Contacts of the helix formed by residues 101 - 115 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98P SER 3.2 14.3 + - - +
99P ASP* 4.5 3.4 - - + +
100P GLN* 1.3 77.4 + - - +
102P GLN* 1.3 67.6 + - - +
103P ASP* 2.9 21.8 + - - +
104P LYS* 3.0 21.2 + - + +
105P GLU* 2.8 32.3 + - - +
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Residues in contact with GLN 102 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101P ASN* 1.3 71.0 + - - +
103P ASP* 1.3 64.4 + - - +
105P GLU* 3.3 8.1 + - - +
106P LEU* 3.1 23.8 + - - +
126P ASN 4.8 0.2 + - - -
128P THR* 2.9 38.2 + - - +
130P GLU* 3.5 30.3 - - - +
131P HIS* 3.0 35.8 + - - -
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Residues in contact with ASP 103 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101P ASN* 2.9 11.4 + - - +
102P GLN* 1.3 76.4 - - - +
104P LYS* 1.3 56.4 + - - +
105P GLU 3.0 1.6 - - - -
106P LEU* 3.1 7.1 + - - +
107P HIS* 2.5 38.0 + - - +
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Residues in contact with LYS 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F GLU* 5.5 2.6 - - - +
87F THR* 3.5 28.3 - - - +
91F TYR 5.9 0.4 + - - -
97P ASN 3.6 8.7 - - - +
98P SER* 3.5 32.1 - - - +
99P ASP* 3.7 18.8 - - - +
101P ASN* 3.0 22.3 + - + +
103P ASP* 1.3 76.1 - - - +
105P GLU* 1.3 55.7 + - - +
107P HIS* 3.8 10.2 - - + -
108P LEU* 2.7 57.0 + - + +
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Residues in contact with GLU 105 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66P ILE* 5.2 1.0 - - - +
68P PRO* 5.1 0.2 - - - +
98P SER* 3.6 27.8 + - - +
100P GLN* 4.4 10.7 + - - +
101P ASN 2.8 23.2 + - - +
102P GLN* 3.4 11.2 + - - +
104P LYS* 1.3 78.4 - - - +
106P LEU* 1.3 57.7 + - - +
108P LEU* 4.1 2.8 - - - +
109P LEU* 3.0 35.8 + - - +
122P PHE* 3.8 20.6 - - + -
123P MET 4.0 1.0 - - - +
124P SER* 2.8 31.2 + - - -
126P ASN 4.0 1.7 - - - +
131P HIS* 2.8 34.8 + - + +
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Residues in contact with LEU 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102P GLN 3.1 11.4 + - - +
103P ASP* 3.1 10.8 + - - +
105P GLU* 1.3 75.3 - - - +
107P HIS* 1.3 65.7 + - - +
109P LEU* 3.1 30.8 - - + +
110P ASN* 3.1 23.6 + - - +
130P GLU 4.9 1.8 - - - +
131P HIS* 4.6 20.2 + - + +
134P GLU* 3.1 53.4 - - + +
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Residues in contact with HIS 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F ASN* 3.4 17.5 + - - -
103P ASP 2.5 23.5 + - - +
104P LYS* 3.7 12.3 - - + +
106P LEU* 1.3 70.2 - - - +
108P LEU* 1.3 64.5 + - + +
109P LEU 2.9 4.0 - - - -
110P ASN* 2.9 22.3 + - - +
111P ASN* 3.0 47.0 + - - +
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Residues in contact with LEU 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F ASN* 5.1 5.8 - - + +
93F ILE 5.5 6.3 - - - +
66P ILE* 3.5 21.3 - - + +
96P SER* 3.8 24.5 - - - +
97P ASN 3.1 35.7 - - - +
98P SER* 3.8 11.4 - - - -
104P LYS* 2.7 39.3 + - + +
105P GLU 4.4 1.8 - - - +
107P HIS* 1.3 77.6 - - + +
109P LEU* 1.3 57.8 + - - +
110P ASN 3.3 0.2 - - - -
111P ASN* 3.7 18.8 - - + +
112P MET* 3.1 33.7 + - + +
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Residues in contact with LEU 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66P ILE* 4.9 6.5 - - + -
105P GLU 3.0 23.7 + - - +
106P LEU* 3.1 37.7 - - + +
107P HIS 2.9 0.2 - - - -
108P LEU* 1.3 79.3 - - - +
110P ASN* 1.3 62.1 + - - +
112P MET* 4.3 3.2 + - - +
113P LEU* 4.5 5.0 + - - +
120P ILE* 4.2 22.3 - - + +
122P PHE* 4.2 28.7 - - + -
131P HIS* 5.0 4.0 - - + +
134P GLU 4.9 2.5 - - - +
135P LEU* 3.4 47.3 - - + +
138P SER* 5.4 3.9 + - - -
139P PRO* 6.0 1.6 - - - +
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Residues in contact with ASN 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106P LEU* 3.1 37.6 + - - +
107P HIS* 2.9 8.7 + - - +
109P LEU* 1.3 79.7 - - - +
111P ASN* 1.3 61.6 + - - +
112P MET 3.2 2.2 - - - -
113P LEU* 3.5 12.4 + - + +
114P GLY* 3.3 20.4 + - - -
134P GLU* 4.4 6.9 + - - +
138P SER* 6.2 0.2 - - - -
139P PRO* 5.6 5.9 - - - +
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Residues in contact with ASN 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F THR* 5.4 3.2 - - + +
92F ASN* 2.9 31.5 + - - +
94F ILE* 6.3 0.7 - - + -
107P HIS* 3.0 44.9 + - - +
108P LEU* 3.5 14.1 + - + +
110P ASN* 1.3 77.6 + - - +
112P MET* 1.3 69.4 + - + +
113P LEU 3.3 0.2 - - - -
114P GLY* 3.5 3.2 + - - +
115P LYS* 3.2 32.4 + - + +
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Residues in contact with MET 112 (chain P).
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* 4.2 7.6 - - + -
64P GLY* 4.3 9.2 - - - -
65P VAL 5.0 0.2 - - - -
66P ILE* 4.3 13.5 - - + -
94P ILE* 3.5 38.1 - - + +
96P SER* 3.1 30.7 - - - +
108P LEU* 3.1 20.6 + - + +
109P LEU 4.4 1.6 - - - +
110P ASN 3.2 0.4 - - - -
111P ASN* 1.3 89.2 - - + +
113P LEU* 1.3 62.3 + - - +
115P LYS* 3.3 4.7 + - + -
117P VAL* 2.9 40.7 + - + +
120P ILE* 3.4 32.5 - - + -
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Residues in contact with LEU 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109P LEU 4.5 4.3 + - - +
110P ASN* 3.5 16.6 + - + +
111P ASN 3.3 0.2 - - - -
112P MET* 1.3 74.5 - - - +
114P GLY* 1.3 73.9 + - - +
115P LYS 3.0 1.8 - - - -
116P GLN* 2.9 19.1 + - - +
117P VAL* 4.3 3.8 - - - +
120P ILE* 5.3 0.6 - - - +
139P PRO* 3.2 43.1 - - + -
140P VAL* 4.6 15.9 - - + -
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Residues in contact with GLY 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110P ASN 3.3 11.5 + - - -
111P ASN* 3.5 5.6 + - - -
112P MET 3.3 0.2 - - - -
113P LEU* 1.3 86.7 - - - +
115P LYS* 1.3 61.6 + - - +
116P GLN* 3.3 8.0 + - - +
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Residues in contact with LYS 115 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F THR* 2.8 47.7 + - - +
94F ILE* 3.4 27.8 - - + +
115F LYS* 3.1 65.3 - - + +
116F GLN 5.6 0.7 - - - -
117F VAL* 5.0 1.4 - - - +
94P ILE* 5.4 3.1 - - + -
111P ASN* 3.2 18.8 + - - +
112P MET* 3.7 7.0 - - + +
113P LEU 3.0 1.2 - - - -
114P GLY* 1.3 79.5 - - - +
116P GLN* 1.3 69.8 + - - +
117P VAL* 2.9 12.0 + - + +
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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