Contacts of the helix formed by residues 93 - 111 (chain e) 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 e).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64c THR 4.6 0.2 - - - -
92e SER* 1.3 78.8 - - - +
94e PRO* 1.3 68.5 - - - -
95e ALA 3.3 2.0 - - - -
96e LEU* 2.7 30.1 + - - +
97e VAL* 3.1 14.0 + - - +
133e VAL* 4.3 18.1 - - - +
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Residues in contact with PRO 94 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64c THR* 3.3 17.9 - - + +
65c GLN* 3.4 28.5 - - + +
66c TYR 4.6 0.4 - - - -
67c GLY* 3.8 11.4 - - - +
92e SER 4.6 0.4 - - - +
93e GLY* 1.3 85.0 - - - -
95e ALA* 1.3 62.1 + - - +
97e VAL* 3.0 12.8 + - + +
98e ASN* 2.9 25.0 + - - +
133e VAL* 4.3 9.1 - - + -
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Residues in contact with ALA 95 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64c THR* 3.3 18.4 + - + +
67c GLY* 3.5 15.2 - - - -
68c ILE 3.7 20.4 - - - +
69c THR* 3.4 14.1 - - + +
90e ILE* 3.5 24.2 - - + -
93e GLY 3.1 0.8 + - - -
94e PRO* 1.3 80.2 - - - +
96e LEU* 1.3 62.7 + - - +
98e ASN* 3.3 1.3 + - - +
99e MET* 3.0 19.5 + - - +
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Residues in contact with LEU 96 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83e VAL* 4.3 6.3 - - + +
86e ALA* 3.9 29.2 - - + -
87e LEU* 3.8 36.8 - - + +
90e ILE* 4.2 5.7 - - + +
91e GLY 3.6 11.4 - - - +
92e SER* 3.9 10.8 - - - -
93e GLY 2.7 16.3 + - - +
95e ALA* 1.3 71.2 - - - +
97e VAL* 1.3 62.3 + - + +
99e MET* 3.1 5.6 + - + +
100e ILE* 2.8 51.3 + - + +
126e THR* 4.6 13.0 - - + -
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Residues in contact with VAL 97 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93e GLY 3.8 7.2 - - - +
94e PRO* 3.0 11.2 + - + +
96e LEU* 1.3 79.5 - - + +
98e ASN* 1.3 66.6 + - - +
100e ILE* 3.3 0.6 + - + -
101e ASN* 3.1 33.1 + - - +
130e THR* 3.4 25.2 + - - +
131e GLY* 3.5 30.1 - - - +
132e TYR 4.8 2.5 - - - +
133e VAL* 3.7 29.4 - - + -
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Residues in contact with ASN 98 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67c GLY* 3.1 35.6 + - - -
69c THR* 4.4 8.1 - - + -
94e PRO* 2.9 14.0 + - - +
95e ALA* 3.5 8.5 - - - +
97e VAL* 1.3 80.0 - - - +
99e MET* 1.3 63.5 + - - +
101e ASN* 3.5 9.0 + - - +
102e GLY 3.3 15.8 + - - -
109f SER 3.5 22.9 - - - +
110f ALA* 3.7 2.3 - - - +
112f ASN* 5.2 8.9 - - - +
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Residues in contact with MET 99 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1848 T 4.1 11.2 - - - +
69c THR* 4.6 5.6 - - + -
82e LYS* 4.7 13.5 - - - +
83e VAL* 6.3 0.9 - - - -
86e ALA* 3.8 23.3 - - + -
90e ILE* 3.7 23.3 - - + -
95e ALA 3.0 12.6 + - - +
96e LEU* 3.1 13.9 + - + +
98e ASN* 1.3 77.7 - - - +
100e ILE* 1.3 59.9 + - + +
102e GLY* 3.2 3.3 + - - -
103e LEU* 2.8 32.0 + - + +
106f TYR* 4.7 10.1 - - - -
110f ALA* 4.2 20.2 + - - +
111f PHE* 3.8 29.6 - - + -
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Residues in contact with ILE 100 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79e PHE* 5.0 3.1 - - + -
83e VAL* 4.3 19.3 - - + -
96e LEU* 2.8 46.8 + - + +
97e VAL* 3.9 3.4 - - - +
99e MET* 1.3 73.4 - - + +
101e ASN* 1.3 57.0 + - - +
103e LEU* 3.5 6.5 - - + +
104e LYS* 2.8 43.2 + - + +
122e VAL* 4.2 16.4 - - + -
126e THR* 4.1 22.9 - - + -
130e THR* 3.5 35.7 - - + +
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Residues in contact with ASN 101 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97e VAL* 3.1 33.5 + - - +
98e ASN* 3.7 10.3 + - - +
100e ILE* 1.3 77.9 - - - +
102e GLY* 1.3 61.9 + - - +
104e LYS* 3.5 8.6 + - - +
105e GLY* 3.2 17.5 + - - -
130e THR* 3.3 21.1 - - - +
131e GLY* 4.3 7.8 + - - -
109f SER* 4.2 7.8 + - - +
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Residues in contact with GLY 102 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98e ASN 3.3 4.4 + - - -
99e MET 3.2 6.4 + - - -
101e ASN* 1.3 76.6 - - - +
103e LEU* 1.3 60.3 + - - +
105e GLY* 3.1 3.9 + - - -
106e TYR* 2.9 24.1 + - - +
106f TYR* 3.5 19.8 - - - -
109f SER* 3.0 23.5 + - - -
110f ALA* 4.0 10.3 - - - -
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Residues in contact with LEU 103 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79e PHE* 3.6 16.4 - - + -
82e LYS* 3.5 47.3 - - + +
83e VAL* 3.6 31.4 - - + +
99e MET* 2.8 22.7 + - + +
100e ILE* 3.2 9.4 + - + +
102e GLY* 1.3 74.0 - - - +
104e LYS* 1.3 66.0 + - - +
106e TYR* 3.1 11.2 + - + +
107e TYR* 3.0 41.0 + - + -
106f TYR* 3.9 9.5 - - + -
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Residues in contact with LYS 104 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79e PHE* 3.8 28.7 - - + -
100e ILE* 2.8 34.7 + - + +
101e ASN* 3.7 8.4 + - - +
103e LEU* 1.3 71.7 - - - +
105e GLY* 1.3 59.3 + - - +
107e TYR* 3.2 1.6 + - - +
108e ILE* 2.8 54.1 + - + +
115e PRO* 5.0 5.8 - - - +
118e LEU* 4.8 5.8 - - + -
119e ASP* 2.7 38.1 + - - +
122e VAL* 5.0 2.0 - - + -
129e PRO* 6.1 0.2 - - - +
130e THR* 4.6 12.1 - - + +
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Residues in contact with GLY 105 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101e ASN 3.2 8.9 + - - -
102e GLY* 3.1 7.8 + - - -
104e LYS* 1.3 77.7 - - - +
106e TYR* 1.3 58.5 + - - +
108e ILE* 4.5 6.7 - - - +
109e SER* 2.6 36.7 + - - -
102f GLY 4.4 3.1 - - - -
105f GLY* 5.9 2.5 - - - -
106f TYR 5.3 2.2 - - - -
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Residues in contact with TYR 106 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1557 A 3.8 5.9 + - - -
1567 T 2.9 18.0 + - - -
82e LYS* 5.6 4.0 - - - -
102e GLY 2.9 11.9 + - - +
103e LEU* 3.2 16.6 - - + +
105e GLY* 1.3 74.8 - - - +
107e TYR* 1.3 84.4 + + - +
110e ALA* 2.8 40.9 + - + +
111e PHE* 3.7 27.0 - + - -
82f LYS* 2.8 40.6 + - - -
99f MET* 4.6 7.4 - - - +
102f GLY 3.7 15.3 + - - -
103f LEU* 4.0 13.5 - - + -
106f TYR* 3.7 31.0 - + + -
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Residues in contact with TYR 107 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1557 A 4.5 4.9 - - + +
1567 T 3.3 34.7 + - - -
75e ILE* 3.5 38.4 - - + -
78e GLY* 3.5 9.6 - - - -
79e PHE* 3.7 31.0 - + + -
82e LYS* 5.2 1.1 - - + -
103e LEU* 3.0 25.5 + - + +
104e LYS 4.0 1.8 - - - +
106e TYR* 1.3 98.5 - + - +
108e ILE* 1.3 66.8 + - - +
111e PHE* 3.1 42.0 + + + -
113e ALA* 3.0 26.5 + - + +
118e LEU* 4.4 8.1 - - + -
71h PRO* 6.5 0.7 - - + -
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Residues in contact with ILE 108 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104e LYS* 2.8 43.8 + - + +
105e GLY* 4.1 4.5 - - - +
107e TYR* 1.3 72.3 - - - +
109e SER* 1.3 61.7 + - - +
112e ASN* 3.1 25.3 - - - +
113e ALA 3.6 15.8 + - - +
115e PRO* 3.9 31.4 - - + -
118e LEU* 3.3 21.5 - - + -
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Residues in contact with SER 109 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105e GLY 2.6 21.1 + - - -
108e ILE* 1.3 85.4 - - - +
110e ALA* 1.3 60.6 + - - +
111e PHE 3.5 0.2 - - - -
112e ASN* 4.0 10.8 - - - +
98f ASN* 3.5 17.3 - - - +
101f ASN* 4.2 6.4 + - - +
102f GLY* 2.9 21.7 - - - -
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Residues in contact with ALA 110 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106e TYR* 2.8 25.4 + - + +
109e SER* 1.3 80.0 + - - +
111e PHE* 1.3 61.9 + - + +
112e ASN* 5.1 1.7 + - - -
98f ASN* 3.6 12.5 - - - +
99f MET* 3.9 35.7 + - - +
102f GLY* 4.1 4.7 - - - -
69h THR* 2.6 34.1 + - - +
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Residues in contact with PHE 111 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1557 A 3.8 24.9 - - - -
75e ILE* 4.8 13.1 - - + +
106e TYR* 3.7 34.5 - + - -
107e TYR* 3.1 47.7 + + + +
110e ALA* 1.3 79.2 - - + +
112e ASN* 1.3 75.0 + - - +
113e ALA* 3.2 1.8 + - - +
99f MET* 3.7 28.0 - - + -
69h THR* 3.4 17.3 - - - +
70h GLY* 3.5 31.6 - - - -
71h PRO* 4.6 4.3 - - + -
72h ASN* 3.3 19.2 + - - +
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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
------------------------------------------------------------
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