Contacts of the helix formed by residues 91 - 107 (chain B) in PDB entry 1UXI
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 LEU 91 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ALA* 3.4 24.9 - - + +
81B PRO 3.5 23.1 - - - +
82B ARG* 4.0 22.0 - - + +
86B MET* 4.5 10.8 - - - -
87B SER 4.3 5.2 - - - +
88B ARG* 3.3 19.1 - - - +
89B GLU 2.9 1.0 - - - -
90B ASP* 1.3 78.5 - - - +
92B ILE* 1.3 63.8 + - - +
93B LYS 3.1 2.8 + - - -
94B VAL* 3.2 9.5 + - + +
95B ASN* 2.9 38.6 + - - +
120B ASN* 3.9 9.4 - - + +
121B PRO* 4.3 0.2 - - - -
1310B NAD 3.7 16.6 - - - +
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Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLU* 2.9 22.0 + - + +
90B ASP 5.0 1.6 - - - +
91B LEU* 1.3 78.2 - - - +
93B LYS* 1.3 64.8 + - + +
95B ASN 4.8 0.2 - - - +
96B ALA* 2.9 34.4 + - - +
121B PRO* 3.7 30.5 - - + +
124B ALA* 4.4 2.2 - - + -
125B MET* 4.2 9.4 - - + -
302B THR* 3.5 32.8 - - - +
305B THR* 4.0 21.5 - - + -
306B LEU* 3.8 19.3 - - + +
309B LEU* 4.0 10.5 - - + -
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Residues in contact with LYS 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ASP 4.7 3.5 + - - +
91B LEU 3.1 1.2 + - - -
92B ILE* 1.3 85.9 - - + +
94B VAL* 1.3 66.9 + - + +
96B ALA* 3.5 6.2 + - - +
97B ASP* 3.3 24.7 + - - +
309B LEU* 4.1 29.4 - - + -
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ALA* 4.3 12.1 - - + -
90B ASP 5.9 1.6 - - - +
91B LEU* 3.2 10.4 + - + +
93B LYS* 1.3 80.2 - - + +
95B ASN* 1.3 75.7 + - - +
97B ASP* 3.2 10.6 + - - +
98B ILE* 3.2 33.5 + - + +
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Residues in contact with ASN 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLY* 3.5 7.9 - - - -
80B ALA* 2.6 50.6 + - - +
91B LEU* 2.9 27.0 + - - +
92B ILE 4.6 0.2 - - - +
94B VAL* 1.3 70.2 - - - +
96B ALA* 1.3 57.8 + - - +
98B ILE* 3.7 9.8 - - - +
99B THR* 2.5 39.6 + - - +
119B ASN* 5.0 0.7 - - + -
120B ASN 2.7 29.8 + - - +
125B MET* 3.7 7.6 - - + -
1310B NAD 3.1 11.7 + - - -
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Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ILE 2.9 22.2 + - - +
93B LYS 3.7 5.4 - - - +
94B VAL 3.2 0.4 - - - -
95B ASN* 1.3 77.8 - - - +
97B ASP* 1.3 59.0 + - - +
100B ARG* 2.8 37.7 + - - +
125B MET* 3.9 8.9 - - + -
128B LEU* 3.4 22.6 - - + +
306B LEU* 4.3 3.6 - - + -
309B LEU* 3.9 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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93B LYS* 3.3 20.4 + - - +
94B VAL* 3.2 9.2 + - - +
96B ALA* 1.3 78.2 - - - +
98B ILE* 1.3 60.9 + - + +
100B ARG* 3.3 14.5 + - - +
101B ALA* 2.9 31.2 + - - +
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B SER* 3.2 49.1 - - - +
79B GLY 4.3 0.9 - - - +
80B ALA* 4.0 7.2 - - + +
94B VAL* 3.2 22.8 + - + +
95B ASN* 3.7 26.5 - - - +
97B ASP* 1.3 76.9 - - + +
99B THR* 1.3 59.2 + - - +
101B ALA* 3.1 6.7 + - - +
102B CYS* 2.9 35.9 + - - -
119B ASN* 4.3 1.1 - - - +
1310B NAD 3.9 22.4 - - + +
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Residues in contact with THR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 5.3 0.7 - - - -
78B SER* 5.1 0.2 - - - -
95B ASN 2.5 25.8 + - - -
96B ALA 3.8 3.4 - - - -
98B ILE* 1.3 78.4 - - - +
100B ARG* 1.3 63.3 + - - +
102B CYS* 3.9 3.5 - - - +
103B ILE* 3.0 36.5 + - + +
117B MET* 3.5 30.3 - - + -
119B ASN* 3.3 21.3 + - - +
125B MET* 3.3 24.5 - - - +
128B LEU* 4.0 15.0 - - + -
129B ALA 4.7 0.4 - - - +
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ALA* 2.8 29.5 + - - +
97B ASP* 3.7 14.9 + - - +
99B THR* 1.3 76.6 - - - +
101B ALA* 1.3 60.6 + - - +
103B ILE* 4.1 0.3 - - - +
104B SER* 2.8 34.1 + - - +
128B LEU* 3.4 27.3 - - + +
131B GLU* 5.4 1.2 + - - -
132B VAL* 4.1 26.1 - - + +
306B LEU* 5.6 3.4 - - - +
309B LEU 5.2 10.0 + - - -
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ASP 2.9 17.7 + - - +
98B ILE* 3.1 8.0 + - - +
100B ARG* 1.3 77.8 - - - +
102B CYS* 1.3 60.9 + - - +
104B SER* 3.0 17.3 + - - -
105B GLN* 2.9 31.0 + - - +
1310B NAD 4.4 10.8 - - - +
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Residues in contact with CYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 3.7 15.5 - - + -
65B TYR* 3.4 25.7 - - - +
76B VAL* 4.6 10.5 - - + -
78B SER* 3.1 28.3 - - - +
98B ILE* 2.9 19.2 + - - +
99B THR 3.9 3.4 - - - +
101B ALA* 1.3 77.4 - - - +
103B ILE* 1.3 58.3 + - + +
105B GLN* 3.3 2.3 + - - +
106B ALA* 2.8 34.1 + - - +
1310B NAD 3.5 20.4 - - - -
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Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 6.0 1.1 - - + -
76B VAL* 4.1 17.3 - - + -
99B THR* 3.0 31.1 + - + +
102B CYS* 1.3 76.0 - - + +
104B SER* 1.3 60.7 + - - +
105B GLN 3.0 0.3 + - - -
106B ALA* 4.5 2.5 - - + +
107B ALA* 2.8 37.2 + - + +
115B ILE* 4.3 14.6 - - + -
117B MET* 4.1 11.2 - - + -
129B ALA* 3.8 24.9 - - + +
132B VAL* 3.6 13.0 - - + -
133B SER* 3.5 40.6 - - - +
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Residues in contact with SER 104 (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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100B ARG* 2.8 25.1 + - - +
101B ALA* 3.0 13.0 + - - -
103B ILE* 1.3 78.3 - - - +
105B GLN* 1.3 60.4 + - - +
107B ALA* 5.3 0.2 - - - -
108B PRO* 3.3 23.0 - - - +
132B VAL* 3.7 17.4 - - - +
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Residues in contact with GLN 105 (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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65B TYR* 3.0 49.1 + - + +
101B ALA* 2.9 32.9 + - - +
102B CYS 3.3 2.2 + - - +
103B ILE 3.0 0.8 - - - -
104B SER* 1.3 82.6 + - - +
106B ALA* 1.3 64.4 + - - +
108B PRO* 3.9 4.3 - - - +
109B LEU* 3.4 24.6 - - - +
1310B NAD 5.3 2.8 + - - -
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Residues in contact with ALA 106 (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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8B ILE* 4.7 7.2 - - + -
65B TYR* 4.2 17.9 - - + -
68B THR* 4.7 5.5 + - - +
74B ILE* 4.0 31.8 - - + +
102B CYS 2.8 19.3 + - - +
103B ILE* 4.2 2.7 - - + +
105B GLN* 1.3 77.8 - - - +
107B ALA* 1.3 67.8 + - - +
109B LEU* 3.0 19.0 + - - +
110B SER* 3.4 8.1 + - - -
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 4.4 6.2 - - - +
103B ILE* 2.8 21.2 + - + +
104B SER* 5.3 0.4 - - - -
106B ALA* 1.3 71.8 - - - +
108B PRO* 1.3 69.6 - - + +
110B SER 3.0 23.2 + - - -
111B PRO* 3.4 2.4 - - - +
115B ILE* 4.6 4.0 - - + +
133B SER* 3.6 24.7 - - - +
135B PHE* 3.4 33.0 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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