Contacts of the helix formed by residues 13 - 31 (chain E) in PDB entry 2QVS
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 GLU 13 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14E SER* 1.3 67.2 + - - +
15E VAL* 3.0 28.2 + - + +
16E LYS* 3.2 35.7 + - - +
17E GLU* 3.4 19.8 + - - +
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Residues in contact with SER 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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13E GLU* 1.3 71.1 - - - +
15E VAL* 1.3 57.2 + - - +
17E GLU* 2.9 16.5 + - - +
18E PHE* 2.6 38.2 + - - +
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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
----------------------------------------------------------
13E GLU* 3.2 27.8 - - + +
14E SER* 1.3 78.2 - - - +
16E LYS* 1.3 95.7 + - + +
18E PHE* 3.5 5.3 + - - +
19E LEU* 3.0 33.9 + - + +
155E GLU* 5.0 9.0 - - - +
292E LYS* 4.6 17.9 - - - +
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Residues in contact with LYS 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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13E GLU* 3.2 42.2 - - - +
15E VAL* 1.3 95.0 - - + +
17E GLU* 1.3 73.0 + - - +
19E LEU* 3.3 5.8 + - - +
20E ALA* 2.8 27.7 + - - +
289E ASN* 5.8 2.2 + - - -
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Residues in contact with GLU 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 GLU 3.4 18.3 + - - +
14E SER* 2.9 18.7 + - - +
16E LYS* 1.3 81.3 - - - +
18E PHE* 1.3 64.1 + - - +
20E ALA* 3.4 4.4 - - - +
21E LYS* 2.9 48.0 + - + +
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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 SER* 2.6 19.8 + - - +
15E VAL* 3.7 5.6 - - - +
17E GLU* 1.3 73.9 - - - +
19E LEU* 1.3 63.3 + - + +
21E LYS* 3.3 7.4 + - - +
22E ALA* 2.6 40.8 + - + +
99E ASN* 5.2 4.7 - - - -
100E PHE* 4.1 23.6 - + - -
101E PRO* 5.6 0.7 - - + -
156E TYR* 4.3 16.4 - + - -
306E TYR* 2.8 44.9 - + - -
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Residues in contact with LEU 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* 3.0 25.0 + - + +
16E LYS* 3.9 5.2 - - - +
18E PHE* 1.3 87.0 - - + +
20E ALA* 1.3 55.5 + - - +
22E ALA* 3.0 6.6 + - + +
23E LYS* 2.6 37.3 + - - +
155E GLU* 4.4 24.7 - - + +
156E TYR* 4.3 16.2 - - + +
159E SER* 3.4 36.9 + - - +
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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 LYS 2.8 22.3 + - - +
17E GLU* 3.4 5.6 - - - +
19E LEU* 1.3 71.1 - - - +
21E LYS* 1.3 66.1 + - + +
22E ALA 3.1 0.2 + - - -
23E LYS* 3.1 7.3 + - - +
24E GLU* 3.0 24.4 + - - +
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Residues in contact with LYS 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 GLU* 2.9 38.8 + - - +
18E PHE* 3.7 6.3 - - - +
20E ALA* 1.3 77.9 - - + +
22E ALA* 1.3 55.0 + - - +
24E GLU* 3.5 14.2 - - - +
25E ASP* 2.7 44.9 + - - +
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Residues in contact with ALA 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* 2.6 31.6 + - + +
19E LEU* 3.1 13.7 - - + +
20E ALA 3.0 0.2 - - - -
21E LYS* 1.3 71.1 - - - +
23E LYS* 1.3 66.5 + - - +
25E ASP* 3.3 9.3 + - - +
26E PHE* 2.9 24.8 + - - +
156E TYR* 4.0 27.9 + - + -
160E LEU* 4.5 3.8 - - + +
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Residues in contact with LYS 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 LEU 2.6 17.7 + - - +
20E ALA* 3.1 5.6 + - - +
22E ALA* 1.3 73.5 - - - +
24E GLU* 1.3 54.9 + - - +
26E PHE* 3.6 3.5 - - + +
27E LEU* 2.7 61.7 + - + +
159E SER* 4.6 14.4 + - - +
160E LEU* 4.0 19.9 - - + +
161E ASP* 4.7 7.9 + - - -
190E ARG* 4.7 13.7 - - - +
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Residues in contact with GLU 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 3.0 10.7 + - - +
21E LYS* 3.5 21.6 - - - +
23E LYS* 1.3 79.9 - - - +
25E ASP* 1.3 68.7 + - - +
26E PHE 3.1 0.2 + - - -
27E LEU* 3.3 5.9 + - - +
28E LYS* 3.1 27.7 + - - +
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Residues in contact with ASP 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 LYS* 2.7 29.6 + - - +
22E ALA* 3.6 7.3 - - - +
24E GLU* 1.3 80.6 - - - +
26E PHE* 1.3 61.5 + - - +
28E LYS* 3.8 10.6 - - - +
29E LYS* 3.3 44.9 + - - +
97E ALA 4.8 0.7 - - - -
99E ASN* 6.4 1.8 - - + -
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Residues in contact with PHE 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 ALA 2.9 16.6 + - - +
23E LYS* 3.6 4.0 - - + +
25E ASP* 1.3 74.9 - - - +
27E LEU* 1.3 66.7 - - + +
28E LYS 3.1 1.6 - - - -
29E LYS* 3.1 2.3 + - - +
30E TRP* 2.7 71.6 + + + +
94E ILE* 5.4 0.4 - - + -
97E ALA* 3.5 41.7 - - + +
98E VAL* 4.2 2.7 - - + -
156E TYR* 5.2 1.3 - - - +
160E LEU* 3.6 38.8 - - + -
162E LEU* 3.9 17.3 - - + -
190E ARG* 3.4 39.7 - - - -
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Residues in contact with LEU 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 LYS* 2.7 50.3 + - + +
24E GLU* 4.0 4.9 - - - +
26E PHE* 1.3 82.6 - - + +
28E LYS* 1.3 57.2 + - - +
30E TRP* 3.8 4.4 - - + +
31E GLU* 2.9 50.1 + - - +
190E ARG* 3.8 30.1 - - - +
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Residues in contact with LYS 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 GLU* 3.1 21.0 + - - +
25E ASP* 3.8 11.4 - - - +
27E LEU* 1.3 79.1 - - - +
29E LYS* 1.3 70.7 + - + +
31E GLU* 3.6 1.9 + - - +
32E THR* 3.5 26.0 + - - -
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Residues in contact with LYS 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 ASP* 3.3 34.8 + - - +
26E PHE 3.1 1.8 + - - -
28E LYS* 1.3 85.2 - - + +
30E TRP* 1.3 60.7 + - - +
32E THR 3.4 6.1 - - - -
33E PRO* 3.3 11.8 - - - +
96E GLN* 2.6 49.6 - - - +
97E ALA* 3.7 22.6 + - + +
99E ASN* 6.1 5.0 - - - +
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Residues in contact with TRP 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 PHE* 2.7 53.6 + + + +
27E LEU* 3.8 5.4 - - + +
29E LYS* 1.3 75.4 - - - +
31E GLU* 1.3 70.0 + - - +
32E THR 3.2 4.0 + - - -
33E PRO* 3.5 5.5 - - - +
90E ASN* 4.1 9.9 - - - -
93E ARG* 2.6 98.8 + - + +
94E ILE* 3.4 33.9 - - + -
96E GLN* 4.2 0.9 - - - -
97E ALA* 3.8 2.4 - - + +
162E LEU* 4.8 0.9 - - + -
190E ARG* 3.7 51.5 - - + +
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Residues in contact with GLU 31 (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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27E LEU* 2.9 32.1 + - - +
28E LYS* 4.0 2.0 - - - +
30E TRP* 1.3 86.8 + - - +
32E THR* 1.3 67.8 + - - +
33E PRO* 3.8 3.8 - - - +
93E ARG* 3.7 19.3 + - - +
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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