Contacts of the helix formed by residues 90 - 101 (chain B) in PDB entry 1N54
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 SER 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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650A LYS* 5.0 10.9 - - - -
40B CYS* 3.5 9.2 - - - -
88B TYR* 3.5 7.3 - - - +
89B TYR* 1.3 80.6 - - - +
91B ARG* 1.3 66.1 - - - +
92B ALA* 3.2 10.9 + - - +
93B ASP* 3.4 21.0 + - - +
94B ALA* 3.4 12.5 + - - +
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Residues in contact with ARG 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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15B VAL* 4.7 3.4 + - - +
17B LEU* 3.6 16.4 - - - +
36B LEU 3.4 10.5 + - - -
37B LYS* 3.2 31.5 + - - +
38B LYS* 4.7 4.5 - - - +
39B SER 2.8 33.3 + - - +
40B CYS* 3.2 14.7 - - - -
90B SER* 1.3 72.8 - - - +
92B ALA* 1.3 52.9 + - - +
94B ALA* 2.7 8.4 + - - +
95B GLU* 2.7 64.4 + - + +
115B TRP* 3.1 41.8 - - + +
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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
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90B SER* 4.0 10.0 - - - +
91B ARG* 1.3 79.0 - - - +
93B ASP* 1.3 71.8 + - - +
95B GLU* 3.3 15.3 + - - +
96B ASN* 3.4 19.4 + - - +
99B ARG* 4.6 1.7 + - - -
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Residues in contact with ASP 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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650A LYS* 5.0 13.3 + - - -
1558A GOL 4.8 7.5 + - - -
63B SER* 3.1 38.1 + - - +
64B GLY* 2.8 26.7 - - - -
65B ASP* 3.1 14.1 + - - +
88B TYR* 3.9 15.2 - - + -
89B TYR* 5.9 1.4 - - - +
90B SER* 3.4 20.3 + - - +
91B ARG 3.3 0.2 - - - -
92B ALA* 1.3 81.0 - - - +
94B ALA* 1.3 62.4 + - - +
96B ASN* 3.3 10.1 + - - +
97B ALA 3.3 0.7 + - - -
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Residues in contact with ALA 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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40B CYS* 4.1 10.3 - - - +
42B LEU* 3.6 10.4 - - + +
88B TYR* 3.4 24.6 - - + -
90B SER 3.4 5.2 + - - +
91B ARG* 2.7 22.8 + - - +
93B ASP* 1.3 80.5 - - - +
95B GLU* 1.3 60.8 + - - +
96B ASN 3.3 0.2 + - - -
97B ALA* 3.5 0.7 + - - +
98B MET* 3.2 19.8 + - - +
115B TRP* 3.7 24.2 - - + -
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Residues in contact with GLU 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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15B VAL* 3.2 39.0 - - + +
91B ARG* 2.7 60.1 + - + +
92B ALA* 3.8 7.7 - - - +
93B ASP 3.3 0.4 - - - -
94B ALA* 1.3 72.2 - - - +
96B ASN* 1.3 51.7 + - - +
98B MET* 2.9 6.6 + - - +
99B ARG* 2.6 65.6 + - - +
115B TRP* 4.2 3.1 - - + -
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Residues in contact with ASN 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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326A TRP* 4.9 3.5 - - - -
368A ILE* 3.7 21.7 - - + +
1558A GOL 4.3 3.2 + - - -
63B SER* 3.5 27.5 + - - -
92B ALA* 3.4 14.2 + - - +
93B ASP* 3.5 9.1 + - - +
94B ALA 3.2 0.4 - - - -
95B GLU* 1.3 77.2 - - - +
97B ALA* 1.3 53.0 + - - +
99B ARG* 2.6 30.0 + - - +
100B TYR* 2.4 54.5 + - + -
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Residues in contact with ALA 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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42B LEU* 4.2 7.9 - - + -
60B PHE* 4.2 5.6 - - + -
63B SER* 3.0 10.7 + - - +
88B TYR* 2.7 42.0 - - + +
93B ASP 3.3 1.4 + - - -
94B ALA 3.9 2.0 - - - +
95B GLU 3.4 0.2 - - - -
96B ASN* 1.3 79.0 - - - +
98B MET* 1.3 52.6 + - - +
101B ILE* 2.8 26.7 + - + +
102B ASN* 2.8 31.7 + - - -
113B THR* 4.6 2.1 + - - +
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Residues in contact with MET 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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14B TYR* 3.6 31.9 - - - +
15B VAL* 4.4 3.8 - - + -
16B GLU 5.8 1.6 - - - +
19B GLN* 5.2 3.4 - - - +
42B LEU* 3.2 27.8 - - + -
94B ALA 3.2 13.3 + - - +
95B GLU* 2.9 15.8 + - - +
97B ALA* 1.3 77.7 - - - +
99B ARG* 1.3 60.0 + - - +
102B ASN* 3.5 21.1 + - - +
113B THR* 3.1 45.1 - - - +
114B ASP* 3.6 16.6 - - - +
115B TRP* 4.1 23.3 - - + +
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Residues in contact with ARG 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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326A TRP* 4.7 11.2 - - - -
327A LYS* 3.5 34.0 - - - +
329A ARG* 2.7 27.2 + - - +
12B ASP* 2.9 35.7 + - - +
14B TYR* 4.1 17.9 - - + -
15B VAL* 4.6 5.6 - - + +
92B ALA 4.6 1.6 + - - -
95B GLU* 2.6 57.7 + - - +
96B ASN* 2.6 34.6 + - - +
98B MET* 1.3 77.7 - - - +
100B TYR* 1.3 81.8 + - + +
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Residues in contact with TYR 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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326A TRP* 3.0 49.1 + - - -
327A LYS* 3.9 7.6 - - - -
329A ARG* 3.1 22.6 + - + +
368A ILE* 3.6 21.8 - - + -
370A VAL* 3.9 33.0 - - + -
371A MET* 3.4 20.8 - - + +
374A THR* 2.7 46.6 - - - +
96B ASN* 2.4 35.5 + - - +
99B ARG* 1.3 96.7 - - + +
101B ILE* 1.3 56.8 + - + +
104B THR* 3.0 8.5 - - - +
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Residues in contact with ILE 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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370A VAL* 4.6 12.6 - - + -
419A HIS* 5.8 1.1 - - + -
59B LEU* 3.5 55.6 - - + +
60B PHE* 3.7 25.6 - - + -
63B SER* 3.7 15.7 - - - +
97B ALA* 2.8 44.7 + - + +
100B TYR* 1.3 73.9 - - - +
102B ASN* 1.3 68.5 + - - +
103B GLY 3.1 0.3 + - - -
104B THR* 2.9 30.2 + - - +
111B ILE* 4.3 6.0 - - + +
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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
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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