Contacts of the helix formed by residues 7 - 28 (chain E) 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 7 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E LEU* 3.4 20.4 + - - +
4E ASP* 3.8 22.8 - - - +
5E GLU 3.1 0.8 - - - -
6E ALA* 1.3 79.9 - - - +
8E ARG* 1.3 62.9 + - + +
9E GLN 3.2 1.3 - - - -
10E TRP* 3.3 9.3 + - - +
11E LYS* 3.0 25.8 + - - +
10F TRP* 4.6 3.1 - - + -
10H TRP* 6.0 4.4 - - - -
11J PRO* 4.1 30.4 - - + +
12J PRO 5.3 2.6 - - - +
14J PHE* 5.5 7.1 - - - +
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Residues in contact with ARG 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E ASP* 3.1 32.5 + - - +
5E GLU* 3.4 17.5 + - - +
7E GLU* 1.3 76.2 - - - +
9E GLN* 1.3 67.6 + - + +
10E TRP 3.1 0.2 - - - -
11E LYS* 3.8 11.4 - - - +
12E ALA* 3.0 26.2 + - - +
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Residues in contact with GLN 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E THR* 6.1 0.2 - - - +
5E GLU 3.4 13.7 - - - +
6E ALA* 3.4 26.1 - - - +
8E ARG* 1.3 80.3 - - + +
10E TRP* 1.3 56.3 + - - +
12E ALA* 3.8 4.8 - - - +
13E GLU* 2.9 36.8 + - + +
11F LYS* 5.8 0.7 - - - -
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Residues in contact with TRP 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ALA 3.8 2.8 + - - +
7E GLU* 3.3 14.2 + - - +
8E ARG 3.1 0.2 - - - -
9E GLN* 1.3 76.3 - - - +
11E LYS* 1.3 78.0 + - + +
12E ALA 3.0 1.3 - - - -
13E GLU* 2.7 26.1 + - + +
14E PHE* 2.7 46.1 + + + -
10F TRP* 3.9 24.5 - + + -
13H GLU* 5.7 4.9 - - + -
17H TRP* 3.7 11.2 - + + -
8J PRO* 3.3 38.4 + - + +
9J LEU 2.8 27.0 + - - -
10J PHE* 3.5 39.0 - + - -
11J PRO* 4.2 9.9 - - + -
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Residues in contact with LYS 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E GLU 3.0 11.5 + - - +
8E ARG* 3.8 10.3 - - - +
10E TRP* 1.3 95.9 - - + +
12E ALA* 1.3 61.5 + - - +
14E PHE* 3.3 15.6 + - + +
15E HIS* 3.6 8.0 + - - +
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Residues in contact with ALA 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ARG 3.0 18.2 + - - +
9E GLN* 3.8 5.8 - - - +
11E LYS* 1.3 78.6 - - - +
13E GLU* 1.3 63.5 + - + +
14E PHE 3.1 1.2 + - - -
15E HIS* 3.9 2.6 + - - +
16E ARG* 3.5 19.1 + - - +
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Residues in contact with GLU 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E GLN* 2.9 26.6 + - + +
10E TRP* 2.7 13.8 + - + +
12E ALA* 1.3 72.9 - - + +
14E PHE* 1.3 61.8 + - - +
16E ARG* 2.7 43.4 + - - +
17E TRP* 3.4 14.0 + - - +
14F PHE* 3.4 29.8 - - + -
17F TRP* 3.3 40.9 - - + -
18F SER* 4.6 2.1 + - - -
8J PRO* 3.9 6.9 - - + +
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Residues in contact with PHE 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E TRP* 2.7 42.7 + + + +
11E LYS* 3.5 12.1 - - + +
12E ALA 3.1 0.2 - - - -
13E GLU* 1.3 75.3 - - - +
15E HIS* 1.3 87.0 + + + +
16E ARG 3.1 1.3 - - - -
17E TRP* 3.0 28.0 + + - +
18E SER* 2.8 27.4 + - - -
16H ARG* 6.3 0.4 - - - -
17H TRP* 4.4 14.1 - + - -
20H TYR* 3.8 41.7 - + - -
7J PRO* 4.6 2.0 - - + -
8J PRO* 3.9 15.3 - - + -
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Residues in contact with HIS 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E LYS 3.6 8.9 + - - +
12E ALA 3.9 2.4 + - - +
14E PHE* 1.3 95.0 - + + +
16E ARG* 1.3 57.1 + - - +
18E SER* 3.5 22.5 - - - -
19E SER* 2.6 36.7 + - - -
20H TYR* 5.6 3.6 - - - -
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Residues in contact with ARG 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ALA 3.5 16.0 + - - +
13E GLU* 2.7 46.4 + - - +
14E PHE 3.1 0.8 - - - -
15E HIS* 1.3 76.8 - - - +
17E TRP* 1.3 54.0 + - - +
19E SER* 3.1 9.8 + - - -
20E TYR* 2.8 68.6 + - + -
17F TRP* 5.0 1.1 - - + -
18F SER* 4.5 11.7 + - - -
21F MSE 3.7 31.7 - - + +
22F VAL* 4.6 6.7 - - - +
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Residues in contact with TRP 17 (chain E).
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 3.4 10.3 + - - +
14E PHE* 3.0 32.2 + + - +
16E ARG* 1.3 77.6 - - - +
18E SER* 1.3 85.5 + - - +
20E TYR* 2.8 26.0 + - - +
21E MSE 2.9 44.4 + - + +
17F TRP* 4.2 5.2 - + + -
21F MSE 4.0 22.0 - - + -
20H TYR* 3.9 37.5 - + + -
23H HIS* 5.9 3.8 - + - -
24H TRP* 3.9 7.9 - + + -
4J PRO* 4.4 1.5 - - + +
5J PRO 2.9 26.7 + - - -
6J PRO 3.7 8.7 - - - -
7J PRO* 3.5 36.1 - - + -
8J PRO* 3.9 7.4 - - + -
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Residues in contact with SER 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E PHE* 2.8 19.8 + - - -
15E HIS* 3.6 35.9 - - - -
17E TRP* 1.3 95.6 - - - +
19E SER* 1.3 56.3 + - - +
21E MSE 3.4 6.6 + - - +
22E VAL* 3.2 30.7 + - - +
20H TYR* 4.7 8.7 + - - -
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Residues in contact with SER 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E HIS* 2.6 23.6 + - - -
16E ARG* 3.2 11.7 - - - -
17E TRP 3.0 0.2 - - - -
18E SER* 1.3 73.7 - - - +
20E TYR* 1.3 68.0 + - - +
21E MSE 3.1 0.2 - - - -
22E VAL* 3.2 23.8 + - - +
23E HIS* 3.4 24.3 + - - -
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Residues in contact with TYR 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ARG* 2.8 47.5 + - + -
17E TRP* 2.8 10.6 + - - +
19E SER* 1.3 82.7 - - - +
21E MSE 1.3 61.9 + - - +
23E HIS* 3.7 7.4 + + - +
24E TRP* 3.3 21.7 + - - +
21F MSE 3.2 56.0 + - + -
22F VAL* 5.5 0.3 - - - -
24F TRP* 3.6 26.4 - + + -
25F LYS* 3.8 38.5 + - + +
4J PRO* 4.4 7.0 - - + -
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Residues in contact with MSE 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E TRP* 2.9 54.7 + - + +
18E SER* 3.6 9.6 - - - +
20E TYR* 1.3 77.5 - - - +
22E VAL* 1.3 62.7 - - - +
24E TRP* 3.5 29.2 - - + +
25E LYS* 3.1 24.1 + - - +
23H HIS* 6.1 4.5 - - - -
24H TRP* 3.8 14.8 - - - -
27H GLN* 5.7 4.5 - - + -
3J THR* 4.0 7.6 - - + -
4J PRO* 3.0 37.7 - - + -
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Residues in contact with VAL 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E SER* 3.2 18.2 + - - +
19E SER* 3.2 14.6 - - - +
21E MSE 1.3 81.0 - - - +
23E HIS* 1.3 79.7 + - + +
25E LYS* 3.2 12.8 + - - +
26E ASN* 3.0 25.3 + - - +
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Residues in contact with HIS 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E SER* 3.4 21.1 + - - -
20E TYR* 4.2 9.1 - + - +
22E VAL* 1.3 91.6 - - + +
24E TRP* 1.3 64.3 + - - +
26E ASN* 3.0 22.2 + - - +
27E GLN 3.2 8.1 + - - -
24F TRP* 6.0 0.2 - - + -
25F LYS* 5.2 10.6 - - - -
28F PHE* 3.7 34.2 - + + -
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Residues in contact with TRP 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E TYR 3.3 17.1 + - - +
21E MSE 3.5 28.7 - - + +
22E VAL 3.2 0.4 - - - -
23E HIS* 1.3 77.8 - - - +
25E LYS* 1.3 81.1 + - + +
27E GLN* 2.9 45.0 + - - +
28E PHE* 4.0 11.0 + + - +
24F TRP* 4.0 11.9 - + + -
28F PHE* 4.2 8.9 - + - -
27H GLN* 3.9 33.7 - - + -
30H HIS* 6.4 0.2 - - + -
31H TYR* 4.9 14.1 - + - -
1J LEU 2.8 27.9 + - - -
2J LEU 3.4 13.2 + - - -
3J THR* 3.4 30.1 - - + -
4J PRO* 4.1 5.6 - - + -
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Residues in contact with LYS 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E MSE 3.1 14.6 + - - +
22E VAL* 3.2 6.7 + - - +
24E TRP* 1.3 94.1 - - + +
26E ASN* 1.3 63.4 + - - +
27E GLN 3.6 0.2 + - - -
28E PHE* 3.7 18.7 + - - +
27H GLN* 6.0 1.8 - - - +
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Residues in contact with ASN 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E VAL* 3.0 35.3 + - - +
23E HIS* 3.0 17.2 + - - +
25E LYS* 1.3 82.9 - - - +
27E GLN* 1.3 64.6 + - - +
28E PHE* 3.1 6.6 - - - -
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Residues in contact with GLN 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E HIS 3.2 5.9 + - - +
24E TRP* 2.9 31.9 + - - +
26E ASN* 1.3 80.0 - - - +
28E PHE* 1.3 83.2 + - + +
28F PHE* 4.0 15.9 - - + -
31H TYR* 4.8 7.9 + - - -
1J LEU 3.3 41.1 + - - +
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Residues in contact with PHE 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E TRP* 5.6 11.4 - + - -
25E LYS* 3.7 17.0 + - + +
26E ASN* 3.1 7.5 - - - -
27E GLN* 1.3 104.6 - - + +
30H HIS* 5.8 10.1 - + - -
31H TYR* 5.4 12.3 - + - -
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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
------------------------------------------------------------
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