Contacts of the helix formed by residues 93 - 111 (chain c) in PDB entry 3J9X
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 GLY 93 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64a THR* 4.6 0.7 - - - -
92c SER* 1.3 76.5 - - - +
94c PRO* 1.3 67.2 - - - -
95c ALA 3.3 1.8 - - - -
96c LEU* 2.7 29.5 + - - +
97c VAL* 3.1 15.9 + - - +
133c VAL* 4.3 19.3 - - - +
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Residues in contact with PRO 94 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64a THR* 3.3 17.9 - - + +
65a GLN* 3.4 27.6 - - + +
66a TYR 4.6 0.4 - - - -
67a GLY* 3.8 11.0 - - - +
92c SER 4.6 0.4 - - - +
93c GLY* 1.3 83.4 - - - -
95c ALA* 1.3 63.0 + - - +
97c VAL* 3.0 13.4 + - + +
98c ASN* 2.9 25.3 + - - +
133c VAL* 4.3 8.9 - - + -
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Residues in contact with ALA 95 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64a THR* 3.3 19.4 + - + +
67a GLY* 3.5 15.4 - - - -
68a ILE 3.7 20.6 - - - +
69a THR* 3.4 14.0 - - + +
90c ILE* 3.5 25.1 - - + -
93c GLY 3.1 0.6 + - - -
94c PRO* 1.3 78.7 - - - +
96c LEU* 1.3 62.0 + - - +
98c ASN* 3.3 1.5 + - - +
99c MET* 3.0 19.4 + - - +
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Residues in contact with LEU 96 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83c VAL* 4.3 6.1 - - + +
86c ALA* 3.9 28.9 - - + +
87c LEU* 3.8 37.5 - - + +
90c ILE* 4.2 5.1 - - + +
91c GLY 3.6 12.5 + - - +
92c SER* 3.9 10.5 - - - -
93c GLY 2.7 17.4 + - - +
95c ALA* 1.3 71.3 - - - +
97c VAL* 1.3 62.3 + - + +
99c MET* 3.1 5.9 + - + +
100c ILE* 2.8 53.2 + - + +
126c THR* 4.6 12.1 - - + -
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Residues in contact with VAL 97 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93c GLY* 3.1 6.9 + - - +
94c PRO* 3.0 10.3 + - + +
96c LEU* 1.3 78.7 - - + +
98c ASN* 1.3 66.5 + - - +
100c ILE* 3.3 0.6 + - + -
101c ASN* 3.1 34.0 + - - +
130c THR* 3.4 25.2 + - - +
131c GLY* 3.5 28.5 - - - +
132c TYR 4.8 2.9 - - - +
133c VAL* 3.7 30.3 - - + -
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Residues in contact with ASN 98 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67a GLY* 3.1 35.2 + - - -
69a THR* 4.4 7.4 - - + -
94c PRO* 2.9 12.3 + - - +
95c ALA* 3.5 8.1 - - - +
97c VAL* 1.3 81.7 - - - +
99c MET* 1.3 62.5 + - - +
101c ASN* 3.5 8.6 + - - +
102c GLY 3.3 15.1 + - - -
109d SER 3.5 22.4 - - - +
110d ALA* 3.7 3.5 - - - +
112d ASN* 5.2 9.8 - - - +
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Residues in contact with MET 99 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1728 T 4.1 11.9 - - - +
69a THR* 4.6 5.8 - - + -
82c LYS* 4.7 12.3 - - - -
83c VAL* 6.3 0.7 - - - -
86c ALA* 3.8 23.3 - - + -
90c ILE* 3.7 23.6 - - + -
95c ALA 3.0 13.6 + - - +
96c LEU* 3.3 13.5 - - + +
98c ASN* 1.3 77.4 - - - +
100c ILE* 1.3 60.1 + - + +
102c GLY* 3.2 3.3 + - - -
103c LEU* 2.8 31.8 + - + +
106d TYR* 4.7 9.6 - - - -
110d ALA* 4.2 20.0 + - - +
111d PHE* 3.8 30.5 - - + -
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Residues in contact with ILE 100 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79c PHE* 5.0 2.7 - - + -
83c VAL* 4.3 19.1 - - + -
96c LEU* 2.8 46.2 + - + +
97c VAL* 3.9 3.4 - - + +
99c MET* 1.3 76.2 - - + +
101c ASN* 1.3 57.5 + - - +
103c LEU* 3.5 6.5 - - + +
104c LYS* 2.8 43.4 + - + +
122c VAL* 4.2 15.9 - - + -
126c THR* 4.1 22.9 - - + -
130c THR* 3.5 35.4 - - + +
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Residues in contact with ASN 101 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97c VAL* 3.1 34.7 + - - +
98c ASN* 3.7 10.1 + - - +
100c ILE* 1.3 77.5 - - - +
102c GLY* 1.3 62.3 + - - +
104c LYS* 3.5 8.2 + - - +
105c GLY* 3.2 17.5 + - - -
130c THR* 3.3 20.9 - - - +
131c GLY* 4.3 7.1 + - - -
109d SER* 4.2 8.4 + - - +
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Residues in contact with GLY 102 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98c ASN 3.3 4.8 + - - -
99c MET 3.2 6.2 + - - -
101c ASN* 1.3 75.7 - - - +
103c LEU* 1.3 59.3 + - - +
105c GLY* 3.1 4.2 + - - -
106c TYR 2.9 24.1 + - - -
105d GLY 4.8 0.2 - - - -
106d TYR* 3.5 20.1 - - - -
109d SER* 3.0 23.9 + - - -
110d ALA* 4.0 10.1 - - - -
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Residues in contact with LEU 103 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79c PHE* 3.6 17.0 - - + -
82c LYS* 3.5 46.9 - - + +
83c VAL* 3.6 31.2 - - + +
99c MET* 2.8 22.0 + - + +
100c ILE* 3.2 8.9 + - + +
102c GLY* 1.3 73.0 - - - +
104c LYS* 1.3 65.6 + - - +
106c TYR* 3.1 11.6 + - + +
107c TYR* 3.0 40.9 + - + -
106d TYR* 3.9 10.8 - - + -
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Residues in contact with LYS 104 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79c PHE* 3.8 28.3 - - + -
100c ILE* 2.8 36.9 + - + +
101c ASN* 3.7 8.0 + - - +
103c LEU* 1.3 71.7 - - - +
105c GLY* 1.3 58.3 + - - +
107c TYR* 3.2 1.6 + - - +
108c ILE* 2.8 54.2 + - + +
115c PRO* 5.0 4.7 - - - +
118c LEU* 4.8 6.5 - - + -
119c ASP* 2.7 37.5 + - - +
122c VAL* 5.0 1.8 - - + -
129c PRO* 6.1 0.2 - - - +
130c THR* 4.6 12.0 - - + +
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Residues in contact with GLY 105 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101c ASN 3.2 8.2 + - - -
102c GLY* 3.1 8.4 + - - -
104c LYS* 1.3 77.2 - - - +
106c TYR* 1.3 57.0 + - - +
108c ILE* 4.1 6.4 - - - +
109c SER* 2.6 35.9 + - - -
102d GLY* 4.4 3.8 - - - -
105d GLY* 5.9 2.0 - - - -
106d TYR 5.3 2.0 - - - -
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Residues in contact with TYR 106 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1677 A 3.8 5.4 + - - -
1687 T 2.9 18.3 + - - -
82c LYS* 5.6 3.8 - - - -
102c GLY 2.9 12.5 + - - +
103c LEU* 3.1 15.5 + - + +
105c GLY* 1.3 75.2 - - - +
107c TYR* 1.3 84.7 + + - +
110c ALA* 2.8 41.7 + - + +
111c PHE* 3.7 25.6 - + - -
82d LYS* 2.8 39.5 + - - -
99d MET* 4.6 7.6 - - - +
102d GLY 3.7 15.3 + - - -
103d LEU* 4.0 13.2 - - + -
106d TYR* 3.7 31.8 - + + +
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Residues in contact with TYR 107 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1677 A 4.5 5.0 - - + +
1687 T 3.3 35.7 + - - -
75c ILE* 3.5 38.4 - - + -
78c GLY* 3.5 9.1 - - - -
79c PHE* 3.7 31.0 - + + -
82c LYS* 5.2 0.9 - - + -
103c LEU* 3.0 26.0 + - + +
104c LYS 4.0 2.0 - - - +
106c TYR* 1.3 98.1 - + - +
108c ILE* 1.3 66.7 + - - +
111c PHE* 3.1 42.4 + + + +
113c ALA* 3.0 26.4 + - + +
118c LEU* 4.4 7.6 - - + -
71f PRO* 6.5 1.1 - - + -
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Residues in contact with ILE 108 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104c LYS* 2.8 44.8 + - + +
105c GLY* 4.1 4.9 - - - +
107c TYR* 1.3 72.1 - - - +
109c SER* 1.3 61.3 + - - +
112c ASN* 3.1 24.9 - - - +
113c ALA 3.6 16.1 - - - +
115c PRO* 3.9 31.9 - - + -
118c LEU* 3.3 20.9 - - + -
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Residues in contact with SER 109 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105c GLY* 2.6 21.3 + - - -
108c ILE* 1.3 84.9 - - - +
110c ALA* 1.3 60.8 + - - +
112c ASN* 4.0 9.7 - - - +
98d ASN* 3.5 17.8 - - - +
101d ASN* 4.2 6.3 - - - +
102d GLY* 2.9 23.4 - - - -
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Residues in contact with ALA 110 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106c TYR* 2.8 25.9 + - + +
109c SER* 1.3 80.2 + - - +
111c PHE* 1.3 63.7 + - + +
112c ASN* 3.6 1.7 + - - -
98d ASN* 3.6 13.0 - - - +
99d MET* 3.9 34.4 + - - +
102d GLY* 4.1 4.7 - - - -
69f THR* 2.6 34.1 + - - +
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Residues in contact with PHE 111 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1677 A 3.8 24.0 - - - -
75c ILE* 4.8 12.6 - - + +
106c TYR* 3.7 34.5 - + - -
107c TYR* 3.1 46.9 + + + +
110c ALA* 1.3 78.8 - - + +
112c ASN* 1.3 75.1 + - - +
113c ALA* 3.3 2.3 + - - +
99d MET* 3.7 28.0 - - + -
69f THR* 3.4 16.4 - - - +
70f GLY* 3.5 32.3 - - - -
71f PRO* 4.6 3.4 - - + -
72f ASN* 3.3 19.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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