Contacts of the helix formed by residues 7 - 30 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E ARG* 1.3 77.1 - - - +
8E VAL* 1.3 59.4 + - - +
9E GLN 3.1 0.2 - - - -
10E MET* 2.9 14.8 + - - +
11E LEU* 2.9 25.9 + - - +
200E MET* 5.5 0.9 - - - -
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Residues in contact with VAL 8 (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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6E ARG 3.1 7.9 - - - +
7E GLY* 1.3 76.4 - - - +
9E GLN* 1.3 57.2 + - - +
11E LEU* 3.3 9.7 + - - +
12E LEU* 2.9 26.9 + - - +
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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
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6E ARG* 3.0 14.4 + - - +
8E VAL* 1.3 78.1 - - - +
10E MET* 1.3 57.5 + - - +
12E LEU* 3.1 10.1 + - - +
13E THR* 2.9 28.1 + - - -
196E LEU* 5.6 7.7 - - + +
200E MET* 3.5 25.3 - - + +
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Residues in contact with MET 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E GLY* 2.9 15.0 + - - +
9E GLN* 1.3 77.2 - - - +
11E LEU* 1.3 58.4 + - - +
13E THR* 3.1 12.1 + - - -
14E THR* 2.9 24.8 + - - -
126E GLU* 6.4 2.7 - - + -
200E MET* 3.5 22.1 - - + +
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Residues in contact with LEU 11 (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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7E GLY 2.9 12.0 + - - +
8E VAL* 3.5 12.6 - - - +
9E GLN 3.2 0.2 - - - -
10E MET* 1.3 73.9 - - - +
12E LEU* 1.3 65.1 + - - +
14E THR* 2.9 18.5 + - - -
15E VAL* 2.9 20.7 + - + +
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Residues in contact with LEU 12 (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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8E VAL 2.9 14.3 + - - +
9E GLN* 3.1 13.0 + - - +
11E LEU* 1.3 74.4 - - - +
13E THR* 1.3 57.4 + - - +
15E VAL* 3.2 13.6 - - + +
16E GLY* 2.9 27.2 + - - -
193E VAL* 4.9 3.7 - - - +
196E LEU* 6.1 4.9 - - + -
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Residues in contact with THR 13 (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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9E GLN 2.9 13.2 + - - -
10E MET* 3.1 17.3 - - - -
12E LEU* 1.3 77.2 - - - +
14E THR* 1.3 55.6 + - - +
16E GLY* 3.9 0.2 - - - -
17E ALA* 2.9 31.4 + - + +
122E ILE* 4.4 22.2 - - + -
142E PHE* 6.1 2.6 - - + -
193E VAL* 4.6 15.4 + - + +
196E LEU* 5.2 2.6 - - - +
197E ALA* 4.5 23.1 + - + +
200E MET* 4.0 10.7 - - - -
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Residues in contact with THR 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 MET 2.9 12.4 + - - -
11E LEU* 2.9 12.7 + - - -
13E THR* 1.3 76.2 - - - +
15E VAL* 1.3 66.0 + - - +
17E ALA* 3.2 5.3 + - - +
18E PHE* 2.9 41.5 + - - +
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Residues in contact with VAL 15 (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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11E LEU* 2.9 20.9 + - + +
12E LEU* 3.2 20.4 - - + +
14E THR* 1.3 76.1 - - - +
16E GLY* 1.3 61.2 + - - +
18E PHE* 5.1 2.9 - - - -
19E ALA* 2.9 38.4 + - + +
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Residues in contact with GLY 16 (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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12E LEU 2.9 17.0 + - - -
13E THR 3.9 0.7 - - - -
15E VAL* 1.3 80.5 - - - +
17E ALA* 1.3 56.0 + - - +
19E ALA* 4.9 0.2 - - - -
20E ALA* 2.8 36.7 + - - +
142E PHE* 5.4 1.3 - - - -
189E ILE* 4.1 20.6 - - - -
193E VAL* 4.5 12.8 - - - -
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Residues in contact with ALA 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 THR* 2.9 24.1 + - + +
14E THR* 3.7 4.3 - - - +
16E GLY* 1.3 75.9 - - - +
18E PHE* 1.3 66.2 + - + +
20E ALA* 4.1 1.0 - - - +
21E PHE* 2.9 32.4 + - - +
118E GLY 6.0 0.2 - - - -
119E GLY* 4.9 15.9 - - - -
122E ILE* 5.5 5.8 - - + -
142E PHE* 4.7 22.0 - - + -
193E VAL* 5.1 1.2 - - - +
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Residues in contact with PHE 18 (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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14E THR* 2.9 30.0 + - - +
15E VAL* 4.5 2.0 - - - +
17E ALA* 1.3 82.8 - - + +
19E ALA* 1.3 65.5 + - - +
21E PHE* 3.0 10.2 + + + +
22E SER* 2.9 26.5 + - - -
119E GLY* 5.6 11.7 - - - -
123E ALA* 5.7 9.2 - - + -
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Residues in contact with ALA 19 (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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15E VAL* 2.9 23.6 + - + +
16E GLY* 4.9 0.7 - - - -
18E PHE* 1.3 77.8 - - - +
20E ALA* 1.3 63.6 + - - +
22E SER* 3.2 6.8 + - - -
23E LEU* 2.9 31.8 + - + +
189E ILE* 6.0 1.8 - - + -
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Residues in contact with ALA 20 (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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16E GLY 2.8 23.3 + - - +
17E ALA* 4.1 1.3 - - - +
19E ALA* 1.3 77.0 - - - +
21E PHE* 1.3 62.3 + - - +
23E LEU* 3.0 15.4 + - - +
24E MET* 2.9 23.0 + - - +
115E LEU* 5.3 5.3 - - + +
142E PHE* 6.0 1.8 - - + -
186E SER* 4.0 20.4 - - - +
189E ILE* 4.3 17.4 - - + +
190E ALA* 4.4 10.3 - - + +
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Residues in contact with PHE 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 ALA 2.9 21.9 + - - +
18E PHE* 3.0 10.3 + + + +
20E ALA* 1.3 77.9 - - - +
22E SER* 1.3 63.4 + - - +
24E MET* 3.3 7.0 + - + +
25E THR* 2.7 42.5 + - + -
112E VAL* 3.4 34.1 - - + -
115E LEU* 4.3 15.4 - - + +
116E PHE* 3.5 44.6 - + + -
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Residues in contact with SER 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 PHE 2.9 13.5 + - - -
19E ALA* 3.7 8.1 - - - -
21E PHE* 1.3 81.4 - - - +
23E LEU* 1.3 59.4 + - - +
25E THR* 3.3 10.1 - - - -
26E ILE* 2.9 30.7 + - - +
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Residues in contact with LEU 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 ALA* 2.9 30.0 + - + +
20E ALA* 3.2 17.5 - - + +
22E SER* 1.3 76.1 - - - +
24E MET* 1.3 60.8 + - - +
26E ILE* 3.5 5.1 + - + +
27E ALA* 2.9 28.5 + - - +
182E PHE* 4.5 18.7 - - + +
185E LEU* 4.3 31.9 - - + +
186E SER* 4.0 16.2 - - - +
189E ILE* 5.3 6.1 - - + -
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Residues in contact with MET 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 ALA 2.9 11.3 + - - +
21E PHE* 3.7 7.6 - - - +
23E LEU* 1.3 75.8 - - - +
25E THR* 1.3 63.0 + - - +
27E ALA* 3.2 10.1 + - - +
28E VAL* 2.9 28.1 + - + +
111E SER* 6.3 1.1 - - - -
112E VAL* 5.0 15.9 - - + +
115E LEU* 4.8 15.5 - - + -
149E ASN* 5.0 5.8 - - - +
183E GLY* 5.4 0.2 - - - -
186E SER* 4.0 16.2 - - - +
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Residues in contact with THR 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 PHE* 2.7 39.5 + - + -
22E SER* 3.3 13.6 - - - -
23E LEU 3.2 0.2 - - - -
24E MET* 1.3 75.4 - - - +
26E ILE* 1.3 57.2 + - - +
28E VAL* 2.7 30.9 + - + +
29E GLY* 2.9 8.8 + - - -
112E VAL* 5.6 4.3 - - - +
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Residues in contact with ILE 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 SER 2.9 19.0 + - - +
23E LEU* 4.1 5.2 - - + +
25E THR* 1.3 74.5 - - - +
27E ALA* 1.3 57.9 + - - +
29E GLY* 2.9 18.2 + - - +
30E THR 3.3 18.0 + - - +
179E SER* 4.1 2.1 - - - -
182E PHE* 6.0 1.8 - - + -
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Residues in contact with ALA 27 (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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23E LEU 2.9 16.0 + - - +
24E MET* 3.2 16.8 - - - +
26E ILE* 1.3 78.7 - - - +
28E VAL* 1.3 58.9 + - + +
29E GLY 3.6 0.2 + - - -
30E THR 4.6 1.0 + - - -
32E TYR* 4.2 12.8 - - - +
62E GLY 4.9 1.2 - - - +
179E SER* 3.6 36.7 - - - +
182E PHE* 4.8 1.5 - - + +
183E GLY* 4.1 13.2 - - - +
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Residues in contact with VAL 28 (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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24E MET* 2.9 16.5 + - + +
25E THR* 2.7 19.5 + - + +
27E ALA* 1.3 73.1 - - + +
29E GLY* 1.3 63.0 + - - +
62E GLY 3.6 14.8 - - - +
64E TRP* 5.6 2.8 - - - +
108E PRO* 5.3 14.6 - - + +
109E ILE* 5.6 11.9 - - + -
112E VAL* 5.0 13.9 - - + -
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Residues in contact with GLY 29 (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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25E THR 2.9 8.0 + - - -
26E ILE* 2.9 13.5 + - - -
28E VAL* 1.3 80.7 - - - +
30E THR* 1.3 63.8 + - - -
62E GLY* 4.4 5.8 - - - +
64E TRP* 6.0 0.9 - - - +
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Residues in contact with THR 30 (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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26E ILE 3.3 5.7 + - - +
27E ALA 4.6 0.8 + - - -
28E VAL 3.8 0.8 - - - -
29E GLY* 1.3 78.8 - - - +
31E ASP* 1.3 73.5 + - - +
32E TYR* 3.1 3.1 - - - -
61E SER 5.8 0.4 - - - -
62E GLY* 4.2 12.6 - - - -
179E SER* 3.1 15.2 - - - -
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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