Contacts of the helix formed by residues 28 - 34 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H GLY 4.4 1.2 + - - -
27H ILE* 1.3 72.7 - - - +
29H PHE* 1.3 65.3 + - - +
30H SER* 3.6 20.6 - - - +
32H ARG* 3.0 37.8 + - + +
34H TYR* 3.2 18.6 + - - -
75H ASN 5.8 2.2 - - - +
78H ASN* 3.6 9.2 - - - +
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Residues in contact with PHE 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 3.5 20.2 - - + -
22H CYS* 3.2 37.9 - - - -
23H THR* 4.0 1.3 - - - -
24H ALA* 3.7 22.7 - - + -
27H ILE* 4.0 8.7 - - + -
28H THR* 1.3 71.3 - - - +
30H SER* 1.3 59.1 - - - +
32H ARG 3.0 1.8 + - - -
34H TYR* 3.2 9.2 + - - +
36H MET* 3.4 42.8 - - + +
73H ARG* 2.9 37.0 + - + -
75H ASN* 6.3 0.2 - - - -
78H ASN* 2.9 43.2 + - - +
79H ILE 3.8 1.3 - - - -
80H LEU* 3.6 17.5 - - + -
97H CYS* 4.4 0.2 - - - -
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Residues in contact with SER 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H THR* 3.0 18.6 + - - +
29H PHE* 1.3 76.9 - - - +
32H ARG* 1.3 64.4 + - - +
34H TYR 3.5 0.2 - - - -
55H SER* 3.5 24.6 - - - +
73H ARG* 3.8 4.8 - - - +
75H ASN* 3.2 44.0 + - - +
78H ASN* 4.4 1.0 + - - -
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Residues in contact with ARG 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H THR* 3.0 34.2 + - + +
30H SER* 1.3 86.6 - - - +
34H TYR* 1.3 93.1 + - + +
55H SER* 3.9 12.2 - - - -
101H GLN* 4.7 1.6 + - - +
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Residues in contact with TYR 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H GLY 5.5 0.9 + - - -
27H ILE* 3.8 20.6 - - + +
28H THR 3.2 30.1 + - - -
29H PHE* 3.2 6.1 + - - +
32H ARG* 1.3 119.4 + - + +
35H ILE* 1.3 65.1 + - - +
36H MET* 3.3 14.3 + - - -
53H ILE 3.5 1.6 - - - +
55H SER* 3.6 9.9 + - - -
73H ARG* 3.1 24.8 + - - -
99H ARG* 3.4 42.7 + - + -
101H GLN* 3.1 20.2 - - + +
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Residues in contact with ILE 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H TYR* 1.3 77.1 - - - +
36H MET* 1.3 59.8 + - - +
37H SER* 4.0 1.5 + - - +
52H SER* 4.1 22.0 - - - -
53H ILE 3.2 13.0 - - - +
54H SER* 4.0 17.7 - - - +
55H SER* 4.8 1.3 - - - +
60H TYR* 5.9 0.2 - - + -
100H GLY 4.2 10.9 + - - -
101H GLN* 2.9 23.3 + - - +
601H SPB 3.3 61.9 - - + +
99L LEU* 4.3 16.4 - - + -
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Residues in contact with MET 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 4.7 1.1 - - + -
29H PHE* 3.4 66.6 - - + +
34H TYR* 4.0 9.6 - - - +
35H ILE* 1.3 71.8 - - - +
37H SER* 1.3 62.6 + - - +
52H SER* 3.1 2.3 - - - -
53H ILE* 2.8 40.6 + - + -
71H ILE* 3.7 4.0 - - - +
73H ARG* 4.0 3.8 - - - +
80H LEU* 4.0 17.9 - - + -
97H CYS* 4.3 12.8 - - - -
98H ALA* 3.5 23.3 - - - +
99H ARG* 3.9 29.4 - - + +
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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