Contacts of the helix formed by residues 14 - 23 (chain A) in PDB entry 2DOS
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 CYS 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLY* 5.9 2.5 - - - -
12A SER 5.5 2.0 - - - -
13A LEU* 1.3 80.9 - - - +
15A ALA* 1.3 60.3 + - - +
16A GLN 4.6 0.7 - - - +
17A HIS* 3.3 53.4 - - + +
18A CYS* 3.1 30.5 + - - +
134A ASN* 4.5 2.5 + - - +
135A SER* 3.3 17.7 - - - +
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Residues in contact with ALA 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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13A LEU* 4.3 2.6 + - - +
14A CYS* 1.3 70.2 - - - +
16A GLN* 1.3 62.0 + - - +
18A CYS* 3.4 1.0 + - - +
19A LEU* 3.0 29.8 + - - +
33A LEU* 3.3 14.4 - - + +
75A PHE* 3.1 60.0 - - + -
80A ILE* 4.5 7.0 - - - -
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Residues in contact with GLN 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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14A CYS* 4.6 1.0 - - + +
15A ALA* 1.3 76.3 - - - +
17A HIS* 1.3 78.9 + - + +
20A ASN* 2.7 69.3 + - - +
28A PHE 3.4 13.3 + - - +
29A SER 3.8 2.2 - - - -
30A PRO* 3.2 51.4 - - + +
33A LEU* 3.3 10.2 - - + +
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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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7A GLU* 5.8 3.7 + - - -
9A GLN* 4.6 22.8 - - + +
14A CYS* 3.3 39.8 + - + +
15A ALA 3.3 0.4 - - - -
16A GLN* 1.3 102.1 + - + +
18A CYS* 1.3 58.0 + - - +
20A ASN* 4.4 4.0 - - - -
21A ASN* 2.6 45.1 + - - +
133A LEU* 4.4 4.2 - - + +
135A SER* 4.1 17.9 - - - +
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Residues in contact with CYS 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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13A LEU* 5.4 4.5 - - + -
14A CYS 3.1 21.3 + - - +
15A ALA* 3.7 5.6 - - - +
17A HIS* 1.3 75.5 - - - +
19A LEU* 1.3 65.4 + - + +
21A ASN* 4.0 1.9 - - - +
22A LEU* 2.7 42.5 + - - +
80A ILE* 4.9 14.1 - - + -
113A ILE* 4.4 10.3 - - - -
120A TRP* 5.2 7.9 - - - -
122A THR* 3.1 36.9 - - - +
133A LEU* 5.5 1.3 - - - -
134A ASN* 6.1 1.3 - - - +
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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 ALA 3.0 19.9 + - - +
16A GLN 4.0 1.8 - - - +
18A CYS* 1.3 79.8 - - - +
20A ASN* 1.3 64.6 + - - +
22A LEU* 3.7 8.7 - - + +
23A LEU* 2.9 38.4 + - - +
28A PHE* 3.9 14.8 - - + -
33A LEU* 3.6 24.7 - - + -
80A ILE* 3.9 29.6 - - + +
83A ALA* 3.6 23.8 - - + -
84A LEU* 5.6 1.8 - - + -
87A TRP* 3.4 31.9 - - + -
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Residues in contact with ASN 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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5A PHE* 6.4 3.8 - - + -
16A GLN* 2.7 56.5 + - - +
17A HIS* 4.1 4.3 - - - +
19A LEU* 1.3 72.9 - - - +
21A ASN* 1.3 58.5 + - - +
23A LEU* 4.9 0.4 - - - -
24A GLN 3.2 2.3 + - - -
25A GLY* 2.7 43.5 + - - +
26A GLU* 3.3 27.5 - - - +
27A TYR 4.7 0.4 - - - +
28A PHE* 3.2 38.1 + - - +
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Residues in contact with ASN 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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5A PHE* 4.0 27.6 + - - +
17A HIS* 2.6 32.2 + - - +
18A CYS* 4.0 2.5 - - - +
20A ASN* 1.3 76.0 - - - +
22A LEU* 1.3 62.4 + - - +
24A GLN* 2.9 23.4 + - - +
25A GLY 4.8 0.2 - - - +
122A THR* 5.4 3.6 - - + -
124A ARG* 5.4 1.6 - - - +
131A PHE* 4.5 21.1 - - + -
133A LEU* 2.9 47.9 - - + +
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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 CYS* 2.7 29.7 + - - +
19A LEU* 3.7 8.7 - - + +
21A ASN* 1.3 74.9 - - - +
23A LEU* 1.3 64.1 + - + +
24A GLN* 3.3 5.0 + - - +
84A LEU* 3.3 37.5 - - + -
87A TRP* 4.7 7.6 - - + -
111A SER* 3.8 17.0 - - - +
113A ILE* 5.3 7.4 - - + -
122A THR* 4.5 13.0 - - + +
123A VAL 5.5 0.2 - - - +
124A ARG* 3.5 37.2 + - + +
169A LEU* 3.6 24.2 - - + +
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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
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19A LEU* 2.9 19.9 + - + +
20A ASN 4.1 1.8 - - - +
22A LEU* 1.3 74.2 - - + +
24A GLN* 1.3 72.6 + - - +
25A GLY 3.4 0.4 + - - +
27A TYR* 3.4 51.4 - - + -
87A TRP* 3.2 55.0 - - + -
169A LEU* 3.9 8.1 - - + -
170A PRO* 3.4 37.2 - - + +
171A ASP* 3.8 9.8 - - - +
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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