Contacts of the helix formed by residues 101 - 115 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B SER 3.0 12.4 + - - +
99B ASP* 3.0 8.2 + - + +
100B GLN* 1.3 77.5 - - - +
102B GLN* 1.3 64.5 + - - +
103B ASP* 3.4 19.4 + - - +
104B LYS* 3.2 29.8 + - + +
105B GLU* 2.9 29.3 + - - +
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Residues in contact with GLN 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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100B GLN 3.6 4.2 + - - -
101B ASN* 1.3 73.0 + - - +
103B ASP* 1.3 74.8 + - - +
105B GLU* 3.0 20.3 + - - +
106B LEU* 3.1 19.6 + - + +
128B THR* 3.9 16.6 + - - +
130B GLU* 2.7 41.2 + - - +
131B HIS* 3.2 30.4 - - + +
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Residues in contact with ASP 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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101B ASN* 3.4 17.1 + - - +
102B GLN* 1.3 85.7 + - - +
104B LYS* 1.3 57.2 + - - +
106B LEU* 4.2 6.4 - - - +
107B HIS* 3.2 25.6 + - - +
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Residues in contact with LYS 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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97B ASN 3.3 19.7 - - - +
98B SER* 3.6 24.7 - - - +
99B ASP* 4.7 7.2 - - + -
101B ASN* 3.2 19.2 + - + +
102B GLN 3.1 0.4 - - - -
103B ASP* 1.3 77.6 - - - +
105B GLU* 1.3 61.7 + - - +
107B HIS* 4.0 15.0 - - + -
108B LEU* 2.8 50.7 + - + +
83I GLU* 6.1 4.5 - - - -
87I THR* 4.3 23.0 - - - +
91I TYR 6.0 0.2 + - - -
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Residues in contact with GLU 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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66B ILE* 4.4 6.3 - - - +
68B PRO* 4.9 1.0 - - - +
98B SER* 3.2 28.9 + - - +
100B GLN* 4.6 9.7 - - - +
101B ASN 2.9 28.7 + - - +
102B GLN* 3.0 10.8 + - - +
104B LYS* 1.3 79.7 - - - +
106B LEU* 1.3 62.5 + - - +
108B LEU* 3.4 3.5 + - - +
109B LEU* 3.2 20.2 + - - +
122B PHE* 3.8 16.5 - - + -
123B MET 4.1 1.2 - - - +
124B SER* 2.8 41.0 + - - -
125B GLY 4.6 0.9 + - - -
126B ASN 4.1 1.4 - - - +
131B HIS* 3.4 27.7 + - + +
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Residues in contact with LEU 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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102B GLN* 3.1 23.2 + - - +
103B ASP* 4.4 5.6 - - - +
105B GLU* 1.3 73.6 - - - +
107B HIS* 1.3 65.1 + - - +
109B LEU* 3.5 16.7 - - + +
110B ASN* 3.2 25.9 + - - +
130B GLU* 3.7 32.3 - - + +
131B HIS* 3.6 29.2 - - + -
134B GLU* 3.6 37.9 - - + -
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Residues in contact with HIS 107 (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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103B ASP 3.2 20.3 + - - +
104B LYS* 3.6 18.2 - - + +
105B GLU 3.2 0.4 - - - -
106B LEU* 1.3 77.9 - - - +
108B LEU* 1.3 70.1 + - + +
110B ASN* 3.0 24.1 + - + +
111B ASN* 3.1 39.4 + - - +
92I ASN* 3.7 16.0 + - - -
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Residues in contact with LEU 108 (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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66B ILE* 4.4 13.5 - - + -
96B SER* 3.8 29.8 - - - +
97B ASN* 3.1 36.3 - - - +
98B SER* 3.6 11.9 - - - +
104B LYS* 2.8 39.7 + - + +
105B GLU* 3.8 3.8 - - - +
107B HIS* 1.3 76.8 - - + +
109B LEU* 1.3 55.9 + - - +
111B ASN* 3.0 16.2 + - + +
112B MET* 2.7 39.0 + - - +
92I ASN* 5.4 3.6 - - - +
93I ILE 5.3 5.6 - - - +
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Residues in contact with LEU 109 (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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66B ILE* 4.4 10.7 - - + +
105B GLU 3.2 13.0 + - - +
106B LEU* 3.5 24.5 - - + +
108B LEU* 1.3 74.2 - - - +
110B ASN* 1.3 76.0 + - - +
112B MET* 3.2 8.7 + - - +
113B LEU* 3.0 54.4 + - + +
120B ILE* 5.1 4.9 - - + -
122B PHE* 6.6 0.4 - - + -
131B HIS* 6.4 0.4 - - + -
134B GLU* 5.0 7.6 - - + +
135B LEU* 3.8 38.4 - - + +
138B SER* 5.6 4.0 - - - +
142B VAL* 5.9 4.9 - - + -
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Residues in contact with ASN 110 (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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106B LEU* 3.2 14.8 + - - +
107B HIS* 3.0 15.6 + - + +
109B LEU* 1.3 91.1 - - - +
111B ASN* 1.3 56.9 + - - +
113B LEU* 4.1 8.7 - - - +
114B GLY* 2.7 31.9 + - - -
134B GLU* 5.1 8.8 + - - +
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Residues in contact with ASN 111 (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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107B HIS* 3.1 39.6 + - - +
108B LEU* 3.0 16.2 + - + +
110B ASN* 1.3 74.0 - - - +
112B MET* 1.3 66.4 + - + +
114B GLY* 3.1 3.5 + - - -
115B LYS* 2.9 53.0 + - + +
60I THR* 5.6 2.6 - - - +
92I ASN* 2.5 37.7 + - - +
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Residues in contact with MET 112 (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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64B GLY* 4.0 11.2 - - - -
66B ILE* 3.5 29.2 - - - -
94B ILE* 3.2 36.3 - - + +
96B SER* 4.2 7.9 - - - +
108B LEU* 2.7 15.2 + - - +
109B LEU* 3.3 7.6 - - - +
111B ASN* 1.3 75.0 - - + +
113B LEU* 1.3 61.5 + - - +
115B LYS* 2.8 28.7 + - + +
116B GLN 3.3 3.3 + - - -
117B VAL* 3.2 29.6 - - + +
120B ILE* 3.1 34.1 - - + -
94I ILE* 5.2 3.8 - - + -
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Residues in contact with LEU 113 (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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109B LEU* 3.0 36.7 + - + +
110B ASN* 4.1 9.4 - - - +
112B MET* 1.3 75.6 - - - +
114B GLY* 1.3 55.0 + - - +
116B GLN* 2.7 27.8 + - - +
117B VAL* 4.0 7.0 - - + +
120B ILE* 4.3 13.5 - - + -
138B SER* 3.8 9.4 - - - +
139B PRO* 3.7 29.8 - - + -
140B VAL* 3.4 33.4 - - + -
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Residues in contact with GLY 114 (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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110B ASN 2.7 20.8 + - - -
111B ASN* 3.3 4.9 - - - -
112B MET 3.0 0.4 - - - -
113B LEU* 1.3 78.3 - - - +
115B LYS* 1.3 60.1 + - - +
116B GLN* 2.8 18.6 + - - -
116I GLN* 6.1 0.3 - - - +
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Residues in contact with LYS 115 (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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62B THR* 5.9 1.7 - - - +
94B ILE* 5.8 3.6 - - + -
111B ASN* 2.9 32.6 + - + +
112B MET* 2.8 18.4 + - + +
114B GLY* 1.3 79.3 + - - +
116B GLN* 1.3 78.9 + - - +
117B VAL* 3.5 6.5 + - + +
62I THR* 3.6 28.9 - - - +
92I ASN* 5.5 0.4 - - - +
94I ILE* 4.1 18.4 - - + -
115I LYS* 3.4 26.4 - - + +
116I GLN* 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
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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