Contacts of the helix formed by residues 81 - 90 (chain A) in PDB entry 1UJU
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLY* 4.2 0.7 - - - -
31A ALA* 3.9 22.0 - - + +
32A ARG* 4.6 22.4 - - + -
46A ILE* 5.4 0.2 - - - -
79A GLY 5.1 2.0 - - - +
80A LEU* 1.3 78.6 - - - +
82A HIS* 1.3 60.2 + - - +
83A GLY* 3.9 7.3 + - - -
84A GLU* 2.5 39.6 + - - +
85A ALA* 2.8 10.7 + - - -
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Residues in contact with HIS 82 (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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27A ILE* 2.6 49.8 + - + +
28A ARG* 3.3 7.3 - - - -
29A GLY* 3.2 35.9 - - - +
30A GLY* 3.3 13.3 - - - -
33A GLY* 5.5 2.7 - - - +
46A ILE* 4.6 1.3 - - + -
81A THR* 1.3 71.5 - - - +
83A GLY* 1.3 65.8 + - - +
85A ALA* 4.3 4.7 - - - -
86A VAL* 2.8 40.7 + - + +
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Residues in contact with GLY 83 (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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81A THR* 2.8 9.4 + - - -
82A HIS* 1.3 79.6 - - - +
84A GLU* 1.3 59.8 + - - +
86A VAL* 3.7 5.4 + - - +
87A GLN* 3.2 28.3 + - - +
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Residues in contact with GLU 84 (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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80A LEU* 3.4 27.0 - - + +
81A THR* 2.5 24.6 + - - +
83A GLY* 1.3 69.6 - - - +
85A ALA* 1.3 66.3 + - - +
87A GLN* 3.3 12.3 + - - +
88A LEU* 3.0 21.3 + - - +
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Residues in contact with ALA 85 (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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27A ILE* 4.3 11.7 - - + +
46A ILE* 3.9 28.3 - - + -
72A VAL* 5.4 0.9 - - - +
77A LEU* 4.3 13.2 - - + +
80A LEU* 3.4 20.5 - - + +
81A THR 2.8 14.3 + - - +
82A HIS* 3.6 7.9 - - - +
84A GLU* 1.3 71.5 - - - +
86A VAL* 1.3 63.8 + - - +
88A LEU* 3.0 18.5 + - - +
89A LEU* 3.3 6.6 + - - +
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Residues in contact with VAL 86 (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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27A ILE* 3.8 26.0 - - + -
82A HIS* 2.8 40.7 + - + +
83A GLY* 3.8 6.1 - - - +
85A ALA* 1.3 72.7 - - - +
87A GLN* 1.3 58.9 + - - +
89A LEU* 2.7 52.6 + - + +
90A ARG* 3.2 31.0 + - - +
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Residues in contact with GLN 87 (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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83A GLY 3.2 15.3 + - - +
84A GLU* 3.3 16.2 + - - +
86A VAL* 1.3 83.3 - - - +
88A LEU* 1.3 56.0 + - - +
90A ARG* 3.0 53.7 + - - +
91A SER* 2.9 31.2 + - - -
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Residues in contact with LEU 88 (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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72A VAL* 3.2 34.9 - - + +
73A ASN* 4.9 4.9 + - + +
75A GLN* 3.6 48.9 - - + +
76A SER 4.8 1.3 - - - +
77A LEU* 3.6 14.8 - - + -
80A LEU* 3.8 16.4 - - + -
84A GLU 3.0 10.1 + - - +
85A ALA 3.0 14.1 + - - +
86A VAL 2.9 0.6 + - - -
87A GLN* 1.3 78.5 - - - +
89A LEU* 1.3 58.1 + - - +
91A SER* 3.5 18.8 + - - -
92A VAL 4.6 0.2 + - - -
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Residues in contact with LEU 89 (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 LYS* 5.1 0.2 + - - -
23A LEU* 4.1 13.4 - - + +
24A GLY 5.7 0.2 - - - +
25A ILE* 3.6 48.2 - - + +
27A ILE* 4.5 19.7 - - + +
69A LEU* 6.1 0.9 - - + -
72A VAL* 3.8 21.7 - - + +
85A ALA 3.3 4.1 + - - +
86A VAL* 2.7 39.0 + - + +
88A LEU* 1.3 81.4 - - - +
90A ARG* 1.3 65.1 + - + +
91A SER 3.3 0.9 - - - -
92A VAL* 3.1 23.2 - - - +
96A LEU* 4.2 7.0 - - + +
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Residues in contact with ARG 90 (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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23A LEU* 6.2 0.4 - - - -
86A VAL* 3.4 22.0 + - - +
87A GLN* 3.0 55.5 + - - +
89A LEU* 1.3 84.3 - - + +
91A SER* 1.3 55.8 + - - +
92A VAL* 3.1 16.8 + - - +
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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