Contacts of the helix formed by residues 10 - 25 (chain B) in PDB entry 3VON
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 PRO 10 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B LYS* 4.2 2.9 - - + +
9B VAL* 1.4 100.4 - - + +
11B ARG* 1.3 67.1 + - - +
12B ASN* 3.4 3.1 - - - +
13B PHE* 4.0 15.0 - - + -
14B ARG* 3.3 19.9 + - - +
74B PRO* 4.7 1.3 - - - -
31C ASN* 4.3 6.5 - - - +
34C TYR* 3.5 42.2 - - + -
55C GLU* 5.6 0.4 - - - +
57C PHE* 3.6 27.6 - - + -
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Residues in contact with ARG 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PRO* 1.3 74.2 - - - +
12B ASN* 1.3 81.3 + - - +
14B ARG* 3.3 2.4 + - - +
15B LEU* 3.0 50.4 + - + +
42B THR 2.7 21.6 + - - -
43B LEU* 3.6 2.6 + - - +
44B THR* 3.3 30.3 + - - +
69B CYS* 2.8 24.5 + - - +
70B GLY 3.0 23.7 + - - -
71B PRO* 4.1 19.2 - - - +
73B TYR* 3.2 27.9 + - + +
74B PRO* 4.5 1.3 - - - +
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Residues in contact with ASN 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PRO* 3.4 2.2 - - - +
11B ARG* 1.3 108.5 + - - +
13B PHE* 1.3 60.2 + - + +
15B LEU* 3.3 3.0 + - - +
16B LEU* 3.1 34.5 + - - +
42B THR 4.5 0.5 - - - +
43B LEU* 4.1 10.0 - - + +
34C TYR* 4.4 2.0 + - - -
55C GLU* 2.7 44.1 + - - +
70C ARG* 3.9 19.9 + - - +
72C MET* 4.5 6.1 - - - -
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Residues in contact with PHE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 4.5 15.4 - - + +
10B PRO* 3.9 16.3 + - + -
11B ARG 3.4 0.2 - - - -
12B ASN* 1.3 75.4 - - + +
14B ARG* 1.3 64.2 + - - +
16B LEU* 4.0 14.0 + - + +
17B GLU* 3.6 24.4 + - - +
34C TYR* 4.0 9.0 - + - -
55C GLU* 3.3 50.0 - - + -
57C PHE* 3.6 28.9 - - + -
68C LYS* 3.4 44.0 - - + -
69C VAL* 3.9 9.2 - - - -
70C ARG* 4.2 9.0 - - + -
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Residues in contact with ARG 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 4.3 25.1 + - + +
10B PRO 3.3 18.8 + - - +
11B ARG 3.3 4.9 + - - +
12B ASN 3.2 0.4 - - - -
13B PHE* 1.3 77.6 - - - +
15B LEU* 1.3 59.2 + - - +
17B GLU* 3.0 23.5 + - - +
18B GLU* 3.0 49.6 + - - +
73B TYR* 4.2 5.4 - - + -
74B PRO* 4.0 23.5 - - + +
111B ASN* 3.1 30.8 + - - +
112B SER* 3.9 14.3 + - - +
113B TYR 3.5 17.2 + - - -
114B SER* 4.7 3.0 - - - +
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ARG* 3.0 51.5 + - + +
12B ASN* 3.3 5.6 + - - +
14B ARG* 1.3 76.5 - - - +
16B LEU* 1.3 58.6 + - - +
18B GLU* 3.5 6.0 + - + -
19B LEU* 3.0 22.0 + - - +
43B LEU* 3.5 30.4 - - + +
46B TRP* 3.3 35.3 - - + +
69B CYS* 3.8 17.3 - - + -
73B TYR* 3.5 31.2 - - + -
115B ILE* 4.3 4.9 - - + -
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ASN 3.1 20.0 + - - +
13B PHE* 4.2 14.4 - - + +
15B LEU* 1.3 73.4 - - - +
17B GLU* 1.3 61.5 + - + +
19B LEU* 3.3 16.0 + - + +
20B GLU* 3.0 33.4 + - + +
43B LEU* 3.8 28.9 - - + -
70C ARG* 3.6 31.6 - - + -
83C LEU* 4.7 9.6 - - + +
85C ARG* 4.0 31.5 + - + +
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 5.2 5.7 - - - +
13B PHE 3.6 16.1 + - - +
14B ARG* 3.0 22.1 + - - +
16B LEU* 1.3 76.6 - - - +
18B GLU* 1.3 65.4 + - + +
20B GLU* 3.1 10.0 + - - +
21B GLU* 3.0 24.6 + - - +
68C LYS* 5.4 8.6 + - - +
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 3.0 36.6 + - + +
15B LEU* 3.5 12.6 - - + +
17B GLU* 1.3 76.1 - - + +
19B LEU* 1.3 55.4 + - - +
21B GLU* 3.5 7.6 + - - +
22B GLY 2.8 14.7 + - - -
33B TRP* 2.8 32.0 + - + +
46B TRP* 4.3 7.2 - - + -
73B TYR* 2.4 35.0 + - - -
114B SER* 3.3 22.2 + - - -
115B ILE* 3.0 29.6 + - + +
116B LYS 4.2 1.9 + - - -
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU 3.0 13.4 + - - +
16B LEU* 3.4 18.2 - - + +
18B GLU* 1.3 73.0 - - - +
20B GLU* 1.3 56.4 + - - +
22B GLY* 3.1 3.3 + - - -
23B GLN* 2.8 52.9 + - + +
34B GLY* 4.5 5.2 - - - -
35B LEU* 3.7 34.5 - - + +
43B LEU* 4.8 0.7 - - + -
46B TRP* 3.7 20.1 - - + -
83C LEU* 3.6 30.7 - - + -
85C ARG* 4.5 11.9 - - - +
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Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 3.0 19.0 + - + +
17B GLU* 3.1 11.4 + - - +
19B LEU* 1.3 76.2 - - - +
21B GLU* 1.3 56.9 + - - +
23B GLN* 3.1 30.5 + - - +
24B LYS* 3.0 56.7 + - - +
85C ARG* 3.4 21.5 + - - +
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLU 3.0 15.9 + - - +
18B GLU* 3.9 6.2 - - - +
20B GLU* 1.3 75.6 - - - +
22B GLY* 1.3 57.0 + - - +
24B LYS* 3.3 10.8 + - + +
25B GLY* 2.9 29.3 + - - -
26B VAL* 3.7 22.8 - - + +
33B TRP* 3.6 13.5 - - - -
114B SER* 5.1 2.3 + - - -
116B LYS* 3.3 30.8 + - - +
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Residues in contact with GLY 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLU 2.8 10.5 + - - -
19B LEU* 3.1 6.0 + - - -
21B GLU* 1.3 77.6 - - - +
23B GLN* 1.3 58.4 + - - +
25B GLY* 3.9 8.1 + - - -
32B SER* 4.7 7.1 + - - -
33B TRP* 3.4 49.4 - - - +
34B GLY* 5.8 0.7 - - - -
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Residues in contact with GLN 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 2.8 31.6 + - + +
20B GLU* 3.1 31.3 + - - +
22B GLY* 1.3 78.1 - - - +
24B LYS* 1.3 64.3 + - + +
25B GLY* 3.6 0.5 + - - -
85C ARG* 4.9 2.8 + - - -
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Residues in contact with LYS 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLU* 3.0 48.6 + - - +
21B GLU* 3.3 9.0 + - + +
23B GLN* 1.3 76.9 - - + +
25B GLY* 1.3 67.1 + - - +
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Residues in contact with GLY 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLU 2.9 12.4 + - - -
22B GLY* 3.9 7.4 + - - -
23B GLN 3.3 3.0 - - - -
24B LYS* 1.3 83.7 - - - +
26B VAL* 1.3 65.3 + - - +
27B GLY 4.2 1.3 + - - +
29B GLY* 6.4 1.3 - - - -
32B SER* 5.1 8.7 - - - -
33B TRP* 6.1 0.7 - - - -
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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