Contacts of the helix formed by residues 7 - 30 (chain F) in PDB entry 5VOT
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 GLY 7 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ARG* 1.3 78.0 - - - +
8F VAL* 1.3 57.0 + - - +
9F GLN 3.0 0.4 - - - -
10F MET* 2.8 36.6 + - - +
11F LEU* 2.9 12.2 + - - +
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Residues in contact with VAL 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ARG 3.5 22.2 - - - +
7F GLY* 1.3 76.9 - - - +
9F GLN* 1.3 60.4 + - + +
11F LEU* 3.7 8.4 - - - +
12F LEU* 2.9 33.6 + - - +
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Residues in contact with GLN 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ARG 3.0 14.6 + - - +
8F VAL* 1.3 82.9 - - + +
10F MET* 1.3 65.7 + - + +
12F LEU* 4.2 3.0 - - - +
13F THR* 2.1 42.2 + - - +
196F LEU* 5.1 10.9 - - + +
200F MET* 4.3 21.3 - - + -
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Residues in contact with MET 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ARG 5.3 0.9 - - - +
7F GLY* 2.8 25.1 + - - +
9F GLN* 1.3 89.0 - - + +
11F LEU* 1.3 62.1 + - - +
13F THR* 3.2 10.3 + - + +
14F THR* 2.9 33.9 + - + +
122F ILE* 6.1 4.7 - - + -
125F SER* 6.2 0.4 - - - -
126F GLU* 6.3 3.4 - - - -
200F MET* 5.5 5.6 - - + -
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Residues in contact with LEU 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F GLY 2.9 11.8 + - - +
8F VAL* 3.3 11.6 + - - +
10F MET* 1.3 75.6 - - - +
12F LEU* 1.3 69.0 + - + +
14F THR* 2.9 23.5 + - - +
15F VAL* 2.9 35.5 + - + +
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Residues in contact with LEU 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F VAL 2.9 18.9 + - - +
9F GLN* 4.3 3.1 - - - +
11F LEU* 1.3 77.5 - - + +
13F THR* 1.3 56.2 + - - +
15F VAL* 3.3 11.7 - - + +
16F GLY* 2.9 26.3 + - - -
193F VAL* 4.6 8.7 - - - +
196F LEU* 5.0 13.7 - - + -
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Residues in contact with THR 13 (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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9F GLN* 2.1 30.1 + - - +
10F MET* 3.3 13.3 - - + +
11F LEU 3.0 0.2 - - - -
12F LEU* 1.3 78.2 - - - +
14F THR* 1.3 59.3 + - + +
16F GLY* 3.2 1.4 + - - -
17F ALA* 2.9 25.9 + - + +
122F ILE* 3.5 45.8 - - + +
193F VAL* 5.0 13.9 + - + +
196F LEU* 5.3 7.3 - - - +
197F ALA* 5.5 9.5 - - + -
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Residues in contact with THR 14 (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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10F MET* 2.9 20.9 + - + +
11F LEU* 2.9 15.9 + - - +
13F THR* 1.3 77.4 - - + +
15F VAL* 1.3 70.0 + - - +
17F ALA* 2.8 24.0 + - - +
18F PHE* 2.9 25.7 + - - +
122F ILE* 5.8 4.3 - - + -
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Residues in contact with VAL 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 LEU* 2.9 44.7 + - + +
12F LEU* 3.3 15.7 - - + +
14F THR* 1.3 85.0 + - - +
16F GLY* 1.3 53.5 + - - +
18F PHE* 4.7 3.3 - - - +
19F ALA* 2.5 41.8 + - + +
189F ILE* 5.7 0.4 - - + -
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Residues in contact with GLY 16 (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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12F LEU 2.9 17.3 + - - -
13F THR 3.6 3.4 - - - -
15F VAL* 1.3 77.1 - - - +
17F ALA* 1.3 65.4 + - - +
19F ALA* 4.1 3.8 - - - -
20F ALA* 2.9 28.6 + - - +
142F PHE* 5.2 3.7 - - - -
189F ILE* 4.4 12.1 - - - -
190F ALA* 6.0 0.2 - - - -
193F VAL* 4.3 17.7 - - - -
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Residues in contact with ALA 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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13F THR* 2.9 13.2 + - + +
14F THR* 2.8 18.8 + - - +
16F GLY* 1.3 70.8 - - - +
18F PHE* 1.3 66.2 + - + +
20F ALA* 4.7 0.2 - - - +
21F PHE* 2.8 35.2 + - - +
115F LEU* 6.2 0.2 - - - +
119F GLY* 4.4 22.9 - - - +
122F ILE* 5.5 6.3 - - + -
142F PHE* 5.6 7.8 - - + -
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Residues in contact with PHE 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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14F THR* 2.9 22.7 + - - +
15F VAL* 4.7 2.7 - - - +
17F ALA* 1.3 81.6 - - + +
19F ALA* 1.3 64.5 + - - +
21F PHE* 4.2 9.6 - + + -
22F SER* 2.9 34.5 + - - +
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Residues in contact with ALA 19 (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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15F VAL 2.5 26.5 + - - +
16F GLY* 3.8 4.3 - - - +
18F PHE* 1.3 78.0 - - - +
20F ALA* 1.3 59.7 + - - +
22F SER* 4.3 0.7 - - - -
23F LEU* 2.9 32.3 + - - +
189F ILE* 4.6 12.3 - - + -
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Residues in contact with ALA 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 GLY 2.9 18.5 + - - +
17F ALA* 4.7 0.4 - - - +
19F ALA* 1.3 74.9 - - - +
21F PHE* 1.3 57.0 + - - +
24F MET* 2.9 30.1 + - - +
115F LEU* 4.0 12.9 - - + +
142F PHE* 5.7 0.9 - - + -
186F SER* 3.3 39.6 - - - +
189F ILE* 5.0 2.9 - - + +
190F ALA* 3.9 18.4 - - + +
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Residues in contact with PHE 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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17F ALA 2.8 24.5 + - - +
18F PHE* 3.9 9.4 - + + +
20F ALA* 1.3 75.7 - - - +
22F SER* 1.3 73.5 + - - +
24F MET* 3.1 5.4 + - - +
25F THR* 2.9 34.1 + - - -
112F VAL* 4.3 15.5 - - + -
115F LEU* 4.0 28.9 - - + +
116F PHE* 4.0 39.7 - + + -
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Residues in contact with SER 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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18F PHE* 2.9 27.0 + - - +
19F ALA* 4.3 0.4 - - - -
21F PHE* 1.3 81.8 - - - +
23F LEU* 1.3 57.4 + - - +
25F THR* 3.2 8.4 + - - -
26F ILE* 2.9 43.3 + - - +
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Residues in contact with LEU 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 ALA 2.9 22.8 + - - +
22F SER* 1.3 78.6 - - - +
24F MET* 1.3 56.8 + - - +
26F ILE* 3.9 9.4 - - - +
27F ALA* 2.9 27.7 + - - +
182F PHE* 4.0 18.1 - - + +
186F SER* 3.5 24.7 - - - -
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Residues in contact with MET 24 (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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20F ALA 2.9 19.4 + - - +
21F PHE* 3.1 4.5 + - + +
23F LEU* 1.3 75.2 - - - +
25F THR* 1.3 60.9 + - - +
27F ALA* 3.2 9.5 + - - +
28F VAL* 2.9 33.1 + - - +
111F SER* 5.3 5.2 - - - +
112F VAL* 5.2 11.2 - - + -
115F LEU* 4.1 17.5 - - + -
183F GLY* 5.3 1.1 - - - -
186F SER* 4.2 7.1 - - - -
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Residues in contact with THR 25 (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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21F PHE* 2.9 27.6 + - - -
22F SER* 3.5 12.0 - - - -
24F MET* 1.3 75.9 - - - +
26F ILE* 1.3 57.6 + - + +
28F VAL* 2.7 32.0 + - + +
29F GLY* 2.9 9.2 + - - -
112F VAL* 5.8 5.7 - - - +
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Residues in contact with ILE 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 SER* 2.9 33.4 + - - +
23F LEU* 3.9 7.9 - - - +
25F THR* 1.3 73.4 - - + +
27F ALA* 1.3 55.6 + - - +
29F GLY* 2.7 24.5 + - - +
30F THR 3.5 9.0 + - - +
179F SER* 3.8 18.8 - - - +
182F PHE* 5.4 5.6 - - + -
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Residues in contact with ALA 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 LEU 2.9 17.1 + - - +
24F MET* 3.2 13.9 - - - +
26F ILE* 1.3 78.0 - - - +
28F VAL* 1.3 59.3 + - + +
29F GLY 3.4 0.3 + - - -
30F THR 3.9 9.5 - - - +
32F TYR* 4.9 8.8 - - - +
62F GLY* 5.3 2.4 - - - +
179F SER* 3.6 28.0 - - - +
180F PHE* 5.5 1.1 - - - -
182F PHE* 5.4 0.2 - - - +
183F GLY* 3.8 16.2 - - - -
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Residues in contact with VAL 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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24F MET 2.9 20.9 + - - +
25F THR* 2.7 20.5 + - + +
27F ALA* 1.3 72.4 - - + +
29F GLY* 1.3 62.7 + - - +
62F GLY 4.3 11.9 - - - +
64F TRP* 3.9 40.5 - - + -
108F PRO* 5.7 8.3 - - + -
109F ILE* 6.1 4.9 - - + -
112F VAL* 4.5 19.1 - - + -
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Residues in contact with GLY 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 THR 2.9 6.9 + - - -
26F ILE* 2.7 14.5 + - - -
28F VAL* 1.3 82.0 - - - +
30F THR* 1.3 69.8 + - - +
62F GLY* 4.8 5.9 - - - +
64F TRP* 6.0 0.5 - - - -
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Residues in contact with THR 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 ILE 3.5 5.0 + - - +
27F ALA 3.9 6.6 - - - +
29F GLY* 1.3 84.8 - - - +
31F ASP* 1.3 73.4 + - - +
32F TYR* 3.3 4.8 + - - -
61F SER 6.0 0.2 - - - -
62F GLY* 4.6 10.3 - - - +
67F CYS* 6.1 5.4 - - - -
179F SER* 3.2 18.3 + - - -
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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