Contacts of the helix formed by residues 12 - 20 (chain A) in PDB entry 2JDC
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
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Residue Dist Surf HB Arom Phob DC
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7A ILE* 3.8 22.9 - - + -
8A ASN 3.9 5.8 - - - +
9A ALA 2.7 20.0 + - - +
11A ASP* 1.3 77.8 - - - +
13A TYR* 1.3 65.5 + - - +
14A GLU 3.3 2.8 + - - -
15A LEU 3.4 3.0 + - - -
16A ARG* 2.9 53.3 + - - +
41A HIS* 4.1 9.0 - - + +
53A ILE* 3.6 20.7 - - + +
54A ALA 5.5 0.2 - - - +
55A SER* 4.0 17.9 - - - +
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Residues in contact with TYR 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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9A ALA* 3.4 21.0 - - - +
10A GLU* 3.5 42.6 + - + +
11A ASP 3.5 2.0 - - - -
12A THR* 1.3 82.1 + - - +
14A GLU* 1.3 58.3 + - - +
16A ARG* 3.7 5.1 - - - +
17A HIS* 2.8 32.2 + - - +
26A ILE* 3.8 17.6 - - + +
29A CYS* 3.6 25.4 - - + +
30A MET* 3.7 44.8 - - + +
34A ASP* 3.9 16.0 + - - +
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Residues in contact with GLU 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 GLU 5.0 0.8 + - - -
11A ASP 4.8 5.3 + - - +
12A THR 3.3 0.8 - - - -
13A TYR* 1.3 77.2 - - - +
15A LEU* 1.3 64.2 + - + +
17A HIS* 3.3 5.5 + - - +
18A ARG* 2.8 56.5 + - + +
26A ILE* 5.1 2.2 - - - -
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Residues in contact with LEU 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 ASP 5.3 1.0 + - - +
12A THR 3.4 2.9 + - - +
13A TYR 3.4 0.4 - - - -
14A GLU* 1.3 81.6 - - + +
16A ARG* 1.3 66.2 + - - +
18A ARG* 4.3 13.5 - - - +
19A ILE* 2.9 42.6 + - + +
49A LYS* 6.2 0.4 - - - -
50A LEU* 3.7 30.7 - - + +
51A ILE 4.0 20.0 - - - +
52A SER* 4.1 0.9 - - - +
53A ILE* 3.7 37.7 - - + -
76A ALA* 4.7 0.5 - - - +
78A LEU* 3.8 34.3 - - + -
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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 THR* 2.9 42.3 + - - +
13A TYR* 3.7 3.4 - - - +
15A LEU* 1.3 75.9 - - - +
17A HIS* 1.3 57.9 - - - +
20A LEU* 2.9 47.0 + - + +
21A ARG 3.0 8.5 + - - -
29A CYS* 2.8 42.9 + - - -
31A PHE* 3.4 32.4 - - + -
34A ASP* 2.9 38.2 + - - -
41A HIS* 4.0 1.8 - - - -
53A ILE* 3.6 14.0 - - + +
55A SER* 2.9 32.1 + - - -
74A GLY* 4.4 4.8 + - - -
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Residues in contact with HIS 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 TYR 2.8 17.9 + - - +
14A GLU* 3.6 5.2 - - - +
16A ARG* 1.3 78.8 - - - +
18A ARG* 1.3 67.9 + - + +
21A ARG 3.2 10.2 + - - -
22A PRO* 2.9 53.7 + - + +
24A GLN 3.1 25.0 + - - -
25A PRO 4.6 0.2 - - - -
26A ILE* 3.5 33.5 - - + +
29A CYS* 3.3 9.6 - - - -
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Residues in contact with ARG 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 GLU* 2.8 46.7 + - + +
15A LEU* 4.1 12.4 - - + +
17A HIS* 1.3 82.0 - - + +
19A ILE* 1.3 67.2 + - + +
22A PRO* 3.9 15.2 - - - +
49A LYS* 4.8 10.9 - - - +
78A LEU* 3.7 35.8 - - + +
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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 LEU* 2.9 31.6 + - + +
18A ARG* 1.3 87.5 - - + +
20A LEU* 1.3 62.5 + - - +
22A PRO* 4.1 5.6 - - - +
76A ALA* 3.8 22.7 - - + +
77A THR 3.6 28.9 - - - +
78A LEU* 3.6 16.6 - - + +
79A GLU 5.5 0.4 - - - +
82A ARG* 3.7 22.7 - - - +
111A ARG* 4.4 7.1 + - - -
1147A CAO 3.7 24.4 - - + +
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Residues in contact with LEU 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* 2.9 28.5 + - + +
19A ILE* 1.3 80.6 - - - +
21A ARG* 1.3 63.9 + - + +
22A PRO* 3.3 7.2 - - - +
31A PHE* 4.9 3.6 - - + -
74A GLY* 3.7 35.0 - - - -
75A MET 4.0 9.0 - - - +
76A ALA* 4.2 9.4 - - + -
111A ARG* 2.9 45.8 + - - +
135A VAL* 3.9 4.5 - - - +
1147A CAO 3.8 28.9 - - + +
1148A SO4 3.7 17.7 - - - +
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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