Contacts of the helix formed by residues 11 - 23 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A VAL* 1.3 81.5 - - - +
12A PHE* 1.3 59.2 + - - +
13A GLY 3.3 4.9 - - - +
14A ASP* 3.2 19.7 + - - +
15A TRP* 2.9 25.8 + - - +
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Residues in contact with PHE 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL 3.8 1.6 + - - -
11A LEU* 1.3 71.5 - - - +
13A GLY* 1.3 56.5 + - - +
15A TRP* 3.2 14.8 + + - +
16A LEU* 2.5 61.5 + - + +
61A TRP* 3.7 44.6 - + + -
95A PHE* 3.4 46.0 - + - -
98A ALA* 3.8 18.6 - - + +
99A LEU* 3.5 25.6 - - + -
102A THR* 3.4 18.6 - - - +
105A PHE* 4.2 2.0 - + - -
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Residues in contact with GLY 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.3 3.6 - - - +
12A PHE* 1.3 79.5 - - - +
14A ASP* 1.3 59.6 + - - +
16A LEU 3.4 0.2 + - - -
17A LEU* 3.0 35.9 + - - +
102A THR* 3.8 15.2 + - - +
104A ARG* 6.0 1.1 - - - -
105A PHE* 3.4 28.7 - - - -
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Residues in contact with ASP 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 3.6 23.8 - - + +
11A LEU* 3.2 22.5 + - - +
13A GLY* 1.3 72.4 - - - +
15A TRP* 1.3 67.7 + - - +
17A LEU* 3.4 8.2 + - - +
18A GLY* 3.2 18.4 + - - -
104A ARG* 4.2 15.9 + - - -
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Residues in contact with TRP 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 3.9 20.2 - - + +
11A LEU 2.9 13.5 + - - +
12A PHE* 3.3 33.9 - + - +
14A ASP* 1.3 77.2 - - - +
16A LEU* 1.3 91.4 + - + +
18A GLY* 3.1 12.9 + - - -
19A GLU* 3.2 37.4 + - + +
57A ILE* 3.9 20.2 - - + -
60A ALA* 3.7 26.4 + - + -
61A TRP* 3.6 43.1 - + + -
64A ALA* 3.8 17.1 - - + +
95A PHE* 4.1 2.2 - + - -
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 2.5 36.4 + - + +
13A GLY 3.8 4.0 - - - +
15A TRP* 1.3 88.2 - - + +
17A LEU* 1.3 58.6 + - - +
19A GLU* 3.1 4.3 + - + +
20A VAL* 2.9 36.8 + - + +
28A LEU* 4.1 23.1 - - + -
38A PHE* 4.2 16.4 - - + -
40A VAL* 4.7 2.7 - - + -
57A ILE* 4.5 1.6 - - + -
95A PHE* 3.9 26.2 - - + -
99A LEU* 4.2 11.9 - - + -
105A PHE* 3.6 23.8 - - + -
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLY 3.0 24.8 + - - +
14A ASP* 3.9 9.2 - - - +
15A TRP 3.3 0.4 - - - -
16A LEU* 1.3 76.5 - - - +
18A GLY* 1.3 57.3 + - - +
20A VAL* 3.6 6.2 - - + +
21A SER* 2.9 35.2 + - - +
30A TRP* 3.7 32.0 + - + -
38A PHE* 3.9 24.9 - - + -
104A ARG* 3.6 27.8 - - - +
105A PHE* 4.1 11.4 - - + -
124A LEU* 4.3 11.7 - - + -
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Residues in contact with GLY 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASP 3.2 9.9 + - - -
15A TRP 3.1 8.8 + - - -
17A LEU* 1.3 78.0 - - - +
19A GLU* 1.3 60.4 + - - +
21A SER* 4.0 5.1 - - - -
22A SER* 3.1 25.1 + - - -
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Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TRP* 3.2 52.8 + - + +
16A LEU* 3.1 8.8 + - + +
18A GLY* 1.3 77.5 - - - +
20A VAL* 1.3 63.9 + - - +
22A SER* 2.5 26.1 + - - -
23A GLY* 3.5 2.8 + - - -
24A GLN 4.3 1.7 + - - -
25A TYR* 2.9 38.0 + - + -
28A LEU* 4.0 21.3 - - + +
57A ILE* 4.3 4.3 - - + -
60A ALA* 4.8 0.6 - - - +
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Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 2.9 26.4 + - + +
17A LEU* 3.6 11.2 - - + +
18A GLY 3.5 0.2 - - - -
19A GLU* 1.3 75.8 - - - +
21A SER* 1.3 61.1 + - - +
23A GLY* 3.1 14.9 + - - -
28A LEU* 3.7 36.4 - - + +
29A GLN* 3.7 12.5 - - - +
30A TRP* 3.6 46.0 + - + +
38A PHE* 4.0 21.5 - - + -
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Residues in contact with SER 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU 2.9 16.6 + - - -
18A GLY* 4.1 5.6 - - - -
20A VAL* 1.3 72.1 - - - +
22A SER* 1.3 65.2 + - - +
23A GLY* 3.3 0.7 + - - -
30A TRP* 2.7 34.2 + - - +
35A ARG* 3.7 28.3 + - - +
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Residues in contact with SER 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLY 3.1 15.1 + - - -
19A GLU* 2.5 28.7 + - - -
21A SER* 1.3 79.4 - - - +
23A GLY* 1.3 59.9 + - - +
24A GLN* 3.1 37.6 + - - +
25A TYR* 4.5 2.1 - - - -
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Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLU 3.5 0.8 + - - -
20A VAL 3.1 9.9 + - - -
21A SER 3.2 1.7 - - - -
22A SER* 1.3 79.8 + - - +
24A GLN* 1.3 62.2 + - - +
25A TYR 3.4 3.3 - - - -
28A LEU 4.7 0.4 - - - -
29A GLN* 3.3 35.7 + - - -
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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