Contacts of the helix formed by residues 8 - 18 (chain A) in PDB entry 1ADN
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 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LEU* 1.5 89.0 - - + +
9A ASP* 1.5 60.2 + - - +
10A ASP* 2.7 37.7 + - - +
11A GLN* 3.0 20.3 + - - +
12A ARG* 3.2 23.7 + - - +
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Residues in contact with ASP 9 (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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8A THR* 1.5 57.3 - - - +
10A ASP* 1.5 57.3 + - - +
11A GLN 3.6 0.2 - - - -
12A ARG* 3.2 16.1 - - + +
13A TRP* 2.9 32.9 + - - +
49A ARG* 4.5 20.1 + - - -
54A PHE* 4.3 11.5 - - + -
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Residues in contact with ASP 10 (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 LEU* 5.1 1.7 - - - +
8A THR* 2.7 30.7 + - - +
9A ASP* 1.5 68.8 - - - +
11A GLN* 1.5 69.3 + - - +
13A TRP* 4.6 3.2 - - - +
14A GLN* 2.7 50.4 + - - +
49A ARG* 5.9 6.5 - - - +
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Residues in contact with GLN 11 (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 LEU* 4.0 23.2 - - + +
8A THR* 3.0 17.9 + - - +
10A ASP* 1.5 69.7 + - - +
12A ARG* 1.5 60.0 + - - +
14A GLN* 3.4 10.1 + - - +
15A SER* 2.8 33.3 + - - -
22A ASN* 3.6 15.1 + - - +
23A ALA* 2.9 31.0 - - + +
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Residues in contact with ARG 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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6A CYS* 2.8 44.0 - - - +
7A LEU 4.5 1.2 - - - +
8A THR* 3.2 33.1 + - - +
9A ASP* 3.2 17.7 - - - +
11A GLN* 1.5 69.4 - - - +
13A TRP* 1.5 55.3 + - - +
15A SER* 2.7 35.4 + - - -
23A ALA* 4.7 8.9 - - - +
24A ASP* 3.6 25.6 + - - +
27A PHE* 3.1 21.7 - - + -
54A PHE* 4.4 17.7 - - + -
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Residues in contact with TRP 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 ASP 2.9 11.3 + - - +
10A ASP* 4.6 2.2 - - - +
12A ARG* 1.5 59.7 - - - +
14A GLN* 1.5 55.7 + - - +
16A VAL* 2.7 71.9 + - + +
17A LEU* 2.8 56.1 + - + +
29A PHE* 4.5 3.6 - + - -
46A HIS* 3.7 26.0 - + - -
48A LEU* 4.6 3.4 - - - -
49A ARG* 2.9 66.5 - - + +
52A VAL* 4.4 13.2 - - + -
54A PHE* 3.3 38.1 - + + -
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Residues in contact with GLN 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* 2.7 39.9 + - - +
11A GLN* 3.4 9.0 - - - +
13A TRP* 1.5 55.5 - - - +
15A SER* 1.5 64.5 + - - +
17A LEU* 3.1 16.5 + - + +
18A ALA* 3.0 27.5 + - + +
22A ASN* 5.2 9.9 - - - +
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Residues in contact with SER 15 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLN 2.8 11.7 + - - -
12A ARG* 2.7 23.3 + - - -
14A GLN* 1.5 56.5 - - - +
16A VAL* 1.5 56.5 + - - +
18A ALA* 3.9 2.6 - - - +
19A ARG 3.7 17.3 + - - +
20A ASP 4.1 6.1 - - - +
21A PRO* 4.2 3.5 - - - +
22A ASN* 3.3 38.7 + - - +
23A ALA* 4.1 5.2 - - - -
27A PHE* 2.9 26.1 - - - -
40A PRO* 4.4 4.4 - - - +
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Residues in contact with VAL 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 ARG 3.3 3.3 + - - +
13A TRP* 2.7 74.7 + - + +
15A SER* 1.5 53.6 + - - +
17A LEU* 1.5 64.6 + - - +
18A ALA 3.0 8.9 + - - -
19A ARG* 3.7 2.1 + - - -
27A PHE* 4.0 17.9 - - + -
29A PHE* 4.4 16.6 - - + -
40A PRO* 3.4 36.4 - - + +
46A HIS* 5.3 4.5 - - + +
54A PHE* 4.5 4.3 - - + -
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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 TRP* 2.8 59.4 + - + +
14A GLN* 3.1 16.4 + - + +
16A VAL* 1.5 68.6 - - - +
18A ALA* 1.5 65.5 + - - +
46A HIS* 5.2 6.1 - - + +
49A ARG* 5.0 6.7 - - - +
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Residues in contact with ALA 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 GLN* 3.0 18.2 + - + +
15A SER* 3.9 7.4 - - - +
16A VAL 3.0 1.7 + - - +
17A LEU* 1.5 68.5 - - - +
19A ARG* 1.5 69.2 + - + +
20A ASP 4.8 4.9 - - - +
22A ASN* 5.7 3.8 - - + -
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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