Contacts of the helix formed by residues 86 - 95 (chain A) in PDB entry 1UJD
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLY 4.1 0.9 - - - -
39A GLY* 4.2 5.6 - - - +
49A ILE* 5.7 0.7 - - + -
85A LYS* 1.3 86.1 - - - +
87A TYR* 1.3 68.7 + - - +
88A GLU* 4.3 4.9 + - - +
89A GLU* 2.7 36.8 + - - +
90A VAL* 2.7 28.8 + - - +
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Residues in contact with TYR 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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35A ARG* 3.8 18.0 + - - -
36A ILE 5.5 2.0 - - - +
37A VAL* 3.2 49.4 - - + +
38A GLY 3.6 23.7 + - - +
39A GLY* 3.9 1.2 - - - +
86A THR* 1.3 71.6 - - - +
88A GLU* 1.3 63.4 + - + +
90A VAL* 3.6 1.4 - - - +
91A GLN* 2.7 59.1 + - + +
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Residues in contact with GLU 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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86A THR* 3.2 5.2 - - - +
87A TYR* 1.3 85.0 - - + +
89A GLU* 1.3 70.4 + - + +
91A GLN* 2.9 8.5 + - - +
92A SER* 2.8 24.2 + - - -
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Residues in contact with GLU 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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85A LYS* 4.1 22.2 + - + +
86A THR* 2.7 44.2 + - - +
88A GLU* 1.3 80.3 - - + +
90A VAL* 1.3 67.4 + - - +
92A SER* 3.1 8.5 + - - -
93A ILE* 3.0 24.9 + - + +
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Residues in contact with VAL 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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36A ILE* 4.4 3.1 - - + +
38A GLY* 3.7 24.2 - - - +
51A ALA* 4.0 8.5 - - + -
82A LEU* 3.4 50.3 - - + +
85A LYS* 3.6 22.9 - - + -
86A THR 2.7 23.5 + - - +
87A TYR 3.6 3.4 - - - +
89A GLU* 1.3 69.8 - - - +
91A GLN* 1.3 66.9 + - - +
93A ILE* 2.6 18.2 + - - +
94A ILE* 2.8 23.7 + - + +
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Residues in contact with GLN 91 (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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35A ARG* 3.8 24.1 + - - +
36A ILE 5.0 9.2 + - - +
87A TYR* 2.7 36.9 + - + +
88A GLU* 2.9 13.3 + - - +
90A VAL* 1.3 71.7 - - - +
92A SER* 1.3 52.6 + - - +
94A ILE* 2.6 15.5 + - + +
95A SER* 2.4 62.7 + - - +
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Residues in contact with SER 92 (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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88A GLU* 2.8 13.9 + - - -
89A GLU* 3.3 12.8 - - - -
91A GLN* 1.3 76.0 - - - +
93A ILE* 1.3 64.6 + - - +
94A ILE 3.2 0.2 + - - -
95A SER* 3.2 9.4 + - - +
96A GLN* 3.2 37.4 + - - +
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Residues in contact with ILE 93 (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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77A TRP* 3.5 21.3 + - + +
78A ASN* 4.7 2.3 + - - -
80A ILE* 3.5 44.3 - - + +
81A PRO 3.9 6.3 - - - +
82A LEU* 3.4 31.0 - - + -
85A LYS* 4.4 12.8 - - + +
89A GLU* 3.0 18.1 + - + +
90A VAL* 2.6 16.2 + - - +
92A SER* 1.3 75.2 - - - +
94A ILE* 1.3 59.1 + - - +
96A GLN* 4.3 10.2 - - - +
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Residues in contact with ILE 94 (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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31A GLY* 5.7 4.3 - - - +
34A ILE* 4.9 11.2 - - + +
36A ILE* 3.6 40.8 - - + +
77A TRP* 3.4 50.1 + - + +
82A LEU* 3.9 9.4 - - + -
90A VAL* 2.9 39.3 - - + +
91A GLN* 2.6 13.0 + - + +
93A ILE* 1.3 72.8 - - + +
95A SER* 1.3 52.5 + - - +
96A GLN* 2.5 24.8 + - - -
97A GLN* 4.2 2.9 + - - +
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Residues in contact with SER 95 (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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31A GLY* 5.9 6.0 - - - -
91A GLN* 2.4 53.2 + - - +
92A SER* 3.2 7.7 - - - +
94A ILE* 1.3 63.9 - - - +
96A GLN* 1.3 73.5 + - - +
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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