Contacts of the helix formed by residues 11 - 23 (chain B) in PDB entry 3QU3
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 LEU 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B VAL* 1.3 78.5 - - - +
12B PHE* 1.3 66.8 + - - +
13B GLY* 3.1 6.1 + - - +
14B ASP* 3.1 21.7 + - - +
15B TRP* 3.1 17.5 + - - +
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Residues in contact with PHE 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 VAL 3.8 1.2 + - - -
11B LEU* 1.3 71.9 - - - +
13B GLY* 1.3 53.9 + - - +
15B TRP* 3.1 17.1 + + - +
16B LEU* 2.7 51.7 + - + +
61B TRP* 3.5 46.8 - + + -
95B PHE* 3.4 50.9 - + - -
98B ALA* 3.5 28.9 - - + +
99B LEU* 3.5 25.4 - - + -
102B THR* 3.7 10.8 - - - +
105B PHE* 4.6 1.8 - + - -
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Residues in contact with GLY 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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11B LEU* 3.1 4.9 + - - +
12B PHE* 1.3 80.0 - - - +
14B ASP* 1.3 58.2 + - - +
16B LEU 3.5 0.2 + - - -
17B LEU* 3.1 34.3 + - - +
102B THR* 4.1 13.5 + - - +
104B ARG* 4.7 6.3 - - - -
105B PHE* 3.5 27.4 - - - -
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Residues in contact with ASP 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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10B VAL* 4.4 15.5 - - + +
11B LEU* 3.1 29.0 + - - +
13B GLY* 1.3 72.4 - - - +
15B TRP* 1.3 65.9 + - - +
17B LEU* 3.6 5.7 + - - +
18B GLY* 3.2 18.9 + - - -
104B ARG* 2.9 26.7 + - - +
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Residues in contact with TRP 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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10B VAL* 3.9 20.1 - - + +
11B LEU 3.1 11.5 + - - +
12B PHE* 3.1 26.1 + + - +
14B ASP* 1.3 77.1 - - - +
16B LEU* 1.3 101.5 + - + +
18B GLY* 3.2 4.7 + - - -
19B GLU* 3.2 43.6 + - + +
57B ILE* 3.5 22.7 - - + -
60B ALA* 3.7 22.0 - - + -
61B TRP* 3.6 44.9 - + + -
64B ALA* 3.7 16.6 - - + +
95B PHE* 4.2 1.6 - + - -
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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 PHE* 2.7 30.9 + - + +
13B GLY 3.9 3.8 - - - +
15B TRP* 1.3 95.4 - - + +
17B LEU* 1.3 60.9 + - - +
19B GLU* 2.9 4.7 + - + +
20B VAL* 2.8 35.7 + - + +
28B LEU* 4.1 21.1 - - + -
38B PHE* 4.3 13.5 - - + -
40B VAL* 4.6 5.2 - - + -
57B ILE* 4.2 1.6 - - + -
95B PHE* 3.8 18.8 - - + -
99B LEU* 3.8 28.7 - - + -
105B PHE* 4.0 13.9 - - + -
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Residues in contact with LEU 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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13B GLY 3.1 14.5 + - - +
14B ASP* 4.0 5.8 - - - +
15B TRP 3.4 0.2 - - - -
16B LEU* 1.3 75.8 - - + +
18B GLY* 1.3 64.4 + - - +
20B VAL* 3.1 7.1 + - + +
21B SER* 2.8 28.9 + - - -
30B TRP* 4.0 16.2 - - + -
38B PHE* 4.1 18.2 - - + -
104B ARG* 3.2 39.7 - - - +
105B PHE* 3.8 22.2 - - + -
124B LEU* 3.9 16.6 - - + -
138B EDO 3.9 24.7 - - - +
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Residues in contact with GLY 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 ASP 3.2 12.1 + - - -
15B TRP* 3.2 5.8 + - - -
16B LEU 3.1 0.6 - - - -
17B LEU* 1.3 78.6 - - - +
19B GLU* 1.3 63.2 + - - +
21B SER 3.4 0.2 + - - -
22B SER* 3.0 10.9 + - - -
137B EDO 2.8 44.8 + - - -
138B EDO 4.4 1.7 - - - -
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Residues in contact with GLU 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 TRP* 3.2 50.2 + - + +
16B LEU* 2.9 7.8 + - - +
18B GLY* 1.3 77.8 - - - +
20B VAL* 1.3 68.2 + - - +
22B SER* 2.7 26.8 + - - -
23B GLY* 3.5 2.4 + - - -
25B TYR* 3.3 37.9 + - + -
28B LEU* 3.9 20.2 - - + +
57B ILE* 4.3 1.8 - - + -
60B ALA* 4.6 0.9 - - - +
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Residues in contact with VAL 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* 2.8 27.7 + - + +
17B LEU* 3.4 10.5 - - + +
19B GLU* 1.3 76.0 - - - +
21B SER* 1.3 57.4 + - - +
23B GLY* 3.0 21.5 + - - -
28B LEU* 3.8 30.4 - - + +
29B GLN* 3.5 13.2 - - - +
30B TRP* 3.4 48.9 - - + +
38B PHE* 3.9 25.1 - - + -
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Residues in contact with SER 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 LEU 2.8 8.0 + - - -
20B VAL* 1.3 73.9 - - - +
22B SER* 1.3 63.7 + - - +
23B GLY* 3.3 1.2 + - - -
30B TRP* 2.7 28.5 + - - +
35B ARG* 3.8 15.1 + - - +
137B EDO 3.3 30.1 + - - -
138B EDO 2.6 24.8 + - - -
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Residues in contact with SER 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 GLY 3.0 14.1 + - - -
19B GLU* 2.7 28.9 + - - -
20B VAL 3.2 0.2 - - - -
21B SER* 1.3 77.5 - - - +
23B GLY* 1.3 57.3 + - - +
24B GLN* 3.0 37.9 + - - +
25B TYR* 4.1 8.3 - - - -
137B EDO 3.1 8.9 + - - -
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Residues in contact with GLY 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 GLU 3.5 1.0 + - - -
20B VAL 3.0 17.1 + - - -
21B SER 3.1 1.9 - - - -
22B SER* 1.3 77.8 + - - +
24B GLN* 1.3 56.1 + - - +
25B TYR 3.3 9.4 + - - -
28B LEU 4.8 0.4 - - - -
29B GLN* 3.5 27.3 + - - -
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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