Contacts of the helix formed by residues 88 - 103 (chain B) in PDB entry 3URZ
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 88 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B TYR* 2.9 24.2 + - + +
86B ASN* 3.2 1.0 - - + -
87B ARG* 1.3 74.0 - - - +
89B TYR* 1.3 60.1 + - - +
90B ASP* 3.8 9.0 + - - +
91B LYS* 3.3 35.5 + - - +
92B ALA* 3.0 23.0 + - - +
300B PG4 3.3 55.2 + - - +
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Residues in contact with TYR 89 (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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84B LYS* 4.1 12.6 - - + -
87B ARG* 3.3 55.6 + - + +
88B ASN* 1.3 73.8 - - - +
90B ASP* 1.3 59.2 + - - +
92B ALA* 3.7 3.7 - - - +
93B TYR* 2.9 32.1 + - - +
116B MSE 3.9 21.5 - - + +
119B CYS* 3.4 49.7 - - + -
120B ARG* 3.5 23.3 - - + -
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Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ASN* 3.3 8.2 - - - +
89B TYR* 1.3 76.1 - - - +
91B LYS* 1.3 59.3 + - + +
93B TYR* 3.6 5.7 + - - +
94B LEU* 3.1 25.1 + - - +
120B ARG* 2.7 46.1 + - - +
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Residues in contact with LYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 2.8 41.1 + - - +
83B TYR* 3.4 31.2 - - + -
88B ASN* 3.3 27.4 + - - +
89B TYR 3.4 0.4 - - - -
90B ASP* 1.3 75.9 - - + +
92B ALA* 1.3 65.8 + - - +
94B LEU* 3.2 19.8 + - + +
95B PHE* 3.1 29.0 + - + -
300B PG4 5.5 7.6 - - - -
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Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ALA* 3.8 11.2 - - - +
83B TYR* 3.6 6.9 - - - +
84B LYS* 3.8 17.9 - - - +
88B ASN 3.0 18.2 + - - +
89B TYR* 3.4 3.1 + - - +
91B LYS* 1.3 73.5 - - - +
93B TYR* 1.3 56.9 + - - +
95B PHE* 3.3 4.0 + - - +
96B TYR* 2.9 37.4 + - + -
116B MSE 3.4 30.7 - - + -
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Residues in contact with TYR 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 TYR 2.9 17.8 + - - +
90B ASP 3.6 5.8 - - - +
92B ALA* 1.3 75.4 - - - +
94B LEU* 1.3 60.0 + - + +
96B TYR* 3.2 2.7 + - - +
97B LYS* 2.8 63.2 + - + +
113B CYS* 4.2 21.8 - - + -
116B MSE 4.0 11.6 - - + +
117B GLN* 3.5 43.3 + - + -
120B ARG* 3.7 28.9 - - - -
125B ASP* 4.3 4.8 + - - -
129B MSE 5.0 3.7 - - - -
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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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58B GLU* 4.2 7.9 - - - +
62B TRP* 4.2 24.5 - - + -
90B ASP 3.1 14.9 + - - +
91B LYS* 3.2 36.8 + - + +
93B TYR* 1.3 81.1 - - + +
95B PHE* 1.3 60.3 + - + +
97B LYS* 3.4 11.2 + - + +
98B GLU* 3.1 31.0 + - + +
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Residues in contact with PHE 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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58B GLU* 3.6 31.4 - - + -
61B TYR* 3.6 29.6 - + - -
62B TRP* 3.7 23.8 - + - -
76B ALA* 3.8 24.0 - - + +
79B LEU* 3.6 24.0 - - + -
80B ALA* 3.7 25.1 - - + -
83B TYR* 3.9 18.6 - + - -
91B LYS* 3.1 18.7 + - + +
94B LEU* 1.3 80.3 - - + +
96B TYR* 1.3 64.4 + - - +
98B GLU* 3.4 10.3 + - + +
99B LEU* 3.2 24.6 + - - +
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Residues in contact with TYR 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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77B THR* 5.1 8.6 + - + +
80B ALA* 3.6 28.9 - - + -
81B LEU* 3.9 17.2 + - - +
84B LYS* 3.5 28.8 + - + -
92B ALA 2.9 24.8 + - - +
93B TYR 4.0 2.0 - - - +
95B PHE* 1.3 75.7 - - - +
97B LYS* 1.3 56.6 + - - +
99B LEU* 3.3 19.4 + - + +
100B LEU* 3.0 22.9 + - - +
109B CSX 4.8 5.0 - - - +
112B ALA* 3.4 31.0 - - + -
113B CYS* 3.3 29.2 - - - +
116B MSE 3.7 28.5 - - + -
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Residues in contact with LYS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B TYR* 2.8 49.8 + - + +
94B LEU* 3.6 11.2 - - + +
95B PHE 3.2 0.2 - - - -
96B TYR* 1.3 74.8 - - - +
98B GLU* 1.3 61.5 + - - +
100B LEU* 3.2 10.9 + - + +
101B GLN* 3.0 41.9 + - + +
113B CYS* 3.7 10.0 - - - -
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Residues in contact with GLU 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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61B TYR* 4.5 13.7 - - - +
62B TRP* 3.9 29.8 - - + -
76B ALA* 5.0 2.9 - - + -
94B LEU* 3.1 23.1 + - + +
95B PHE* 3.4 17.0 + - + +
97B LYS* 1.3 75.7 - - - +
99B LEU* 1.3 61.5 + - - +
101B GLN* 3.6 20.6 + - - +
102B LYS* 3.9 22.2 + - - +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B SER* 3.3 42.8 - - - +
76B ALA* 3.9 9.4 - - + +
77B THR* 3.5 31.4 - - + +
80B ALA* 4.7 0.2 - - + -
95B PHE 3.2 16.6 + - - +
96B TYR* 3.6 28.5 - - + +
97B LYS 3.3 0.2 - - - -
98B GLU* 1.3 72.5 - - - +
100B LEU* 1.3 64.6 + - - +
102B LYS* 3.2 21.3 + - + +
103B ALA* 3.4 11.4 + - - +
109B CSX 3.9 21.9 - - - +
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Residues in contact with LEU 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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96B TYR 3.0 17.5 + - - +
97B LYS* 3.5 13.0 - - + +
99B LEU* 1.3 77.6 - - - +
101B GLN* 1.3 57.0 + - + +
103B ALA 3.1 7.0 - - - +
104B PRO* 3.0 46.9 - - + +
106B ASN 4.4 0.2 - - - +
109B CSX 3.8 21.2 - - + +
110B LEU* 3.7 33.4 - - + +
113B CYS* 3.9 10.3 - - - -
129B MSE 3.8 27.4 - - + -
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Residues in contact with GLN 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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97B LYS* 3.0 36.5 + - + +
98B GLU* 4.0 13.9 - - - +
99B LEU 3.3 0.6 - - - -
100B LEU* 1.3 75.5 - - + +
102B LYS* 1.3 61.7 + - + +
104B PRO* 3.6 13.5 - - - +
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Residues in contact with LYS 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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61B TYR* 3.7 14.8 + - - -
67B LYS* 4.2 16.6 - - - +
72B SER* 3.0 27.2 + - - -
73B SER* 3.5 33.5 + - - +
76B ALA* 4.6 4.6 - - - +
98B GLU* 3.9 18.7 + - - +
99B LEU* 3.2 13.0 + - + +
101B GLN* 1.3 80.1 - - + +
103B ALA* 1.3 58.0 + - + +
104B PRO* 3.7 3.3 - - - +
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Residues in contact with ALA 103 (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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99B LEU 3.4 6.9 + - - +
100B LEU* 3.1 14.5 + - - +
102B LYS* 1.3 80.1 - - + +
104B PRO* 1.4 65.0 - - - +
105B ASN 3.3 2.7 - - - -
106B ASN* 3.2 37.1 + - + +
109B CSX 4.4 4.2 - - - +
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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