Contacts of the strand formed by residues 43 - 47 (chain E) in PDB entry 1U1T
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 43 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39E PHE* 3.3 4.7 - - - +
40E ASP* 2.8 57.2 + - - +
42E PHE* 1.3 80.8 - - - +
44E ILE* 1.3 64.2 + - - +
53E MET* 3.7 31.6 - - + -
54E VAL 3.2 11.4 - - - +
55E TYR* 3.5 31.6 - - + -
56E LYS* 4.3 1.1 - - - +
7F LEU* 3.9 15.7 - - + -
8F GLN* 4.0 14.4 - - + +
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Residues in contact with ILE 44 (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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55D TYR* 4.0 16.6 - - - +
12E LEU* 4.2 19.3 - - + -
24E ILE* 4.4 16.8 - - + -
36E ILE* 4.1 21.5 - - + -
38E SER 3.7 10.3 - - - +
39E PHE* 3.9 10.1 - - + -
43E VAL* 1.3 81.4 - - - +
45E LEU* 1.3 71.8 + - - +
46E LEU* 3.5 3.8 + - + +
53E MET* 3.6 1.8 - - - -
54E VAL* 2.8 43.5 + - + +
56E LYS* 4.0 9.2 - - + -
59E ILE* 3.8 24.7 - - + -
62E VAL* 5.0 3.8 - - + -
7F LEU* 4.6 1.1 - - - -
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Residues in contact with LEU 45 (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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36E ILE* 3.7 2.8 - - - -
37E GLU* 2.8 50.6 + - + +
38E SER* 2.8 37.7 + - - +
44E ILE* 1.3 71.4 - - - +
46E LEU* 1.3 55.4 + - - +
51E SER* 3.2 28.0 - - - +
52E GLN 3.4 19.3 - - - +
53E MET* 4.3 4.3 - - + +
7F LEU* 3.8 19.9 - - + +
11F TYR* 3.8 24.5 - - + -
70F LEU* 4.8 9.6 - - + -
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Residues in contact with LEU 46 (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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22E VAL* 4.2 6.3 - - + -
24E ILE* 4.0 28.0 - - + -
32E LEU* 3.6 38.6 - - + -
33E GLN 4.2 13.2 - - - +
34E GLY* 3.8 6.5 - - - +
35E GLN* 3.5 33.4 - - - +
36E ILE* 4.2 2.2 - - + +
37E GLU* 4.2 1.8 - - - -
44E ILE* 3.5 2.2 + - + +
45E LEU* 1.3 72.5 - - - +
47E LYS* 1.3 59.5 + - - +
48E ASN* 3.5 12.9 - - - +
51E SER* 3.4 1.2 - - - -
52E GLN* 2.8 49.3 + - + +
54E VAL* 4.3 8.7 - - + -
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Residues in contact with LYS 47 (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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34E GLY* 3.0 5.6 - - - -
35E GLN* 2.8 63.8 + - + +
37E GLU* 2.8 38.7 + - + +
46E LEU* 1.3 70.8 - - - +
48E ASN* 1.3 77.4 + - - +
50E VAL 3.8 4.5 - - - +
51E SER* 5.0 2.7 - - - -
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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