Contacts of the helix formed by residues 101 - 115 (chain F) in PDB entry 1SXG
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 101 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98F SER 3.6 14.0 + - - +
99F ASP* 4.4 5.4 - - + +
100F GLN* 1.3 74.7 - - - +
102F GLN* 1.3 64.6 + - - +
103F ASP* 2.6 32.6 + - - +
104F LYS* 3.0 20.9 + - + +
105F GLU* 3.0 26.0 + - - +
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Residues in contact with GLN 102 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100F GLN 4.1 1.4 + - - -
101F ASN* 1.3 73.6 - - - +
103F ASP* 1.3 69.5 + - - +
105F GLU* 2.9 14.6 + - - +
106F LEU* 2.8 22.5 + - - +
126F ASN* 5.5 2.7 - - + +
128F THR* 3.1 20.5 + - - +
130F GLU* 3.1 18.2 - - - +
131F HIS* 2.7 35.7 + - + +
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Residues in contact with ASP 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F ASN* 2.6 18.1 + - - +
102F GLN* 1.3 72.5 - - - +
104F LYS* 1.3 65.4 + - - +
106F LEU* 2.8 12.7 + - - +
107F HIS* 2.8 22.1 + - - +
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Residues in contact with LYS 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F ASN* 3.0 26.5 + - - +
98F SER 3.0 17.3 - - - +
99F ASP* 2.6 33.0 + - + +
101F ASN* 3.0 24.1 + - + +
103F ASP* 1.3 78.2 - - - +
105F GLU* 1.3 53.2 + - - +
107F HIS* 3.1 12.2 - - + +
108F LEU* 2.7 51.9 + - + +
83P GLU* 4.9 9.7 + - - +
87P THR* 5.1 14.2 - - + +
93P ILE* 6.6 0.2 - - - -
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Residues in contact with GLU 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F ILE* 4.1 1.5 - - - +
98F SER* 3.6 20.2 + - - -
100F GLN* 3.8 20.3 - - - +
101F ASN 3.0 25.3 + - - +
102F GLN* 2.9 8.7 + - - +
104F LYS* 1.3 74.1 - - - +
106F LEU* 1.3 66.6 + - - +
108F LEU* 3.3 9.0 + - - +
109F LEU* 2.9 30.8 + - + +
122F PHE* 3.3 22.2 - - + -
124F SER* 2.4 26.6 + - - -
131F HIS* 3.0 31.4 - - + -
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F GLN 2.8 9.5 + - - +
103F ASP* 2.8 15.6 + - - +
105F GLU* 1.3 73.5 - - - +
107F HIS* 1.3 60.5 + - - +
109F LEU* 3.4 13.9 + - + +
110F ASN* 3.0 50.0 + - - +
130F GLU* 4.9 16.4 - - - +
131F HIS* 6.6 0.4 - - + -
134F GLU* 4.2 35.0 - - + +
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Residues in contact with HIS 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F ASP 2.8 10.9 + - - +
104F LYS* 3.1 18.4 - - + +
106F LEU* 1.3 74.8 - - - +
108F LEU* 1.3 58.0 + - + +
110F ASN* 3.0 9.8 + - - +
111F ASN* 2.8 67.4 + - - -
92P ASN* 3.2 20.8 + - + -
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Residues in contact with LEU 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F ILE* 3.7 23.1 - - + -
96F SER* 3.1 29.6 - - - +
97F ASN 3.3 27.4 - - - +
98F SER* 3.5 24.2 - - - -
104F LYS* 2.7 30.8 + - + +
105F GLU 3.6 4.5 - - - +
107F HIS* 1.3 75.1 - - + +
109F LEU* 1.3 52.6 + - - +
111F ASN* 3.3 13.4 + - + +
112F MET* 2.8 39.4 + - - +
92P ASN* 6.1 3.1 - - + -
93P ILE* 5.3 4.0 - - + +
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Residues in contact with LEU 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F ILE* 3.5 20.4 - - + -
105F GLU* 2.9 22.4 + - + +
106F LEU* 3.5 16.8 - - + +
107F HIS 3.1 0.2 - - - -
108F LEU* 1.3 73.4 - - - +
110F ASN* 1.3 68.5 + - - +
112F MET* 3.0 5.3 + - - +
113F LEU* 2.9 31.6 + - + +
120F ILE* 3.9 25.5 - - + +
122F PHE* 5.0 11.7 - - + -
131F HIS* 6.2 1.3 - - + -
134F GLU* 5.6 7.0 - - + -
135F LEU* 3.8 41.7 - - + +
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Residues in contact with ASN 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F LEU* 3.0 37.7 + - - +
107F HIS* 3.0 8.6 + - - +
109F LEU* 1.3 75.6 - - - +
111F ASN* 1.3 57.5 + - - +
113F LEU* 3.0 17.4 + - - +
114F GLY* 2.6 34.5 + - - -
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Residues in contact with ASN 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F HIS* 2.8 50.9 + - - +
108F LEU* 3.4 16.8 - - + +
110F ASN* 1.3 82.6 - - - +
112F MET* 1.3 63.6 + - + +
114F GLY* 3.8 2.1 - - - +
115F LYS* 3.0 33.5 + - + +
62P THR* 5.9 0.4 - - - +
92P ASN* 3.3 20.3 + - - +
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Residues in contact with MET 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F GLY* 3.2 33.2 - - - -
65F VAL 4.6 4.3 - - - +
66F ILE* 4.3 16.6 - - + -
94F ILE* 3.4 29.4 - - + +
96F SER* 4.3 16.2 - - - -
108F LEU* 2.8 30.8 + - - +
109F LEU 3.0 4.9 + - - +
111F ASN* 1.3 74.9 - - - +
113F LEU* 1.3 63.3 + - - +
115F LYS* 3.2 12.5 + - + +
117F VAL* 3.1 43.9 + - + +
120F ILE* 4.1 18.6 - - + -
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Residues in contact with LEU 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F LEU* 2.9 19.8 + - + +
110F ASN* 3.4 18.8 - - - +
112F MET* 1.3 78.3 - - - +
114F GLY* 1.3 61.3 + - - +
116F GLN* 3.0 22.0 + - - -
117F VAL* 4.5 2.5 - - - -
120F ILE* 4.2 7.6 - - + -
138F SER* 4.1 8.1 - - - +
139F PRO* 3.6 36.1 - - + -
140F VAL* 3.6 34.5 - - + -
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Residues in contact with GLY 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F ASN 2.6 18.9 + - - -
111F ASN* 3.4 3.6 + - - -
112F MET 3.3 0.2 - - - -
113F LEU* 1.3 73.5 - - - +
115F LYS* 1.3 60.3 + - - +
116F GLN* 3.0 19.2 + - - +
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Residues in contact with LYS 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F ILE* 6.0 2.7 - - + -
111F ASN* 3.0 24.8 + - + +
112F MET* 3.7 10.8 - - + +
113F LEU 3.1 0.8 - - - -
114F GLY* 1.3 78.0 - - - +
116F GLN* 1.3 71.2 + - - +
117F VAL* 3.4 8.5 + - + +
62P THR* 3.1 41.4 + - - +
94P ILE* 4.9 13.1 - - + +
115P LYS* 3.1 68.4 + - + +
116P GLN* 5.0 2.1 + - + -
117P VAL* 4.9 1.6 - - - -
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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