Contacts of the helix formed by residues 94 - 117 (chain J) in PDB entry 4LLL
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 THR 94 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75J LYS* 2.6 29.8 + - + +
76J LEU* 3.0 17.0 + - - -
77J ILE 4.5 7.9 - - - +
78J TYR* 4.0 21.1 - - + -
92J GLY 3.9 1.4 + - - -
93J LEU* 1.3 75.1 - - - +
95J THR* 1.3 55.2 + - - +
96J SER* 3.8 5.1 - - - -
97J GLY 3.4 3.1 + - - -
98J ILE* 2.7 35.3 + - - +
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Residues in contact with THR 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94J THR* 1.3 73.1 - - - +
96J SER* 1.3 55.4 + - - +
98J ILE* 3.0 12.9 + - - +
99J LYS* 2.7 50.9 + - - +
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Residues in contact with SER 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74J LYS 4.5 4.5 + - - -
75J LYS* 3.9 10.4 + - - -
76J LEU* 3.3 17.1 - - - +
94J THR* 3.8 12.3 - - - -
95J THR* 1.3 77.5 - - - +
97J GLY* 1.3 62.9 + - - -
99J LYS* 3.3 7.3 + - - +
100J LEU* 3.0 23.0 + - - +
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Residues in contact with GLY 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J LEU* 4.9 2.6 - - - +
76J LEU* 3.4 36.5 - - - +
93J LEU* 4.4 6.7 - - - -
94J THR* 3.1 8.9 + - - -
96J SER* 1.3 79.3 + - - +
98J ILE* 1.3 61.7 + - - +
100J LEU* 3.3 2.8 + - - +
101J VAL* 3.0 30.8 + - - +
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Residues in contact with ILE 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J TYR* 4.1 11.3 - - + -
93J LEU* 3.6 37.6 - - + +
94J THR 2.7 26.6 + - - +
95J THR* 3.4 9.2 - - - +
97J GLY* 1.3 73.4 - - - +
99J LYS* 1.3 66.4 + - + +
101J VAL* 3.3 4.3 + - - +
102J GLU* 3.1 43.3 + - - +
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Residues in contact with LYS 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95J THR* 2.7 35.7 + - - +
96J SER* 3.9 6.7 - - - +
98J ILE* 1.3 77.9 - - + +
100J LEU* 1.3 62.6 + - - +
102J GLU* 3.5 13.0 + - - +
103J ALA* 3.3 20.3 + - - +
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Residues in contact with LEU 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J PHE* 3.4 41.7 - - + +
29J ILE* 4.1 15.0 - - + -
37J LEU* 3.9 14.1 - - + -
76J LEU* 3.9 32.8 - - + -
96J SER 3.0 13.7 + - - +
97J GLY 3.5 9.4 - - - +
98J ILE 3.2 0.2 - - - -
99J LYS* 1.3 75.1 - - - +
101J VAL* 1.3 60.9 + - - +
103J ALA* 2.8 21.4 + - + +
104J PHE* 3.0 27.2 + - + -
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Residues in contact with VAL 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J LEU* 3.8 33.9 - - + -
38J GLY* 4.4 9.0 - - - -
41J TYR* 3.6 35.4 - - + -
93J LEU* 4.4 11.4 - - + -
97J GLY 3.0 16.8 + - - +
98J ILE 3.3 6.5 + - - +
100J LEU* 1.3 74.5 - - - +
102J GLU* 1.3 62.3 + - - +
103J ALA 3.2 0.7 + - - -
104J PHE* 3.4 14.4 - - + -
105J THR* 2.4 41.0 + - - +
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Residues in contact with GLU 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J TYR* 2.7 32.6 + - + +
98J ILE* 3.1 29.2 + - - +
99J LYS* 3.7 12.2 + - - +
100J LEU 3.2 0.6 - - - -
101J VAL* 1.3 76.6 - - - +
103J ALA* 1.3 62.6 + - - +
105J THR* 4.4 5.4 + - - -
106J SER* 4.9 3.6 + - - -
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Residues in contact with ALA 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J PHE* 3.5 26.1 - - + -
99J LYS 3.3 10.0 + - - +
100J LEU* 2.8 12.2 + - + +
102J GLU* 1.3 82.8 - - - +
104J PHE* 1.3 62.0 + - - +
105J THR 3.5 0.9 + - - -
106J SER* 3.6 15.1 + - - -
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Residues in contact with PHE 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J LEU* 3.8 18.6 - - + -
27J PHE* 3.5 33.7 - + + -
29J ILE* 3.9 8.1 - - + -
34J GLY* 3.4 35.0 - - - -
37J LEU* 3.8 13.0 - - + -
38J GLY* 5.2 1.1 - - - -
100J LEU* 3.0 40.6 + - + -
101J VAL* 3.4 34.1 - - + -
103J ALA* 1.3 72.3 - - - +
105J THR* 1.3 67.2 + - - +
106J SER* 3.0 6.7 - - - -
107J ILE* 2.8 29.1 + - - +
108J PHE* 3.7 20.5 + + - -
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Residues in contact with THR 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J GLY* 5.8 0.5 - - - -
101J VAL* 2.4 37.4 + - - +
102J GLU* 4.7 4.3 - - - -
103J ALA 3.3 2.4 - - - -
104J PHE* 1.3 83.9 - - - +
106J SER* 1.3 65.0 + - - +
108J PHE* 3.5 11.8 + - + +
109J ASP* 3.3 32.8 + - - +
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Residues in contact with SER 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J GLU 4.9 3.4 + - - -
103J ALA 3.6 14.2 + - - -
104J PHE 4.7 0.2 - - - -
105J THR* 1.3 78.5 - - - +
107J ILE* 1.3 59.5 + - - +
109J ASP* 2.9 9.2 + - - +
110J GLU* 2.9 46.5 + - - +
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Residues in contact with ILE 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J ALA* 6.3 0.2 - - - -
23J LYS* 4.1 32.9 - - + +
24J LEU* 4.7 13.2 - - + -
27J PHE* 5.7 2.5 - - + -
104J PHE* 2.8 14.0 + - + +
106J SER* 1.3 80.2 - - - +
108J PHE* 1.3 65.0 + - + +
110J GLU* 3.7 15.4 + - - +
111J MET* 3.7 22.6 + - + +
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Residues in contact with PHE 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I SER* 5.0 10.7 + - - +
20J ALA* 4.5 14.1 - - + -
24J LEU* 4.1 20.9 - - + -
31J ASN* 3.6 19.7 - - + -
34J GLY* 3.5 22.4 - - - -
35J HIS* 3.2 52.3 - + - +
38J GLY* 6.0 1.1 - - - -
104J PHE* 3.7 23.9 + + - -
105J THR* 3.5 14.7 + - + +
106J SER 3.2 0.8 - - - -
107J ILE* 1.3 81.9 - - + +
109J ASP* 1.3 69.4 + - - +
111J MET* 3.8 9.7 + - - +
112J GLU* 3.6 14.6 + - - +
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Residues in contact with ASP 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J THR* 3.5 22.8 - - - +
106J SER* 2.9 10.1 + - - +
108J PHE* 1.3 81.9 - - - +
110J GLU* 1.3 68.0 + - - +
112J GLU* 2.9 11.3 + - + +
113J GLN* 2.9 26.0 + - + +
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Residues in contact with GLU 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106J SER* 2.9 43.6 + - - +
107J ILE* 3.9 9.4 - - - +
108J PHE 3.4 0.2 - - - -
109J ASP* 1.3 72.7 - - - +
111J MET* 1.3 53.1 + - + +
113J GLN* 3.1 9.4 + - - +
114J THR* 2.4 43.7 + - - +
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Residues in contact with MET 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I SER* 6.2 1.6 - - - -
138I LEU* 6.5 0.7 - - + -
16J MET* 4.5 28.9 - - + +
19J LYS* 3.4 19.7 - - + +
20J ALA* 3.2 47.3 - - + +
23J LYS* 4.1 15.3 - - + -
107J ILE* 3.7 15.2 + - + +
108J PHE* 4.0 12.8 - - - +
110J GLU* 1.3 76.2 - - + +
112J GLU* 1.3 56.4 + - - +
114J THR* 3.5 8.7 - - - -
115J LEU* 2.7 45.4 + - + +
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Residues in contact with GLU 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I PHE 4.4 1.0 - - - +
4I THR* 3.1 27.5 + - - +
5I TYR* 2.7 44.8 + - - +
6I SER* 3.6 10.6 + - - -
16J MET* 5.5 1.2 - - - +
108J PHE 3.6 5.8 + - - +
109J ASP* 2.9 16.5 + - + +
111J MET* 1.3 77.4 - - - +
113J GLN* 1.3 60.2 + - + +
115J LEU* 3.0 2.7 + - - -
116J VAL* 2.8 46.5 + - + +
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Residues in contact with GLN 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J ASP* 2.9 13.9 + - + +
110J GLU* 3.6 10.8 - - - +
112J GLU* 1.3 78.4 - - + +
114J THR* 1.3 51.9 + - - +
116J VAL* 4.8 8.3 - - - +
117J SER* 2.6 44.0 + - - +
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Residues in contact with THR 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137I SER* 5.6 6.7 - - - +
138I LEU* 6.3 1.6 - - + -
110J GLU* 2.4 37.4 + - - +
111J MET* 3.7 9.7 - - - -
112J GLU 3.0 0.2 - - - -
113J GLN* 1.3 74.9 - - - +
115J LEU* 1.3 66.8 + - + +
117J SER* 3.2 13.3 + - - -
118J GLN* 3.3 17.4 - - - +
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Residues in contact with LEU 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I TYR* 4.2 25.1 - - + -
134I MET* 4.5 20.4 - - + +
137I SER* 4.3 0.9 - - - +
138I LEU* 4.2 24.9 - - + -
12J ILE* 5.2 7.6 - - + -
16J MET* 4.0 30.7 - - + -
111J MET* 2.7 35.2 + - + +
112J GLU* 3.8 1.8 - - - +
114J THR* 1.3 76.5 - - + +
116J VAL* 1.3 58.2 + - - +
117J SER 3.1 1.3 - - - -
118J GLN* 2.8 47.9 + - - +
119J LEU 4.1 0.9 + - - -
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Residues in contact with VAL 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I TYR* 3.5 32.5 - - + -
112J GLU* 2.8 41.7 + - + +
113J GLN* 4.8 7.9 - - - +
115J LEU* 1.3 71.2 - - - +
117J SER* 1.3 58.4 + - - +
119J LEU* 2.9 28.1 + - - +
124J ASN* 3.4 22.3 + - - +
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Residues in contact with SER 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J GLN* 2.6 34.8 + - - +
114J THR* 3.2 12.0 + - - -
116J VAL* 1.3 77.7 - - - +
118J GLN* 1.3 64.0 + - - +
119J LEU 3.1 2.8 + - - -
120J SER* 4.0 14.0 + - - +
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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