Contacts of the strand formed by residues 20 - 24 (chain E) in PDB entry 1DM0
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 PHE 20 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU* 4.1 18.8 - - + -
68D PHE* 4.7 5.6 - + - -
12E THR* 3.6 36.8 - - + -
13E LYS 3.6 8.3 - - - -
14E TYR* 3.9 26.9 - + + -
15E ASN* 4.2 0.4 - - - -
18E ASP 4.1 0.8 + - - -
19E THR* 1.3 72.6 - - - +
21E THR* 1.3 65.0 + - - +
22E VAL* 4.0 1.9 + - + +
30E PHE* 3.7 1.8 - - - -
31E THR* 3.2 37.6 + - + +
37E GLN* 3.0 52.1 - - + +
40E LEU* 3.8 21.5 - - + +
41E LEU* 4.0 11.2 - - + -
63E PHE* 5.1 1.2 - - - -
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Residues in contact with THR 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E TYR* 4.8 4.7 - - + -
12E THR* 3.0 9.4 - - - +
13E LYS* 2.7 57.4 + - + +
15E ASN* 3.7 15.3 + - - +
20E PHE* 1.3 72.8 - - - +
22E VAL* 1.3 73.1 + - - +
28E GLU* 4.0 26.0 + - + +
29E LEU 3.8 7.6 - - - +
30E PHE* 3.9 11.6 - - - +
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Residues in contact with VAL 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E VAL* 4.3 5.6 - - + -
11E TYR 3.8 3.4 - - - -
12E THR* 3.8 20.6 - - + -
20E PHE* 4.0 3.3 + - + +
21E THR* 1.3 75.0 - - - +
23E LYS* 1.3 63.2 + - - +
24E VAL* 3.4 30.5 + - + +
27E LYS 4.1 0.3 - - - +
28E GLU* 3.5 3.3 - - - -
29E LEU* 3.2 33.3 + - + +
40E LEU* 3.5 37.0 - - + -
52E ILE* 4.2 14.1 - - + -
63E PHE* 4.7 7.2 - - + -
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Residues in contact with LYS 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 3.4 0.9 - - - -
10E GLU* 2.7 63.1 + - + +
11E TYR* 2.9 61.2 + - + +
21E THR* 4.8 0.2 - - - +
22E VAL* 1.3 73.9 - - - +
24E VAL* 1.3 62.3 + - - +
25E GLY 4.1 10.2 + - - +
26E ASP* 4.2 14.0 - - - +
27E LYS 3.5 17.5 - - - +
28E GLU* 4.2 5.8 - - + -
59E ASN* 5.8 0.4 - - - -
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Residues in contact with VAL 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E VAL* 3.4 36.4 - - + +
6E THR 4.1 1.3 - - - -
7E GLY 3.8 28.3 - - - +
8E LYS 3.7 12.3 - - - +
9E VAL* 3.5 21.8 - - + -
10E GLU* 5.2 1.1 - - - -
22E VAL* 3.4 22.9 - - + +
23E LYS* 1.3 79.4 - - - +
25E GLY* 1.3 68.8 + - - +
26E ASP 3.4 1.2 + - - -
27E LYS* 3.3 11.7 + - - +
29E LEU* 5.8 0.4 - - + +
50E VAL* 4.1 12.1 - - + +
52E ILE* 4.3 4.3 - - + -
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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