Contacts of the helix formed by residues 90 - 102 (chain B) 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 ASP 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B GLN 5.0 4.9 - - - +
89B ASN* 1.3 99.5 + - - +
91B ILE* 1.3 73.1 + - - +
92B HIS 3.1 1.6 - - - +
93B THR* 3.3 15.3 + - - +
94B LEU* 3.3 27.2 + - - +
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Residues in contact with ILE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B GLN 6.0 0.4 - - - +
82B VAL* 6.0 2.0 - - + +
89B ASN* 4.2 15.9 - - + +
90B ASP* 1.3 87.8 + - - +
92B HIS* 1.3 84.6 + - + +
94B LEU* 3.2 21.1 + - + +
95B LEU* 2.6 56.1 + - + +
124B LEU* 5.5 1.3 - - + -
127B PHE* 3.6 58.1 - - + +
131B LEU* 5.3 3.1 - - + -
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Residues in contact with HIS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ASN 4.0 22.7 - - - +
90B ASP* 3.1 0.8 - - - +
91B ILE* 1.3 103.9 - - + +
93B THR* 1.3 59.8 + - - +
95B LEU* 4.4 1.8 - - + +
96B MSE 3.1 24.6 + - - +
131B LEU* 3.9 15.7 - - + +
135B GLU* 3.6 38.3 + - + -
139B TYR* 2.6 29.6 + + - +
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Residues in contact with THR 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ASN 5.2 0.7 + - - -
90B ASP* 3.3 18.7 + - - +
92B HIS* 1.3 75.7 - - - +
94B LEU* 1.3 63.5 + - - +
96B MSE 3.5 4.8 + - - +
97B ASP* 3.2 32.2 + - - +
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B TYR* 3.3 24.4 + - + +
81B GLN* 3.9 45.5 - - + +
82B VAL* 4.2 17.7 - - + -
90B ASP* 3.3 16.8 + - - +
91B ILE* 3.2 26.4 + - + +
93B THR* 1.3 78.5 - - - +
95B LEU* 1.3 59.7 + - + +
97B ASP* 3.1 7.7 + - - +
98B LEU* 2.9 30.1 + - - +
124B LEU* 4.7 9.4 - - + -
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ILE* 2.6 46.1 + - + +
92B HIS* 4.1 1.6 - - - +
94B LEU* 1.3 73.9 - - + +
96B MSE 1.3 53.9 + - - +
98B LEU* 3.4 5.7 + - + +
99B ASN* 2.7 35.7 + - - +
124B LEU* 4.4 21.8 - - + -
127B PHE* 5.3 4.3 - - + -
128B ILE* 4.1 21.3 - - + -
131B LEU* 4.1 24.0 - - + -
139B TYR* 3.8 38.6 - - + -
142B VAL* 3.8 16.5 - - + +
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Residues in contact with MSE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B HIS 3.1 19.0 + - - +
93B THR* 3.8 5.8 - - - +
95B LEU* 1.3 76.0 - - - +
97B ASP* 1.3 65.7 - - - +
99B ASN* 3.4 27.6 - - + +
100B SER* 3.2 32.0 - - - +
138B LYS* 4.5 19.1 - - - +
139B TYR* 3.7 18.8 - - + -
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Residues in contact with ASP 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ARG* 4.2 14.5 + - - +
93B THR* 3.2 19.6 + - - +
94B LEU* 3.1 10.1 + - - +
96B MSE 1.3 81.1 + - - +
98B LEU* 1.3 63.7 + - - +
100B SER* 3.4 7.6 + - - -
101B TYR* 3.1 21.9 + - - +
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B TRP* 3.8 30.1 - - + -
77B TYR* 4.1 13.6 + - - +
94B LEU 2.9 16.5 + - - +
95B LEU* 3.7 7.9 - - + +
97B ASP* 1.3 73.4 - - - +
99B ASN* 1.3 60.6 + - - +
101B TYR* 3.2 7.2 + - + +
102B LEU* 2.9 48.8 + - + +
108B LEU* 3.9 17.5 - - + -
120B LEU* 4.1 7.9 - - + -
124B LEU* 3.8 28.9 - - + -
142B VAL* 3.9 21.8 - - + -
145B TRP* 4.8 1.8 - - + -
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Residues in contact with ASN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU 2.7 22.3 + - - +
96B MSE 3.4 27.9 - - + +
97B ASP 3.2 0.2 - - - -
98B LEU* 1.3 75.4 - - - +
100B SER* 1.3 61.0 + - - +
103B GLU 3.5 3.6 + - - -
138B LYS 3.6 13.3 + - - -
139B TYR* 3.0 18.9 - - + +
140B LEU* 4.2 2.2 - - - +
141B ASN* 2.8 67.9 + - - +
142B VAL* 3.3 11.5 + - + +
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Residues in contact with SER 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ASN* 2.8 22.9 + - - -
96B MSE 3.2 23.4 - - - +
97B ASP* 3.7 8.9 + - - -
98B LEU 3.3 0.2 - - - -
99B ASN* 1.3 75.5 - - - +
101B TYR* 1.3 64.1 + - - +
103B GLU* 3.2 21.3 - - - +
141B ASN* 5.1 0.2 - - - +
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Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ASN* 3.4 25.9 + - + +
168A ARG* 3.3 49.1 + - + +
169A LEU* 4.4 0.9 - - - +
70B MSE 3.2 21.9 - - + +
73B GLN* 5.3 0.9 - - - -
74B TRP* 3.4 29.8 - + + -
97B ASP 3.1 14.0 + - - +
98B LEU* 3.2 18.6 + - + +
100B SER* 1.3 78.4 - - - +
102B LEU* 1.3 63.0 + - + +
103B GLU 3.4 1.0 + - - -
104B ASP* 3.5 2.1 - - - +
105B LYS* 2.7 51.8 + - + -
108B LEU* 2.8 33.4 + - + -
109B THR* 4.3 1.0 - - - -
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 2.9 43.0 + - + +
99B ASN 3.5 0.6 + - - -
100B SER 3.2 0.4 - - - -
101B TYR* 1.3 80.9 - - + +
103B GLU* 1.3 62.0 + - - +
104B ASP 3.1 4.4 + - - -
105B LYS* 3.2 18.5 - - + +
107B TYR 4.7 5.4 - - - +
108B LEU* 4.0 28.7 - - + -
141B ASN* 3.9 14.1 - - + +
142B VAL* 3.9 18.6 - - - -
144B ARG* 2.8 23.7 + - - +
145B TRP* 3.8 40.8 - - + -
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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