Contacts of the strand formed by residues 14 - 21 (chain A) in PDB entry 1DUS
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 VAL 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A SER 3.7 7.9 + - - +
13A ASP* 1.3 78.8 - - - +
15A LYS* 1.3 75.7 + - - +
16A ILE* 4.8 6.7 - - + +
29A LYS* 3.7 31.4 - - + -
30A THR 3.3 12.3 - - - +
31A ASP* 4.0 3.6 - - + +
37A TYR* 4.3 0.7 + - - -
88A ARG* 3.6 26.9 - - - +
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Residues in contact with LYS 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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14A VAL* 1.3 77.4 - - - +
16A ILE* 1.3 64.5 + - - +
17A VAL* 3.8 1.9 + - + +
30A THR* 2.8 42.4 + - - +
37A TYR* 3.1 48.7 - - + +
38A GLY* 3.9 19.9 - - - +
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Residues in contact with ILE 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 VAL* 4.8 9.4 - - + -
15A LYS* 1.3 75.6 - - - +
17A VAL* 1.3 66.4 + - - +
18A GLU* 5.2 2.9 - - + -
27A LYS* 3.7 34.8 - - + -
28A PHE 3.4 7.4 - - - +
29A LYS* 4.5 15.9 - - + -
99A LEU* 5.3 5.8 - - + -
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LYS* 3.8 4.5 - - + +
16A ILE* 1.3 80.7 - - - +
18A GLU* 1.3 72.9 + - - +
19A ASP* 5.3 1.1 - - - +
27A LYS* 3.4 1.6 - - - +
28A PHE* 2.7 47.5 + - + +
30A THR* 3.7 17.7 - - + -
38A GLY* 3.4 35.4 - - - +
39A LYS* 3.7 21.3 - - - +
40A VAL* 4.1 15.7 - - + +
66A TYR* 5.5 0.2 - - - +
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Residues in contact with GLU 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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16A ILE* 5.2 2.9 - - + -
17A VAL* 1.3 80.8 - - - +
19A ASP* 1.3 68.6 + - - +
26A LEU 3.2 10.8 - - - +
27A LYS* 3.8 38.4 + - + +
28A PHE* 5.6 0.4 - - - -
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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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17A VAL* 4.4 1.6 + - - +
18A GLU* 1.3 78.1 - - - +
20A ILE* 1.3 87.2 + - - +
21A LEU* 4.1 7.9 - - + -
25A LYS* 3.8 0.7 - - - -
26A LEU* 2.9 34.0 + - - +
28A PHE* 5.3 2.5 - - + -
40A VAL* 4.0 27.7 + - + +
45A LYS* 2.7 36.9 + - - -
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Residues in contact with ILE 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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19A ASP* 1.3 90.6 + - - +
21A LEU* 1.3 73.0 + - - +
23A GLY* 3.9 24.2 - - - +
24A LYS 3.1 11.2 - - - +
25A LYS* 4.4 26.7 - - + -
45A LYS* 5.1 1.4 - - - -
49A GLU* 4.0 4.0 - - - +
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Residues in contact with LEU 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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19A ASP* 4.7 4.9 - - + -
20A ILE* 1.3 84.8 - - - +
22A ARG* 1.3 64.7 + - - +
23A GLY 2.9 1.3 - - - -
24A LYS* 2.7 38.9 + - - +
26A LEU* 4.0 24.9 - - + +
28A PHE* 4.4 9.2 - - + -
40A VAL* 4.6 6.1 - - + -
45A LYS* 4.1 41.1 - - + +
48A VAL* 4.2 14.6 - - + -
49A GLU* 3.2 9.0 - - + +
68A VAL* 3.5 32.8 - - + -
72A ALA* 4.2 6.9 - - + +
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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