Contacts of the helix formed by residues 28 - 34 (chain A) in PDB entry 1UB5
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 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLY 5.4 0.7 + - - -
27A ILE* 1.3 72.1 - - - +
29A PHE* 1.3 65.9 + - - +
30A SER* 3.5 20.0 - - - +
32A ARG* 3.0 38.0 + - + +
34A TYR* 3.3 18.8 + - - -
75A ASN 5.8 2.5 - - - +
78A ASN* 3.7 9.6 - - - +
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Residues in contact with PHE 29 (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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4A LEU* 3.4 21.3 - - + -
22A CYS* 3.3 36.8 - - - -
23A THR* 4.0 1.6 - - - -
24A ALA* 3.6 23.1 - - + -
27A ILE* 4.0 8.1 - - + -
28A THR* 1.3 70.8 - - - +
30A SER* 1.3 62.4 + - - +
32A ARG 3.0 1.4 + - - -
34A TYR* 3.2 11.9 + - - +
36A MET* 3.4 40.5 - - + +
73A ARG* 3.0 33.8 + - + -
75A ASN* 6.2 0.4 - - - -
78A ASN* 2.9 44.0 + - - +
79A ILE 3.8 4.0 - - - -
80A LEU* 3.6 14.4 - - + -
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Residues in contact with SER 30 (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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28A THR* 3.2 18.7 - - - +
29A PHE* 1.3 77.2 - - - +
32A ARG* 1.3 64.2 + - - +
34A TYR 3.5 0.2 - - - -
55A SER* 3.4 26.3 - - - +
73A ARG* 3.7 5.5 - - - +
75A ASN* 3.3 42.6 + - - +
78A ASN* 4.4 1.2 + - - -
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Residues in contact with ARG 32 (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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28A THR* 3.0 34.7 + - + +
30A SER* 1.3 86.6 - - - +
34A TYR* 1.3 93.1 + - + +
55A SER* 3.9 11.8 - - - -
101A GLN* 4.7 1.4 + - - +
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Residues in contact with TYR 34 (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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26A GLY 5.5 1.0 + - - -
27A ILE* 3.7 20.9 - - + +
28A THR 3.3 29.3 + - - -
29A PHE* 3.2 5.7 + - - -
30A SER 3.5 0.2 - - - -
32A ARG* 1.3 117.5 + - + +
35A ILE* 1.3 68.8 + - - +
36A MET* 3.3 9.6 + - - -
53A ILE 3.5 1.4 - - - +
55A SER* 3.6 10.4 + - - -
73A ARG* 3.1 24.1 + - - -
99A ARG* 3.4 42.3 + - + -
101A GLN* 3.2 20.2 - - + +
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Residues in contact with ILE 35 (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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34A TYR* 1.3 74.7 - - - +
36A MET* 1.3 60.6 + - - +
37A SER* 4.1 2.6 + - - +
52A SER* 4.1 21.8 - - - +
53A ILE 3.3 12.6 - - - +
54A SER* 4.1 17.0 - - - +
55A SER 4.9 1.3 - - - +
60A TYR* 5.9 0.2 - - + -
100A GLY 4.2 9.9 + - - -
101A GLN* 2.9 34.1 + - - +
99B LEU* 4.3 16.2 - - + -
701B SPB 3.6 48.7 - - + +
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Residues in contact with MET 36 (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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4A LEU* 4.7 1.3 - - + -
29A PHE* 3.4 66.2 - - + +
34A TYR* 3.3 9.8 + - - +
35A ILE* 1.3 71.6 - - - +
37A SER* 1.3 64.7 + - - +
52A SER* 3.1 2.6 - - - -
53A ILE* 2.8 41.1 + - + -
71A ILE* 3.7 4.2 - - - +
73A ARG* 4.0 4.9 - - - +
80A LEU* 4.0 17.5 - - + -
97A CYS* 4.3 13.5 - - - -
98A ALA 3.5 22.2 - - - +
99A ARG* 3.9 28.0 - - + +
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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