Contacts of the helix formed by residues 14 - 24 (chain A) in PDB entry 3QS7
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 ASP 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A SER* 3.4 5.4 + - - -
13A SER* 1.3 78.1 - - - +
15A PHE* 1.3 58.9 + - - -
16A ALA* 3.3 2.7 - - - +
17A VAL* 3.4 32.9 - - + +
18A LYS* 3.7 6.9 + - - +
78A GLU* 4.7 2.0 - - - +
225E PHE* 5.1 7.2 - - + -
301E SER 3.6 1.4 + - - +
302E THR* 3.4 25.6 + - + +
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Residues in contact with PHE 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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11A ILE* 3.9 18.4 - - + -
12A SER* 3.0 29.7 + - - +
13A SER 3.3 7.7 - - - -
14A ASP* 1.3 74.4 - - - +
16A ALA* 1.3 70.4 - - + +
17A VAL 3.0 6.5 + - - -
18A LYS* 3.3 8.5 + - - +
19A ILE* 3.2 26.6 - - + +
78A GLU* 3.3 36.0 - - + +
109A SER* 3.6 29.6 - - - -
112A LEU* 3.5 29.4 - - + -
113A VAL* 3.6 28.3 - - + -
116A LYS* 5.5 2.9 - - + -
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Residues in contact with ALA 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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13A SER 5.3 3.6 - - - +
14A ASP* 3.3 0.4 - - - -
15A PHE* 1.3 99.2 - - + +
17A VAL* 1.3 65.2 + - + +
19A ILE* 3.7 4.9 + - - +
20A ARG* 3.2 23.0 + - - +
109A SER* 4.4 9.9 - - - +
113A VAL* 6.3 0.7 - - + -
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Residues in contact with VAL 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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14A ASP* 3.4 28.7 - - + +
15A PHE 3.0 0.2 - - - -
16A ALA* 1.3 78.1 - - + +
18A LYS* 1.3 59.5 + - - +
19A ILE 3.1 1.8 - - - -
20A ARG* 3.2 6.1 + - - +
21A GLU* 3.0 52.8 + - - +
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Residues in contact with LYS 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 3.7 5.5 + - - +
15A PHE 3.3 9.0 + - - +
17A VAL* 1.3 78.7 - - - +
19A ILE* 1.3 56.3 + - - +
21A GLU* 3.7 12.7 + - - +
22A LEU* 3.2 16.8 + - - +
71A LEU* 4.7 1.4 - - - +
74A ARG* 4.1 27.5 - - + +
75A VAL* 3.1 21.6 - - + +
78A GLU* 4.3 12.3 - - + +
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Residues in contact with ILE 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 PHE* 3.2 30.7 + - + +
16A ALA* 4.1 5.4 - - - +
17A VAL 3.1 0.8 - - - -
18A LYS* 1.3 77.6 - - + +
20A ARG* 1.3 59.4 + - - +
21A GLU 3.2 1.1 - - - -
22A LEU* 3.8 1.3 - - - +
23A SER* 3.0 28.4 + - - -
75A VAL* 4.1 20.9 - - + -
78A GLU* 5.8 3.1 - - + -
105A LEU* 3.8 39.2 - - + +
106A GLN* 5.8 0.2 - - - -
108A THR* 4.4 13.5 - - + -
109A SER* 4.0 32.5 - - - +
112A LEU* 4.5 3.6 - - + -
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Residues in contact with ARG 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 ALA 3.2 17.3 + - - +
17A VAL* 3.2 7.5 + - - +
19A ILE* 1.3 75.7 - - - +
21A GLU* 1.3 59.3 + - - +
23A SER* 3.6 7.1 + - - -
24A ASP* 3.1 59.9 + - - +
66B SER* 4.4 10.1 + - - -
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Residues in contact with GLU 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 VAL* 3.0 38.0 + - + +
18A LYS* 3.9 11.5 - - - +
19A ILE 3.2 0.2 - - - -
20A ARG* 1.3 77.6 - - + +
22A LEU* 1.3 63.9 + - - +
24A ASP* 3.4 12.3 + - - +
25A TYR* 3.4 27.4 - - + -
71A LEU* 4.1 14.2 - - + +
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Residues in contact with LEU 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 LYS 3.2 18.1 + - - +
19A ILE 3.5 2.9 + - - +
21A GLU* 1.3 75.4 - - - +
23A SER* 1.3 64.9 + - - +
25A TYR* 3.1 15.1 + - - +
26A LEU* 3.3 27.5 + - + +
57A MET* 4.6 1.8 - - + -
68A MET* 3.4 33.2 - - - -
71A LEU* 3.9 19.0 - - + +
72A LEU* 3.7 23.1 - - + -
75A VAL* 3.8 23.1 - - + -
101A ILE* 5.7 0.7 - - + -
105A LEU* 3.4 32.8 - - + -
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Residues in contact with SER 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 ILE* 3.0 19.8 + - - -
20A ARG* 3.8 8.5 - - - -
21A GLU 3.4 0.2 - - - -
22A LEU* 1.3 78.6 - - - +
24A ASP* 1.3 61.9 + - - +
25A TYR 3.2 1.2 + - - -
26A LEU* 3.3 16.6 + - - -
28A GLN* 3.1 33.7 + - - +
105A LEU* 4.2 9.6 - - - +
65B GLY* 3.8 5.7 - - - -
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Residues in contact with ASP 24 (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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20A ARG* 3.1 50.1 + - - +
21A GLU* 3.5 13.9 - - - +
22A LEU 3.1 0.8 - - - -
23A SER* 1.3 78.1 + - - +
25A TYR* 1.3 55.2 + - + +
65B GLY 4.7 0.7 - - - -
66B SER* 2.8 25.3 + - - +
67B LYS* 2.6 41.2 + - + +
68B MET* 2.7 18.4 + - - -
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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