Contacts of the helix formed by residues 12 - 23 (chain A) in PDB entry 6I53
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 THR 12 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASN* 1.3 76.9 - - + +
13A THR* 1.3 64.3 + - - +
14A VAL 3.2 2.9 + - - -
15A PHE* 3.6 10.6 + - - +
16A THR* 3.0 24.5 + - - +
24B ASP* 6.4 0.4 - - + -
27B LEU* 3.3 23.6 - - - +
28B ARG 5.5 0.3 + - - -
31B PHE* 4.7 11.5 - - - +
71B ARG* 4.3 28.2 + - + +
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Residues in contact with THR 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASP* 3.8 34.3 + - - +
11A ASN 3.2 1.9 + - - -
12A THR* 1.3 78.3 - - - +
14A VAL* 1.3 60.0 + - - +
16A THR* 3.8 10.2 - - + -
17A ARG* 3.0 49.9 + - + +
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Residues in contact with VAL 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 ASP 5.2 4.9 - - - +
11A ASN 4.2 14.6 - - - +
12A THR 3.2 0.6 - - - -
13A THR* 1.3 78.2 - - - +
15A PHE* 1.3 63.9 + - + +
17A ARG* 3.2 22.8 + - - +
18A ILE* 3.1 31.8 + - + +
80A PRO* 4.4 27.6 - - + -
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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
----------------------------------------------------------
11A ASN 5.2 2.2 - - - -
12A THR* 3.6 12.2 + - - +
14A VAL* 1.3 80.4 - - + +
16A THR* 1.3 64.6 + - - +
18A ILE* 3.5 15.4 + - + +
19A LEU* 3.2 28.9 + - - +
77A PHE* 6.4 0.4 - + - -
80A PRO* 3.8 41.5 - - + -
81A MET* 4.0 32.5 - - + -
84A LEU* 4.0 15.2 - - + +
27B LEU* 4.1 14.8 - - + -
31B PHE* 3.6 38.6 - + + -
32B GLY* 4.6 13.7 - - - -
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Residues in contact with THR 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR* 3.0 20.5 + - - +
13A THR* 3.8 11.6 - - + -
14A VAL 3.3 0.6 - - - -
15A PHE* 1.3 76.6 - - - +
17A ARG* 1.3 59.5 + - - +
19A LEU* 3.4 1.8 + - - +
20A ASP* 3.0 50.7 + - - +
22B GLY 6.0 1.6 - - - +
24B ASP* 3.3 36.7 + - + +
26B ARG* 5.0 0.7 - - - +
27B LEU* 3.4 6.3 - - - +
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Residues in contact with ARG 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 3.0 45.1 + - + +
14A VAL* 3.2 26.3 + - - +
16A THR* 1.3 75.0 - - - +
18A ILE* 1.3 64.2 + - + +
20A ASP* 4.1 5.6 - - - +
21A ARG* 3.2 25.6 + - + +
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Residues in contact with ILE 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 VAL* 3.1 21.3 + - + +
15A PHE* 3.8 27.6 - - + +
16A THR 3.3 0.4 - - - -
17A ARG* 1.3 77.5 - - + +
19A LEU* 1.3 62.3 + - + +
21A ARG* 3.2 15.5 + - - +
22A LEU* 3.1 25.6 + - + +
77A PHE* 3.9 35.7 - - + -
78A LYS 4.4 5.8 - - - +
79A GLY* 4.0 27.1 - - - +
80A PRO* 4.3 4.7 - - + -
84A LEU* 4.4 13.7 - - + -
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Residues in contact with LEU 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 18.2 + - - +
16A THR 4.0 2.2 - - - +
18A ILE* 1.3 76.9 - - + +
20A ASP* 1.3 63.8 + - - +
22A LEU* 3.5 16.3 + - + +
23A LEU* 3.6 22.9 + - - +
84A LEU* 4.0 19.5 - - + -
86A LEU* 3.7 36.1 - - + -
90A MET* 4.3 12.3 - - + -
24B ASP* 4.3 6.1 - - - +
26B ARG* 3.8 35.9 - - + +
27B LEU* 3.8 25.4 - - + -
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Residues in contact with ASP 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 THR* 3.0 35.3 + - - +
17A ARG* 4.2 5.6 - - - +
19A LEU* 1.3 76.5 - - - +
21A ARG* 1.3 62.1 + - - +
23A LEU* 3.5 10.2 + - - +
24A ASP* 3.0 26.8 + - - +
26B ARG* 3.2 20.9 + - - -
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Residues in contact with ARG 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 ARG* 3.2 21.0 + - + +
18A ILE* 3.2 13.8 + - - +
20A ASP* 1.3 77.4 - - - +
22A LEU* 1.3 69.7 + - - +
23A LEU 3.4 0.7 + - - -
24A ASP* 3.6 22.4 + - - +
25A GLY 5.0 0.9 + - - -
76A LYS 3.8 9.4 + - - -
77A PHE* 3.4 37.0 - - - +
78A LYS 4.1 6.5 + - - +
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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 ILE* 3.1 27.9 + - + +
19A LEU* 3.5 17.0 + - + +
20A ASP 3.3 0.4 - - - -
21A ARG* 1.3 85.0 - - - +
23A LEU* 1.3 63.3 + - + +
24A ASP 3.5 0.8 + - - -
25A GLY 5.1 0.5 + - - -
26A TYR* 3.3 22.9 + - - +
74A ARG 4.1 8.7 - - - +
75A LEU* 3.9 44.3 - - + +
76A LYS 3.4 25.8 - - - +
77A PHE* 4.3 11.9 - - + -
84A LEU* 4.7 1.6 - - + -
90A MET* 5.2 2.0 - - + -
121A ILE* 4.6 15.0 - - + -
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU 3.6 10.5 + - - +
20A ASP* 3.5 8.1 + - - +
21A ARG 3.2 0.8 - - - -
22A LEU* 1.3 81.4 - - + +
24A ASP* 1.3 64.8 + - - +
25A GLY 3.8 0.4 - - - -
26A TYR* 3.9 31.6 + - + +
75A LEU* 5.4 1.1 - - + -
90A MET* 3.7 22.9 - - + -
93A LYS* 4.1 33.2 - - + +
94A ILE* 4.6 4.0 - - + -
26B ARG* 3.4 29.6 - - - +
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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