Contacts of the helix formed by residues 101 - 115 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98I SER 2.9 16.2 + - - +
99I ASP* 4.2 7.0 - - + +
100I GLN* 1.3 76.4 - - - +
102I GLN* 1.3 67.7 + - - +
103I ASP* 3.2 20.6 + - - +
104I LYS* 3.0 34.6 + - + +
105I GLU* 3.0 28.9 + - - +
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Residues in contact with GLN 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I GLN 4.0 2.4 + - - -
101I ASN* 1.3 72.8 + - - +
103I ASP* 1.3 63.5 + - - +
105I GLU* 3.9 11.6 + - - -
106I LEU* 3.1 28.2 + - + +
128I THR* 2.9 36.8 + - - +
129I GLU* 5.2 0.9 - - - +
130I GLU* 3.4 35.6 + - - +
131I HIS* 3.2 25.5 + - - +
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Residues in contact with ASP 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101I ASN* 3.1 15.5 + - - +
102I GLN* 1.3 86.9 - - - +
104I LYS* 1.3 54.3 + - + +
106I LEU* 3.3 5.5 + - - +
107I HIS* 2.5 35.8 + - - +
130I GLU* 5.4 1.2 - - - +
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Residues in contact with LYS 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLU* 4.4 8.7 + - - -
87B THR* 4.4 10.9 + - - +
97I ASN 2.9 27.7 + - - -
98I SER* 3.2 21.9 - - - +
99I ASP* 2.9 29.2 + - - +
101I ASN* 3.0 19.1 + - + +
103I ASP* 1.3 72.8 - - - +
105I GLU* 1.3 56.8 + - - +
106I LEU 3.1 1.6 - - - -
107I HIS* 3.8 19.7 - - + +
108I LEU* 2.6 53.4 + - + +
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Residues in contact with GLU 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66I ILE* 4.4 3.3 - - - +
68I PRO* 4.8 0.5 - - - +
98I SER* 3.4 27.8 + - - +
100I GLN* 4.7 5.1 - - - -
101I ASN 3.0 19.5 + - - +
102I GLN* 3.9 5.9 + - - -
104I LYS* 1.3 75.3 - - - +
106I LEU* 1.3 57.5 + - - +
108I LEU* 3.7 4.5 - - - +
109I LEU* 2.8 31.1 + - - +
122I PHE* 3.4 28.4 - - + -
123I MET 4.2 0.3 - - - +
124I SER* 2.9 35.6 + - - +
126I ASN 4.3 0.9 - - - +
131I HIS* 2.9 36.2 + - + -
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Residues in contact with LEU 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102I GLN* 3.1 19.2 + - - +
103I ASP* 3.4 6.1 - - - +
105I GLU* 1.3 78.4 - - - +
107I HIS* 1.3 67.6 + - - +
109I LEU* 3.4 12.5 + - + +
110I ASN* 3.2 35.8 + - + +
130I GLU* 5.2 8.7 - - - +
131I HIS* 4.7 16.4 - - + +
134I GLU* 3.6 46.0 - - + +
135I LEU* 6.3 0.2 - - + -
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Residues in contact with HIS 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B THR* 6.3 1.3 - - + -
92B ASN* 3.4 25.0 + - - -
103I ASP 2.5 22.3 + - - +
104I LYS* 3.4 22.5 - - + +
106I LEU* 1.3 73.7 - - - +
108I LEU* 1.3 53.8 + - + +
110I ASN* 3.0 7.9 + - + +
111I ASN* 2.6 53.4 + - + +
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Residues in contact with LEU 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ASN* 5.4 2.5 - - - +
93B ILE 5.6 1.6 - - - +
66I ILE* 3.9 15.9 - - + -
96I SER* 3.2 32.5 - - - +
97I ASN 3.2 29.8 - - - +
98I SER* 3.8 11.9 - - - -
104I LYS* 2.6 38.5 + - + +
105I GLU 3.7 4.0 - - - +
107I HIS* 1.3 77.9 - - + +
109I LEU* 1.3 54.0 + - - +
111I ASN* 3.2 21.3 - - - +
112I MET* 2.6 40.9 + - + +
115I LYS* 4.4 5.6 - - - +
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Residues in contact with LEU 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66I ILE* 4.2 9.3 - - + +
105I GLU 2.8 23.5 + - - +
106I LEU* 3.8 15.9 - - + +
107I HIS 3.3 0.4 - - - -
108I LEU* 1.3 73.8 - - - +
110I ASN* 1.3 67.2 + - - +
113I LEU* 2.6 29.5 - - - +
120I ILE* 4.4 12.3 - - + -
122I PHE* 5.5 4.0 - - + -
134I GLU* 4.3 4.0 - - + +
135I LEU* 3.2 51.1 - - + +
138I SER* 3.7 11.6 + - - +
142I VAL* 3.7 30.5 - - + -
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Residues in contact with ASN 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106I LEU* 3.2 31.0 + - + +
107I HIS* 3.0 5.2 + - - +
109I LEU* 1.3 99.0 + - - +
111I ASN* 1.3 62.3 + - - +
112I MET 3.4 0.9 - - - -
113I LEU* 3.3 24.3 - - + +
114I GLY* 3.8 6.2 + - - -
134I GLU* 5.3 6.5 + - - +
138I SER* 4.6 9.1 + - - +
139I PRO* 5.0 1.0 - - - +
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Residues in contact with ASN 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ASN* 4.2 6.3 + - - +
107I HIS* 2.6 41.2 + - + +
108I LEU* 3.2 32.7 + - - +
110I ASN* 1.3 73.0 - - - +
112I MET* 1.3 59.8 + - - +
114I GLY* 3.3 3.4 + - - -
115I LYS* 2.6 62.1 + - - +
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Residues in contact with MET 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ILE* 3.8 4.7 - - + -
64I GLY* 3.8 29.6 - - - -
65I VAL 4.8 0.2 - - - -
66I ILE* 4.5 10.8 - - + -
94I ILE* 3.3 33.7 - - + +
96I SER* 4.5 15.5 - - - +
108I LEU* 2.6 32.0 + - + +
111I ASN* 1.3 72.2 - - - +
113I LEU* 1.3 68.5 + - + +
114I GLY 2.9 1.6 - - - -
115I LYS* 3.0 52.2 + - + +
116I GLN 3.1 7.6 + - - -
117I VAL* 3.1 17.6 + - + +
120I ILE* 3.6 22.0 - - + -
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Residues in contact with LEU 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I LEU 2.6 30.3 - - - +
110I ASN* 3.3 26.5 - - - +
112I MET* 1.3 71.7 - - - +
114I GLY* 1.3 63.1 + - - +
116I GLN* 3.2 14.7 + - - +
117I VAL* 3.4 16.3 + - - +
120I ILE* 3.8 10.5 - - + -
138I SER* 3.8 4.3 - - - +
139I PRO* 3.2 36.8 - - + -
140I VAL* 3.6 36.3 - - + -
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Residues in contact with GLY 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I ASN 3.8 5.0 + - - -
111I ASN* 3.3 9.9 + - - -
112I MET 2.9 1.8 - - - -
113I LEU* 1.3 79.5 - - - +
115I LYS* 1.3 50.9 + - - -
116I GLN* 2.6 39.9 + - - -
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Residues in contact with LYS 115 (chain I).
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* 4.8 7.2 - - + -
92B ASN* 3.8 24.7 + - - +
93B ILE 4.5 4.0 + - - +
94B ILE* 3.3 31.5 - - + +
115B LYS* 3.4 24.3 - - + +
94I ILE* 4.6 4.0 - - + +
96I SER* 5.7 0.2 - - - -
108I LEU* 4.4 5.9 - - - +
111I ASN* 2.6 58.7 + - - +
112I MET* 3.0 36.2 + - + +
114I GLY* 1.3 67.5 - - - +
116I GLN* 1.3 73.9 + - - +
117I VAL* 5.2 0.2 - - + -
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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