Contacts of the helix formed by residues 7 - 30 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6G ARG* 1.3 77.1 - - - +
8G VAL* 1.3 59.8 + - - +
10G MET* 2.9 14.2 + - - +
11G LEU* 2.9 25.8 + - - +
200G MET* 5.5 0.7 - - - -
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Residues in contact with VAL 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ARG 3.1 8.8 - - - +
7G GLY* 1.3 76.6 - - - +
9G GLN* 1.3 57.2 + - - +
11G LEU* 3.3 9.4 + - - +
12G LEU* 2.9 27.9 + - - +
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Residues in contact with GLN 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ARG 3.0 14.9 + - - +
8G VAL* 1.3 78.4 - - - +
10G MET* 1.3 57.6 + - - +
12G LEU* 3.1 10.7 + - - +
13G THR* 2.9 27.7 + - - -
196G LEU* 5.6 8.1 - - + +
200G MET* 3.5 24.7 - - + -
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Residues in contact with MET 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G GLY* 2.9 15.2 + - - +
9G GLN* 1.3 79.0 - - - +
11G LEU* 1.3 57.8 + - - +
13G THR* 3.1 11.6 + - - -
14G THR* 2.9 24.9 + - - -
126G GLU* 6.4 2.5 - - + -
200G MET* 3.5 22.5 - - + +
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Residues in contact with LEU 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G GLY 2.9 11.8 + - - +
8G VAL* 3.5 13.2 - - - +
9G GLN 3.2 0.2 - - - -
10G MET* 1.3 73.8 - - - +
12G LEU* 1.3 65.2 + - - +
14G THR* 2.9 19.2 + - - -
15G VAL* 2.9 22.0 + - + +
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Residues in contact with LEU 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G VAL 2.9 14.0 + - - +
9G GLN* 3.3 12.3 - - - +
11G LEU* 1.3 75.1 - - - +
13G THR* 1.3 58.1 + - - +
15G VAL* 3.1 13.3 - - + +
16G GLY* 2.9 27.4 + - - -
193G VAL* 4.9 3.3 - - - +
196G LEU* 6.1 4.7 - - + -
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Residues in contact with THR 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G GLN 2.9 13.2 + - - -
10G MET* 3.1 17.5 + - - -
12G LEU* 1.3 77.0 - - - +
14G THR* 1.3 54.8 - - - +
17G ALA* 2.9 30.6 + - + +
122G ILE* 4.4 22.4 - - + -
142G PHE* 6.3 2.7 - - + -
193G VAL* 4.6 16.3 + - + +
196G LEU* 5.2 2.4 - - - +
197G ALA* 4.5 23.9 + - + +
200G MET* 4.1 10.6 - - - -
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Residues in contact with THR 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G MET 2.9 12.4 + - - -
11G LEU* 2.9 13.0 + - - -
13G THR* 1.3 76.6 - - - +
15G VAL* 1.3 65.8 + - - +
17G ALA* 3.2 4.9 + - - +
18G PHE* 2.9 43.2 + - - +
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Residues in contact with VAL 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G LEU* 2.9 18.8 + - + +
12G LEU* 3.1 20.2 - - + +
14G THR* 1.3 77.3 - - - +
16G GLY* 1.3 60.6 + - - +
18G PHE* 5.0 3.1 - - - -
19G ALA* 2.9 38.2 + - + +
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Residues in contact with GLY 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G LEU 2.9 16.7 + - - -
13G THR 3.9 0.7 - - - -
15G VAL* 1.3 80.0 - - - +
17G ALA* 1.3 55.7 + - - +
19G ALA* 4.9 0.4 - - - -
20G ALA* 2.8 36.6 + - - +
142G PHE* 5.4 1.1 - - - -
189G ILE* 4.1 21.1 - - - -
193G VAL* 4.5 12.6 - - - -
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Residues in contact with ALA 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G THR* 2.9 23.7 + - + +
14G THR* 3.7 4.5 - - - +
16G GLY* 1.3 75.1 - - - +
18G PHE* 1.3 67.0 + - + +
20G ALA* 4.1 1.0 - - - +
21G PHE* 2.9 31.9 + - - +
118G GLY 6.0 0.2 - - - -
119G GLY* 4.9 17.0 - - - -
122G ILE* 5.6 5.2 - - + -
142G PHE* 4.7 21.5 - - + -
193G VAL* 5.1 1.2 - - - +
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Residues in contact with PHE 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G THR* 2.9 32.2 + - - +
15G VAL* 4.4 2.5 - - - +
17G ALA* 1.3 82.3 - - + +
19G ALA* 1.3 65.9 + - - +
21G PHE* 3.0 10.3 + + + +
22G SER* 2.9 25.9 + - - -
119G GLY* 5.7 10.3 - - - -
123G ALA* 5.8 8.1 - - + -
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Residues in contact with ALA 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G VAL* 2.9 25.6 + - + +
16G GLY* 4.5 1.3 - - - +
18G PHE* 1.3 74.9 - - - +
20G ALA* 1.3 62.7 + - - +
22G SER* 3.2 6.1 + - - -
23G LEU* 2.9 33.5 + - + +
189G ILE* 6.0 2.2 - - + -
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Residues in contact with ALA 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G GLY* 2.8 23.4 + - - +
17G ALA* 4.1 2.0 - - - +
19G ALA* 1.3 76.6 - - - +
21G PHE* 1.3 62.1 + - - +
23G LEU* 2.9 15.5 + - - +
24G MET* 2.9 23.9 + - - +
115G LEU* 5.3 6.5 - - + +
142G PHE* 5.9 1.3 - - + -
186G SER* 4.0 21.6 - - - +
189G ILE* 4.5 13.4 - - + +
190G ALA* 4.5 11.2 - - + +
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Residues in contact with PHE 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G ALA 2.9 21.6 + - - +
18G PHE* 3.3 8.3 - + + +
20G ALA* 1.3 77.3 - - - +
22G SER* 1.3 60.0 + - - +
24G MET* 3.3 5.9 + - + +
25G THR* 2.7 47.8 + - + -
112G VAL* 3.5 24.9 - - + +
113G ILE* 5.4 0.2 - - - -
115G LEU* 4.4 13.6 - - + +
116G PHE* 3.5 52.9 - + + -
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Residues in contact with SER 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G PHE 2.9 12.0 + - - -
19G ALA* 3.7 9.0 - - - -
21G PHE* 1.3 82.8 - - - +
23G LEU* 1.3 57.9 + - - +
25G THR* 3.3 9.9 - - - -
26G ILE* 2.9 31.2 + - - +
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Residues in contact with LEU 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G ALA* 2.9 30.4 + - + +
20G ALA* 2.9 17.2 + - + +
22G SER* 1.3 75.5 - - - +
24G MET* 1.3 59.7 + - - +
26G ILE* 3.5 5.9 + - + +
27G ALA* 2.9 28.5 + - - +
182G PHE* 4.4 19.7 - - + +
185G LEU* 4.2 32.1 - - + -
186G SER* 3.9 16.6 - - - +
189G ILE* 5.4 6.1 - - + -
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Residues in contact with MET 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ALA 2.9 12.1 + - - +
21G PHE* 3.8 7.4 - - + +
23G LEU* 1.3 75.8 - - - +
25G THR* 1.3 63.2 + - - +
27G ALA* 3.2 9.7 + - - +
28G VAL* 2.9 28.0 + - + +
111G SER* 5.9 1.3 - - - -
112G VAL* 4.9 16.2 - - + +
115G LEU* 4.8 15.9 - - + -
149G ASN* 5.0 5.8 - - - +
183G GLY* 5.4 0.2 - - - -
186G SER* 4.0 15.1 - - - +
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Residues in contact with THR 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G PHE* 2.7 40.0 + - + -
22G SER* 3.3 13.7 - - - -
23G LEU 3.1 0.2 - - - -
24G MET* 1.3 75.4 - - - +
26G ILE* 1.3 57.1 + - - +
28G VAL* 2.7 31.7 + - + +
29G GLY* 2.9 8.3 + - - -
112G VAL* 5.6 4.9 - - - +
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Residues in contact with ILE 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G SER 2.9 18.6 + - - +
23G LEU* 4.1 5.6 - - + +
25G THR* 1.3 74.5 - - - +
27G ALA* 1.3 57.0 + - - +
29G GLY* 2.9 17.4 + - - +
30G THR 3.3 18.9 + - - +
179G SER* 4.0 2.4 - - - -
182G PHE* 6.0 2.2 - - + -
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Residues in contact with ALA 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G LEU 2.9 15.4 + - - +
24G MET* 3.2 17.3 - - - +
25G THR 3.1 0.4 - - - -
26G ILE* 1.3 77.7 - - - +
28G VAL* 1.3 58.6 + - + +
30G THR 4.6 0.7 + - - -
32G TYR* 4.1 14.2 - - - +
62G GLY 4.8 1.7 - - - +
179G SER* 3.7 36.3 - - - +
182G PHE* 4.9 1.7 - - + +
183G GLY* 4.2 13.5 - - - +
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Residues in contact with VAL 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G MET* 2.9 16.1 + - + +
25G THR* 2.7 18.3 + - + +
27G ALA* 1.3 73.9 - - + +
29G GLY* 1.3 63.8 + - - +
62G GLY 3.5 15.4 - - - +
64G TRP* 5.5 2.9 - - - +
108G PRO* 5.3 14.6 - - + +
109G ILE* 5.6 11.9 - - + -
112G VAL* 5.0 13.5 - - + -
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Residues in contact with GLY 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G THR 2.9 7.8 + - - -
26G ILE* 2.9 12.8 + - - -
28G VAL* 1.3 81.6 - - - +
30G THR* 1.3 63.5 + - - -
62G GLY* 4.4 6.1 - - - +
64G TRP* 5.9 1.9 - - - +
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Residues in contact with THR 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G ILE 3.3 5.8 + - - +
27G ALA 4.6 0.6 + - - -
28G VAL 3.8 0.6 - - - -
29G GLY* 1.3 78.1 - - - +
31G ASP* 1.3 74.6 + - - +
32G TYR* 3.1 2.9 - - - -
61G SER 5.7 0.2 - - - -
62G GLY* 4.2 11.4 - - - -
179G SER* 3.1 15.0 - - - -
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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