Contacts of the helix formed by residues 15 - 28 (chain E) in PDB entry 2VUU
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 15 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E ASN* 2.7 22.8 + - - -
14E THR* 1.3 75.0 - - - +
16E ARG* 1.3 60.4 + - - -
17E GLN 3.2 0.8 + - - -
18E ALA 3.4 1.8 + - - -
19E ALA* 2.8 28.1 + - - +
1353E NAP 3.1 36.6 + - - -
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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
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14E THR 3.7 1.4 + - - +
15E GLY* 1.3 70.4 - - - -
17E GLN* 1.3 65.4 + - - +
19E ALA* 4.2 4.4 - - - +
20E SER* 3.3 20.1 + - - -
153E TYR* 3.3 30.1 - - + -
155E ASN* 2.6 57.3 + - - +
156E ASN* 3.7 10.7 + - - +
192E ALA* 3.8 22.1 - - + +
193E GLU* 4.4 22.4 + - + +
1353E NAP 2.9 47.6 + - - +
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Residues in contact with GLN 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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16E ARG* 1.3 78.6 - - - +
18E ALA* 1.3 67.5 + - - +
20E SER* 3.0 10.2 + - - -
21E LEU* 3.2 8.8 + - - +
78E PHE* 3.4 21.6 - - + -
80E ASN* 2.7 31.4 + - - +
111E SER* 2.8 29.2 + - - -
148E VAL* 5.0 1.2 - - - +
150E ALA* 4.7 8.4 - - + +
153E TYR* 3.0 28.6 + - + +
196E VAL* 3.5 29.8 - - + +
218E LEU* 5.7 2.3 - - - +
1353E NAP 3.1 22.1 + - - +
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Residues in contact with ALA 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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10E VAL* 4.9 3.8 - - + -
11E VAL 3.8 11.0 - - - +
12E ASN* 3.3 27.4 - - + +
13E ALA* 3.6 13.5 - - - +
15E GLY 3.4 1.8 + - - +
17E GLN* 1.3 78.7 - - - +
19E ALA* 1.3 65.1 + - - +
21E LEU* 2.9 7.5 + - - +
22E ILE* 2.8 29.5 + - + +
78E PHE* 3.9 18.7 - - + -
80E ASN* 5.2 2.6 - - + +
1353E NAP 4.5 0.4 + - - -
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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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13E ALA 3.1 13.4 + - - +
14E THR 4.5 0.7 - - - +
15E GLY 2.8 24.2 + - - +
16E ARG* 4.2 4.3 - - - +
18E ALA* 1.3 71.8 - - - +
20E SER* 1.3 64.8 + - - +
22E ILE* 3.2 6.4 + - - +
23E ARG* 2.9 50.2 + - - +
43E ILE* 4.3 15.7 - - + -
47E LEU* 4.4 5.1 - - + +
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Residues in contact with SER 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 ARG 3.3 12.5 + - - -
17E GLN 3.0 11.5 + - - -
19E ALA* 1.3 80.8 - - - +
21E LEU* 1.3 65.7 + - - +
23E ARG* 3.4 14.2 + - - +
24E VAL* 3.2 17.2 + - - +
192E ALA 3.3 10.0 + - - -
193E GLU* 2.5 29.1 + - - -
196E VAL* 4.0 0.7 - - - -
197E GLY* 3.1 27.2 + - - -
198E PRO* 4.4 1.2 - - - +
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Residues in contact with LEU 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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8E ILE* 4.5 11.7 - - + -
10E VAL* 3.9 17.3 - - + -
17E GLN 3.2 6.3 + - - +
18E ALA* 2.9 12.0 + - - +
20E SER* 1.3 74.6 - - - +
22E ILE* 1.3 58.0 + - + +
24E VAL* 3.0 4.3 + - - +
25E ALA* 2.6 51.6 + - + +
32E VAL* 6.3 0.7 - - + -
78E PHE* 3.4 38.4 - - + -
197E GLY* 3.5 16.4 - - - +
200E LEU* 4.1 28.7 - - + -
201E LEU* 4.7 8.3 - - + +
204E PHE* 4.5 11.0 - - + -
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Residues in contact with ILE 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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10E VAL* 3.4 33.4 - - + -
13E ALA* 3.6 29.6 - - + +
18E ALA 2.8 17.2 + - - +
19E ALA 3.5 7.2 - - - +
21E LEU* 1.3 74.4 - - + +
23E ARG* 1.3 59.0 + - - +
25E ALA* 3.9 4.4 - - - +
26E ALA* 2.9 30.8 + - - +
32E VAL* 3.6 17.8 - - + +
34E ALA* 4.0 7.2 - - + -
47E LEU* 3.6 22.7 - - + -
50E ILE* 4.4 3.1 - - + -
53E VAL* 3.8 26.9 - - + -
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Residues in contact with ARG 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 55.3 + - - +
20E SER* 3.6 11.1 - - - +
22E ILE* 1.3 74.4 - - - +
24E VAL* 1.3 63.8 + - + +
26E ALA* 4.1 1.6 - - - +
27E ALA* 3.2 24.8 + - - +
43E ILE* 3.8 17.4 - - - +
46E GLU* 2.6 43.9 + - - +
47E LEU* 4.9 3.8 - - + -
50E ILE* 4.5 18.2 - - + +
193E GLU* 4.8 15.5 + - - +
708M PRO* 3.5 19.7 - - + +
709M LEU 4.0 10.3 - - - -
710M SER* 3.2 36.0 - - - +
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Residues in contact with VAL 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 SER* 3.2 11.6 + - - +
21E LEU 3.0 6.8 + - - +
23E ARG* 1.3 79.6 - - + +
25E ALA* 1.3 65.0 + - - +
27E ALA* 3.4 3.3 + - - +
28E VAL* 3.1 22.7 + - - +
197E GLY 4.4 9.0 - - - -
198E PRO* 4.3 17.5 - - + -
201E LEU* 3.1 36.3 - - + -
699M PHE* 3.1 22.7 - - + -
707M ARG* 5.6 2.7 - - + -
708M PRO* 3.6 25.4 - - + +
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Residues in contact with ALA 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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8E ILE* 4.0 27.4 - - + -
21E LEU* 2.6 32.1 + - + +
22E ILE* 3.9 2.7 - - - +
24E VAL* 1.3 74.4 - - - +
26E ALA* 1.3 63.5 + - - +
28E VAL* 3.3 15.0 - - - +
30E HIS* 3.0 31.3 + - + +
32E VAL* 4.2 9.9 - - + -
201E LEU* 5.0 3.1 - - + -
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Residues in contact with ALA 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 ILE 2.9 19.4 + - - +
23E ARG 4.1 1.6 - - - +
25E ALA* 1.3 73.6 - - - +
27E ALA* 1.3 59.6 + - - +
29E GLY* 2.9 22.9 + - - -
30E HIS 3.6 14.2 + - - +
32E VAL* 4.6 1.9 - - + +
50E ILE* 3.5 31.4 - - + -
52E ASN* 4.5 13.7 + - + +
53E VAL* 4.0 12.3 - - + -
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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 ARG 3.2 17.6 + - - +
24E VAL 3.6 5.2 - - - +
25E ALA 3.3 0.2 - - - -
26E ALA* 1.3 79.6 - - - +
28E VAL* 1.3 59.9 + - - +
29E GLY 3.5 1.0 + - - -
705M VAL* 3.7 24.2 - - + +
706M VAL 5.0 1.1 - - - +
708M PRO* 3.7 26.5 - - + -
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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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5E LYS* 3.5 24.6 - - + +
24E VAL 3.1 8.4 + - - +
25E ALA* 3.3 16.2 - - - +
26E ALA 3.1 0.2 + - - -
27E ALA* 1.3 75.3 - - - +
29E GLY* 1.3 56.8 + - - +
30E HIS* 3.4 22.2 - - + +
201E LEU* 4.4 9.4 - - + -
699M PHE* 3.6 21.8 - - + -
703M HIS* 3.5 40.8 - - + +
705M VAL* 3.8 15.3 - - + +
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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
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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