Contacts of the helix formed by residues 11 - 23 (chain A) in PDB entry 1TQM
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 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LYS 3.8 3.2 + - - -
10A MET* 1.3 73.2 - - - +
12A LYS* 1.3 66.9 + - - -
13A HIS 3.3 4.0 - - - -
14A SER* 3.1 12.0 + - - -
15A TRP* 3.0 29.0 + - - -
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Residues in contact with LYS 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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11A GLY* 1.3 71.3 - - - -
13A HIS* 1.3 70.2 + - + +
15A TRP* 3.2 12.3 + - + +
16A ARG* 3.0 31.2 + - - +
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Residues in contact with HIS 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 GLY 3.3 0.8 - - - -
12A LYS* 1.3 79.8 + - + +
14A SER* 1.3 57.4 + - - +
16A ARG* 3.2 36.6 + - - +
17A ILE* 2.9 35.0 + - - +
42A ILE* 4.0 12.9 - - + +
46A LYS* 4.2 28.4 + - - -
50A ILE* 4.0 20.0 - - + -
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Residues in contact with SER 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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9A LYS 4.8 2.1 + - - -
10A MET* 4.0 21.5 - - - -
11A GLY* 3.1 25.1 + - - -
13A HIS* 1.3 76.9 - - - +
15A TRP* 1.3 63.8 + - - +
17A ILE* 3.2 4.7 + - - +
18A MET* 3.0 27.7 + - - +
50A ILE* 4.2 16.8 - - - +
53A TYR* 5.3 5.5 - - - -
54A LEU* 4.0 14.8 - - - +
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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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7A TYR* 3.8 25.5 + + - -
10A MET* 3.4 39.5 + - + +
11A GLY 3.0 26.3 + - - -
12A LYS* 3.7 9.0 - - + +
14A SER* 1.3 77.8 - - - +
16A ARG* 1.4 56.2 + - + +
18A MET* 3.2 29.7 + - - +
19A ASP* 2.9 35.9 + - - +
79A LEU* 3.9 24.0 - - + -
80A TYR* 4.2 6.7 - + - -
83A HIS* 3.3 69.0 - + + +
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Residues in contact with ARG 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 LYS* 3.0 22.0 + - - +
13A HIS* 3.2 37.6 + - - +
15A TRP* 1.4 74.6 - - + +
17A ILE* 1.3 63.7 + - - +
19A ASP* 3.3 15.2 + - - +
20A ALA* 3.1 23.0 + - - +
39A HIS* 5.1 0.7 - - - -
40A ALA* 2.6 36.4 + - + +
41A ARG* 3.3 23.6 + - - +
42A ILE* 3.7 13.8 - - + +
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Residues in contact with ILE 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 HIS 2.9 17.3 + - - +
14A SER 3.2 7.6 + - - +
16A ARG* 1.3 77.2 - - - +
18A MET* 1.3 63.6 + - - +
20A ALA* 3.2 5.0 + - - +
21A ILE* 3.1 23.1 + - + +
36A ILE* 3.8 21.4 - - + +
40A ALA* 4.1 8.5 - - + -
42A ILE* 3.9 19.1 - - + -
47A ALA* 3.9 27.8 - - + +
50A ILE* 3.9 18.4 - - + -
51A LEU* 3.6 32.8 - - + -
54A LEU* 4.1 11.4 - - + -
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Residues in contact with MET 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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10A MET* 5.0 4.9 - - - +
14A SER 3.0 14.3 + - - +
15A TRP* 3.2 33.0 + - - +
17A ILE* 1.3 77.2 - - + +
19A ASP* 1.3 62.8 + - - +
21A ILE* 3.3 4.4 + - + +
22A PHE* 2.9 20.4 + - - +
54A LEU* 4.1 16.8 - - + -
59A VAL* 3.0 33.7 - - + -
60A VAL* 5.2 2.9 - - + -
72A PHE* 3.4 28.4 - - + -
76A GLY* 3.2 24.7 - - - +
79A LEU* 4.2 7.4 - - + -
80A TYR* 3.7 21.5 - - + +
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Residues in contact with ASP 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* 2.9 20.9 + - - +
16A ARG* 3.5 18.4 - - - +
18A MET* 1.3 75.4 - - - +
20A ALA* 1.4 59.4 + - - +
22A PHE* 3.3 0.5 + - - +
23A LYS* 2.9 49.8 + - - +
39A HIS* 4.4 6.3 - - + +
80A TYR* 3.0 35.8 + - - +
83A HIS* 5.0 5.0 - - - -
84A ARG* 5.0 1.7 + - - -
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Residues in contact with ALA 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 ARG 3.1 9.5 + - - +
17A ILE 3.2 8.0 + - - +
19A ASP* 1.4 79.0 - - - +
21A ILE* 1.3 64.2 + - - +
24A ASN* 2.8 30.0 + - - +
31A VAL* 4.5 1.7 - - - +
36A ILE* 3.6 31.9 - - + +
39A HIS* 3.4 31.2 - - + -
40A ALA* 4.2 2.5 - - + +
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Residues in contact with ILE 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 ILE* 3.1 16.0 + - + +
18A MET* 3.3 11.0 + - - +
20A ALA* 1.3 75.1 - - - +
22A PHE* 1.3 65.1 + - - +
24A ASN 3.0 14.2 + - - -
25A LEU* 3.2 15.7 + - + +
31A VAL* 3.7 13.5 - - + +
36A ILE* 3.8 20.2 - - + -
51A LEU* 3.9 18.2 - - + -
60A VAL* 3.9 28.3 - - + -
70A SER* 4.1 23.3 - - - +
71A THR* 4.2 7.4 - - - -
72A PHE* 3.8 24.2 - - + -
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Residues in contact with PHE 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 MET 2.9 16.6 + - - +
19A ASP 3.3 4.2 + - - +
21A ILE* 1.3 76.6 - - - +
23A LYS* 1.3 75.3 + - + +
24A ASN 3.3 0.7 + - - -
25A LEU* 3.4 18.0 + - + +
26A TRP* 3.4 39.1 - + - -
72A PHE* 3.8 11.4 - + + -
77A LEU* 4.3 4.7 - - + -
80A TYR* 3.4 40.8 - + + -
84A ARG* 4.6 14.6 - - - -
148A ILE* 3.6 22.9 - - + -
174A GLY* 4.0 25.1 - - - -
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Residues in contact with LYS 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 ASP* 2.9 35.3 + - - +
20A ALA 4.4 2.0 - - - +
21A ILE 3.2 0.6 - - - -
22A PHE* 1.3 88.0 - - + +
24A ASN* 1.3 63.7 + - - +
25A LEU 3.5 0.4 - - - -
26A TRP* 4.8 8.9 + - - +
39A HIS* 3.9 30.2 + - + +
80A TYR* 4.8 0.4 + - - -
84A ARG* 4.1 26.8 - - - +
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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