Contacts of the helix formed by residues 89 - 102 (chain A) in PDB entry 2UZ8
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 ASN 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ASP* 1.3 67.5 + - - +
91A ILE* 3.2 9.4 - - - +
92A HIS* 3.8 28.4 + - - +
93A THR* 3.5 14.9 + - - +
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Residues in contact with ASP 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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89A ASN* 1.3 78.1 - - - +
91A ILE* 1.3 70.4 + - + +
93A THR* 2.9 25.5 - - - +
94A LEU* 3.3 9.4 + - - +
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Residues in contact with ILE 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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81A GLN 5.1 1.6 - - - +
82A VAL* 4.8 8.5 - - - +
89A ASN 3.2 4.6 - - - +
90A ASP* 1.3 85.5 - - + +
92A HIS* 1.3 65.0 + - + +
93A THR 3.3 0.2 - - - -
94A LEU* 3.3 25.4 + - + -
95A LEU* 2.7 50.5 + - + +
124A LEU* 4.9 2.2 - - + -
127A PHE* 3.4 65.7 - - + -
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Residues in contact with HIS 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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89A ASN* 3.8 25.0 + - - +
90A ASP 3.3 0.8 - - - -
91A ILE* 1.3 82.6 - - + +
93A THR* 1.3 57.0 + - - +
95A LEU* 4.4 4.5 - - + -
96A MSE 3.0 29.1 + - - +
131A LEU* 4.2 15.8 - - + +
135A GLU* 3.4 39.4 + - + +
139A TYR* 2.9 30.7 + + - +
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Residues in contact with THR 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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89A ASN 3.5 13.6 + - - +
90A ASP* 2.9 24.7 - - - +
92A HIS* 1.3 75.2 - - - +
94A LEU* 1.3 63.1 + - - +
96A MSE 3.4 6.0 + - - +
97A ASP* 3.3 29.9 + - - -
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Residues in contact with LEU 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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77A TYR* 3.3 24.0 + - + +
81A GLN* 3.5 50.7 - - + +
82A VAL* 4.0 20.0 - - + -
90A ASP 3.3 13.0 + - - +
91A ILE* 3.3 31.1 + - + +
93A THR* 1.3 76.5 + - - +
95A LEU* 1.3 59.0 + - + +
97A ASP* 3.2 7.4 + - + +
98A LEU* 3.0 28.9 + - + +
124A LEU* 4.8 8.7 - - + -
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Residues in contact with LEU 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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91A ILE* 2.7 47.7 + - + +
92A HIS* 3.9 7.0 - - + +
93A THR 3.4 0.2 - - - -
94A LEU* 1.3 73.4 - - + +
96A MSE 1.3 52.8 - - - +
98A LEU* 3.6 6.6 - - + +
99A ASN* 2.7 35.3 + - - +
124A LEU* 4.4 15.7 - - + -
127A PHE* 5.4 0.9 - - + -
128A ILE* 4.1 21.8 - - + -
131A LEU* 4.1 23.3 - - + -
139A TYR* 3.7 35.7 - - + -
142A VAL* 3.6 19.1 - - + +
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Residues in contact with MSE 96 (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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92A HIS 3.0 17.9 + - - +
93A THR* 3.9 6.3 - - - +
94A LEU 3.3 0.2 - - - -
95A LEU* 1.3 77.5 - - - +
97A ASP* 1.3 63.5 - - - +
99A ASN* 3.4 31.1 - - + +
100A SER* 3.1 35.8 - - - +
138A LYS* 4.5 20.2 - - - +
139A TYR* 3.8 20.8 - - + +
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Residues in contact with ASP 97 (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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93A THR* 3.3 16.8 + - - +
94A LEU* 3.2 10.2 + - + +
96A MSE 1.3 77.7 + - - +
98A LEU* 1.3 65.0 + - - +
100A SER* 3.4 5.1 + - - -
101A TYR* 3.1 19.8 + - - +
168B ARG* 3.4 23.2 + - - +
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Residues in contact with LEU 98 (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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74A TRP* 4.3 15.0 - - + -
77A TYR* 3.9 16.5 + - + +
94A LEU* 3.0 17.8 + - + +
95A LEU* 3.6 9.0 - - + +
97A ASP* 1.3 74.5 - - - +
99A ASN* 1.3 63.9 + - - +
101A TYR* 3.4 6.8 + - + -
102A LEU* 3.0 43.1 + - + +
108A LEU* 4.3 17.9 - - + -
120A LEU* 4.1 10.5 - - + -
124A LEU* 3.8 28.7 - - + -
142A VAL* 4.0 21.3 - - + -
145A TRP* 4.9 1.1 - - + -
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Residues in contact with ASN 99 (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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95A LEU 2.7 22.1 + - - +
96A MSE 3.4 29.7 - - + +
97A ASP 3.3 0.2 - - - -
98A LEU* 1.3 72.7 - - - +
100A SER* 1.3 60.2 + - - +
103A GLU 3.4 3.5 + - - -
138A LYS 3.7 12.5 + - - -
139A TYR* 3.1 18.7 - - + -
140A LEU* 4.1 2.6 - - - +
141A ASN* 2.8 69.1 + - - +
142A VAL* 3.3 11.7 + - + +
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Residues in contact with SER 100 (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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96A MSE 3.1 22.5 - - - +
97A ASP* 3.7 8.6 + - - -
98A LEU 3.3 0.2 - - - -
99A ASN* 1.3 74.7 - - - +
101A TYR* 1.3 67.5 + - - +
103A GLU* 3.0 25.3 - - - +
141A ASN* 5.0 0.4 - - - +
167B ASN* 2.9 17.9 + - - -
168B ARG* 4.3 8.3 - - - -
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Residues in contact with TYR 101 (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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70A MSE 3.5 13.5 - - + +
73A GLN* 5.2 1.6 - - - -
74A TRP* 3.3 42.0 + + + -
97A ASP 3.1 11.1 + - - +
98A LEU* 3.6 11.0 - - + +
100A SER* 1.3 79.5 - - - +
102A LEU* 1.3 71.0 + - + +
104A ASP* 3.5 0.2 - - - +
105A LYS* 2.7 61.3 + - + -
108A LEU* 2.5 38.7 + - + -
167B ASN* 3.3 17.8 + - + +
168B ARG* 3.7 42.3 - - + +
169B LEU* 3.6 4.7 - - + +
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Residues in contact with LEU 102 (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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98A LEU* 3.0 37.5 + - + +
99A ASN 3.5 0.6 + - - -
100A SER 3.2 0.2 - - - -
101A TYR* 1.3 81.2 - - + +
103A GLU* 1.3 63.2 + - - +
104A ASP 3.0 4.8 + - - -
105A LYS* 3.1 24.6 - - + +
107A TYR 4.7 0.9 - - - +
108A LEU* 4.2 26.5 - - + -
141A ASN* 3.9 20.4 - - + +
142A VAL* 4.0 13.5 - - + -
144A ARG* 3.0 20.4 + - - +
145A TRP* 3.7 46.9 - - + -
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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