Contacts of the helix formed by residues 93 - 111 (chain o) 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 o).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64m THR* 4.6 0.4 - - - -
92o SER* 1.3 77.4 + - - +
94o PRO* 1.3 67.8 - - - -
95o ALA 3.3 1.8 - - - -
96o LEU* 2.7 29.4 + - - +
97o VAL* 3.1 15.4 + - - +
133o VAL* 4.3 19.4 - - - +
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Residues in contact with PRO 94 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64m THR* 3.3 17.3 - - + +
65m GLN* 3.4 28.0 - - + +
66m TYR 4.6 0.2 - - - -
67m GLY* 3.8 10.1 - - - +
92o SER 4.6 0.4 - - - +
93o GLY* 1.3 84.0 - - - -
95o ALA* 1.3 64.4 + - - +
97o VAL* 3.0 13.2 + - + +
98o ASN* 2.9 25.4 + - - +
133o VAL* 4.3 9.1 - - + -
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Residues in contact with ALA 95 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64m THR* 3.3 18.5 + - + +
67m GLY* 3.5 15.7 - - - -
68m ILE 3.7 20.2 - - - +
69m THR* 3.4 13.8 - - + +
90o ILE* 3.5 24.7 - - + -
93o GLY 3.1 0.8 + - - -
94o PRO* 1.3 79.5 - - - +
96o LEU* 1.3 63.4 + - - +
98o ASN* 3.3 1.9 + - - +
99o MET* 3.0 18.9 + - - +
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Residues in contact with LEU 96 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83o VAL* 4.3 5.8 - - + +
86o ALA* 3.9 28.7 - - + -
87o LEU* 3.8 37.0 - - + +
90o ILE* 4.2 5.5 - - + +
91o GLY 3.6 11.6 + - - +
92o SER* 3.9 10.8 - - - -
93o GLY 2.7 16.3 + - - +
95o ALA* 1.3 71.8 - - - +
97o VAL* 1.3 62.4 + - + +
99o MET* 3.1 5.0 + - + +
100o ILE* 2.8 52.0 + - + +
126o THR* 4.6 13.9 - - + -
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Residues in contact with VAL 97 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93o GLY 3.1 7.8 + - - +
94o PRO* 3.0 10.5 + - + +
96o LEU* 1.3 78.3 - - + +
98o ASN* 1.3 67.1 + - - +
100o ILE* 3.3 0.8 + - + -
101o ASN* 3.1 32.7 + - - +
130o THR* 3.4 25.4 + - - +
131o GLY* 3.5 28.7 - - - +
132o TYR 4.8 2.7 - - - +
133o VAL* 3.7 30.7 - - + -
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Residues in contact with ASN 98 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67m GLY* 3.1 35.7 + - - +
69m THR* 4.4 7.9 - - + -
94o PRO* 2.9 12.4 + - - +
95o ALA* 3.5 7.4 - - - +
96o LEU 3.2 0.2 - - - -
97o VAL* 1.3 80.1 - - - +
99o MET* 1.3 63.1 + - - +
101o ASN* 3.5 9.9 + - - +
102o GLY 3.3 16.1 + - - -
109p SER 3.5 23.0 - - - +
110p ALA* 3.7 2.7 - - - +
112p ASN* 5.2 9.3 + - - +
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Residues in contact with MET 99 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2448 T 4.1 11.2 - - - +
69m THR* 4.6 7.0 - - + -
70m GLY 5.3 0.2 - - - +
82o LYS* 4.8 12.6 - - + -
83o VAL* 6.3 0.2 - - - -
86o ALA* 3.8 24.2 - - + -
90o ILE* 3.7 23.3 - - + -
95o ALA 3.0 13.0 + - - +
96o LEU* 3.1 14.3 + - + +
98o ASN* 1.3 77.3 - - - +
100o ILE* 1.3 59.4 + - + +
102o GLY* 3.2 3.3 + - - -
103o LEU* 2.8 32.6 + - + +
106p TYR* 4.7 9.9 - - - -
110p ALA* 4.2 19.9 + - - +
111p PHE* 3.8 29.2 - - + -
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Residues in contact with ILE 100 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79o PHE* 5.0 2.9 - - + -
83o VAL* 4.3 19.3 - - + -
96o LEU* 2.8 46.4 + - + +
97o VAL* 3.3 3.3 + - + +
99o MET* 1.3 73.4 - - + +
101o ASN* 1.3 58.1 + - - +
103o LEU* 3.5 7.1 - - + +
104o LYS* 2.8 44.0 + - + +
122o VAL* 4.2 15.7 - - + -
126o THR* 4.1 22.4 - - + -
130o THR* 3.5 35.9 - - + +
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Residues in contact with ASN 101 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97o VAL* 3.1 34.8 + - - +
98o ASN* 3.7 10.3 + - - +
99o MET 3.2 0.2 - - - -
100o ILE* 1.3 77.9 - - - +
102o GLY* 1.3 61.1 + - - +
104o LYS* 3.5 8.4 + - - +
105o GLY* 3.2 17.5 + - - -
130o THR* 3.3 20.9 - - - +
131o GLY* 4.3 7.1 + - - -
109p SER* 4.2 8.9 + - - +
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Residues in contact with GLY 102 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98o ASN 3.3 4.6 + - - -
99o MET 3.2 6.0 + - - -
101o ASN* 1.3 76.2 - - - +
103o LEU* 1.3 59.5 + - - +
105o GLY* 3.1 4.1 + - - -
106o TYR 2.9 23.9 + - - -
105p GLY 5.3 0.2 - - - -
106p TYR* 3.5 19.5 - - - -
109p SER* 3.0 24.3 + - - -
110p ALA* 4.0 10.3 - - - -
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Residues in contact with LEU 103 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79o PHE* 3.6 17.3 - - + -
82o LYS* 3.5 47.6 - - + +
83o VAL* 3.6 30.5 - - + +
99o MET* 2.8 22.2 + - + +
100o ILE* 3.5 9.2 - - + +
102o GLY* 1.3 72.4 - - - +
104o LYS* 1.3 65.1 + - - +
106o TYR* 3.1 12.0 + - + +
107o TYR* 3.0 40.8 + - + -
106p TYR* 3.9 11.4 - - + -
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Residues in contact with LYS 104 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79o PHE* 3.8 27.6 - - + -
100o ILE* 2.8 35.6 + - + +
101o ASN* 3.7 7.7 + - - +
103o LEU* 1.3 72.6 - - - +
105o GLY* 1.3 57.5 + - - +
107o TYR* 3.2 1.6 + - - +
108o ILE* 2.8 54.2 + - + +
115o PRO* 5.0 6.0 - - - +
118o LEU* 4.8 6.5 - - + -
119o ASP* 2.7 36.9 + - - +
122o VAL* 5.0 2.0 - - + -
129o PRO* 6.1 0.4 - - - +
130o THR* 4.6 12.5 - - + +
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Residues in contact with GLY 105 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101o ASN 3.2 8.5 + - - -
102o GLY* 3.1 8.5 + - - -
104o LYS* 1.3 77.9 - - - +
106o TYR* 1.3 57.6 + - - +
108o ILE* 4.5 6.3 - - - +
109o SER* 2.6 36.9 + - - -
102p GLY 4.4 3.4 - - - -
105p GLY* 5.9 1.8 - - - -
106p TYR 5.3 2.5 - - - -
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Residues in contact with TYR 106 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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957 A 3.8 5.7 + - - -
967 T 2.9 17.9 + - - -
82o LYS* 5.6 4.0 - - - -
102o GLY 2.9 11.9 + - - +
103o LEU* 3.1 15.5 + - + +
105o GLY* 1.3 75.2 - - - +
107o TYR* 1.3 84.6 + + - +
110o ALA* 2.8 41.3 + - + +
111o PHE* 3.7 25.9 - + - -
82p LYS* 2.8 40.6 + - - -
99p MET* 4.6 7.8 - - - +
102p GLY 3.7 15.3 + - - -
103p LEU* 4.0 12.3 - - + -
106p TYR* 3.7 31.6 - + + -
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Residues in contact with TYR 107 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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957 A 4.5 5.0 - - + +
967 T 3.3 34.8 + - - -
75o ILE* 3.5 37.9 - - + -
78o GLY* 3.5 9.5 - - - -
79o PHE* 3.7 31.4 - + + -
82o LYS* 5.2 0.9 - - + -
103o LEU* 3.0 25.2 + - + +
104o LYS 4.0 2.0 - - - +
106o TYR* 1.3 97.6 - + - +
108o ILE* 1.3 66.4 + - - +
111o PHE* 3.1 39.7 + + - -
113o ALA* 3.0 26.0 + - + +
118o LEU* 4.4 8.1 - - + -
71r PRO* 6.5 0.9 - - + -
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Residues in contact with ILE 108 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104o LYS* 2.8 45.4 + - + +
105o GLY* 4.1 5.4 - - - +
107o TYR* 1.3 72.4 - - - +
109o SER* 1.3 61.8 + - - +
112o ASN* 3.1 25.1 - - - +
113o ALA 3.6 16.1 + - - +
115o PRO* 3.9 31.4 - - + -
118o LEU* 3.3 21.1 - - + -
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Residues in contact with SER 109 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105o GLY* 2.6 20.6 + - - -
108o ILE* 1.3 84.0 - - - +
110o ALA* 1.3 61.2 + - - +
112o ASN* 4.0 11.1 - - - +
98p ASN* 3.5 16.6 - - - +
101p ASN* 4.2 5.6 + - - +
102p GLY* 2.9 22.8 - - - -
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Residues in contact with ALA 110 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106o TYR* 2.8 25.7 + - + +
109o SER* 1.3 79.7 + - - +
111o PHE* 1.3 62.5 + - + +
112o ASN* 3.6 1.9 + - - -
98p ASN* 3.6 12.8 - - - +
99p MET* 3.9 36.0 + - - +
102p GLY* 4.1 4.7 - - - -
69r THR* 2.6 33.6 + - - +
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Residues in contact with PHE 111 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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957 A 3.8 23.8 - - - -
75o ILE* 4.8 12.4 - - + +
106o TYR* 3.7 34.5 - + - -
107o TYR* 3.1 48.0 + + + +
110o ALA* 1.3 79.1 - - + +
112o ASN* 1.3 74.7 + - - +
113o ALA* 3.2 2.2 + - - +
99p MET* 3.7 28.0 - - + -
69r THR* 3.4 17.9 - - - +
70r GLY* 3.5 31.2 - - - -
71r PRO* 4.6 3.6 - - + -
72r ASN* 3.3 20.0 + - - +
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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
------------------------------------------------------------
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