 - - - -
27E GLN* 4.0 26.2 - - + -
24F TRP* 2.9 32.9 + + + +
25F LYS* 2.7 28.1 + - + +
27F GLN* 1.3 79.1 - - - +
29F ASP* 1.3 71.3 + - - +
31F TYR* 4.4 0.9 - - - +
32F SER* 3.0 40.8 + - - -
1J LEU* 5.0 9.2 - - - +
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Residues in contact with ASP 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F LYS* 3.0 41.4 + - - +
26F ASN* 3.8 10.0 + - - +
28F PHE* 1.3 91.5 - - - +
30F HIS* 1.3 70.4 + - + +
32F SER* 2.6 23.7 + - - +
33F LYS* 3.2 25.8 - - - +
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Residues in contact with HIS 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F ASN* 3.0 31.1 + - + +
27F GLN* 3.9 4.7 + - - +
29F ASP* 1.3 84.6 - - + +
31F TYR* 1.3 64.1 + - + +
33F LYS* 4.5 9.2 + - + +
34F GLN* 4.3 10.9 + - - +
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Residues in contact with TYR 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F GLN* 3.6 34.9 + - + +
28F PHE* 4.4 1.1 - - - +
29F ASP 3.3 0.4 - - - -
30F HIS* 1.3 80.2 - - + +
32F SER* 1.3 57.9 + - - +
33F LYS 3.3 0.4 - - - -
34F GLN* 2.7 43.4 + - + +
31G TYR 4.9 4.7 + - - -
32G SER* 6.4 1.6 - - - -
34G GLN* 4.3 23.2 + - - +
1J LEU* 5.3 20.4 - - + +
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Residues in contact with SER 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F PHE* 3.0 32.8 + - - -
29F ASP* 2.6 25.2 + - - -
31F TYR* 1.3 77.1 - - - +
33F LYS* 1.3 77.1 + - - +
34F GLN 3.2 4.9 + - - -
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Residues in contact with LYS 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F ASP* 3.2 30.0 + - - +
30F HIS* 4.6 9.9 - - + +
31F TYR 3.3 0.2 - - - -
32F SER* 1.3 89.1 + - - +
34F GLN* 1.3 61.4 + - - +
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Residues in contact with GLN 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F HIS 4.3 7.1 + - - +
31F TYR* 2.7 32.8 + - + +
32F SER 3.8 4.0 - - - -
33F LYS* 1.3 80.5 - - - +
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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