Contacts of the helix formed by residues 102 - 117 (chain B) in PDB entry 1LK9
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 SER 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ASP* 4.2 17.8 + - - +
94B PHE* 3.5 22.7 - - - -
101B ILE* 1.3 73.7 - - - +
103B PHE* 1.3 64.6 + - - +
104B GLU* 3.6 6.8 + - - +
105B LEU* 3.2 25.8 + - - +
106B GLU* 3.0 21.5 + - - +
128B PHE* 3.8 0.4 - - - -
290B GLN* 2.8 29.4 + - - -
294B LEU* 5.2 0.5 - - - +
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Residues in contact with PHE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 4.0 36.6 - - + -
94B PHE* 5.5 1.0 - - - -
98B SER* 4.9 5.5 + - - +
101B ILE 3.2 6.3 + - - +
102B SER* 1.3 72.1 + - - +
104B GLU* 1.3 89.1 + - - +
106B GLU* 3.2 20.8 + - + +
107B LYS* 3.0 38.4 + - + +
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASP* 3.9 10.5 + - - +
30A GLY 3.5 19.1 - - - +
31A ILE* 3.5 9.0 - - + +
32A ILE* 2.9 40.4 + - + +
102B SER* 3.4 2.5 + - - +
103B PHE* 1.3 92.4 - - + +
105B LEU* 1.3 58.0 + - - +
107B LYS* 3.3 19.9 + - - +
108B THR* 3.0 31.2 + - - -
294B LEU* 3.8 22.2 - - + -
298B LYS* 4.8 8.9 + - - +
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B SER* 3.2 19.7 + - - +
103B PHE 3.2 0.6 - - - -
104B GLU* 1.3 76.7 - - - +
106B GLU* 1.3 64.5 + - - +
108B THR* 3.2 2.8 + - - -
109B ILE* 2.9 39.5 + - + +
128B PHE* 3.7 16.6 - - + -
260B PHE* 3.5 29.6 - - + -
290B GLN* 3.6 30.7 - - + +
293B SER* 4.0 7.0 - - - -
294B LEU* 3.7 36.2 - - + +
297B LEU* 4.1 12.8 - - + -
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Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ILE* 4.5 7.5 - - + +
102B SER 3.0 13.3 + - - +
103B PHE* 3.2 22.2 + - + +
105B LEU* 1.3 75.5 - - - +
107B LYS* 1.3 64.1 + - - +
109B ILE* 3.3 4.6 + - - +
110B LYS* 3.0 54.1 + - + +
124B ARG 4.5 1.0 - - - +
125B TYR* 5.5 0.3 - - - -
126B ILE* 3.2 36.0 + - + +
128B PHE* 3.9 11.1 - - + -
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Residues in contact with LYS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B PHE* 3.0 34.3 + - + +
104B GLU* 3.5 26.5 + - - +
105B LEU 3.2 0.2 - - - -
106B GLU* 1.3 80.0 - - - +
108B THR* 1.3 58.3 + - - +
110B LYS* 3.4 7.2 + - - +
111B GLU* 2.9 38.1 + - + +
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Residues in contact with THR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLU 3.0 13.5 + - - -
105B LEU* 3.7 4.9 - - + -
107B LYS* 1.3 74.6 - - - +
109B ILE* 1.3 61.4 - - - +
111B GLU* 3.2 10.1 + - - +
112B LEU* 2.9 27.5 + - - +
294B LEU* 3.5 7.1 - - + +
297B LEU* 3.7 42.4 - - + +
298B LYS* 3.0 36.8 + - + +
301B VAL* 4.2 6.5 - - + +
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Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LEU* 2.9 30.1 + - + +
106B GLU 3.7 3.6 - - - +
108B THR* 1.3 78.3 - - - +
110B LYS* 1.3 63.4 + - - +
112B LEU* 3.2 8.8 + - - +
113B HIS* 3.1 29.3 + - + +
126B ILE* 3.8 11.9 - - + -
128B PHE* 3.6 31.4 - - + -
260B PHE* 4.2 2.7 - - + -
262B TRP* 3.4 53.2 - - + +
264B LEU* 4.9 0.9 - - + -
297B LEU* 3.8 20.9 - - + -
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLU* 3.0 46.9 + - + +
107B LYS* 3.7 6.5 - - - +
109B ILE* 1.3 74.7 - - + +
111B GLU* 1.3 63.7 + - - +
113B HIS* 3.3 3.3 + - - +
114B GLU* 3.1 22.9 + - - +
121B ALA* 3.3 42.6 + - + +
122B LYS* 5.0 4.5 - - - +
123B ASP* 4.4 4.9 - - - +
124B ARG* 2.8 29.8 + - - +
126B ILE* 4.8 12.6 - - + -
264B LEU* 5.1 1.6 - - - -
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LYS* 2.9 28.1 + - + +
108B THR* 3.2 10.4 + - - +
110B LYS* 1.3 76.9 - - - +
112B LEU* 1.3 57.6 + - - +
114B GLU* 3.2 6.4 + - + +
115B VAL* 2.9 31.4 + - + +
301B VAL* 3.7 27.9 - - + +
305B LYS* 3.9 18.9 - - - +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B THR* 2.9 14.4 + - + +
109B ILE* 3.3 9.9 - - - +
111B GLU* 1.3 74.9 - - - +
113B HIS* 1.3 59.5 + - + +
115B VAL* 3.3 4.6 + - + +
116B VAL* 3.0 50.5 + - + +
230B TRP* 3.6 25.6 - - + -
252B PHE* 3.7 17.0 - - + -
262B TRP* 4.4 13.5 - - + -
297B LEU* 4.2 19.7 - - + +
300B VAL* 3.8 27.6 - - + -
301B VAL* 3.9 19.7 - - + +
304B VAL* 5.2 0.2 - - + -
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Residues in contact with HIS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ILE* 3.1 29.7 + - + -
110B LYS 3.9 5.4 - - - +
111B GLU 3.3 0.2 - - - -
112B LEU* 1.3 77.5 - - + +
114B GLU* 1.3 58.1 - - - +
117B GLY* 2.8 28.1 + - - -
118B ASN* 2.9 26.6 + - - +
119B ALA* 3.6 25.7 - - + +
121B ALA* 4.0 10.5 - - + -
230B TRP* 3.7 18.1 - + - -
247B PHE* 3.5 34.8 - + - -
262B TRP* 2.9 25.4 + + - -
264B LEU* 3.7 19.8 - - + +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LYS 3.1 17.4 + - - +
111B GLU* 3.6 7.4 - - + +
113B HIS* 1.3 78.8 - - - +
115B VAL* 1.3 63.3 + - - +
117B GLY* 3.5 11.2 + - - -
119B ALA 5.0 0.3 - - - +
121B ALA* 5.8 0.2 - - - +
122B LYS* 5.7 0.5 - - - +
239B LYS* 3.0 17.0 + - - +
908B SO4 3.0 34.2 + - - -
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B GLU* 2.9 17.7 + - + +
112B LEU* 3.3 13.0 + - + +
114B GLU* 1.3 79.0 - - - +
116B VAL* 1.3 65.3 + - + +
117B GLY* 4.7 0.2 - - - -
301B VAL* 4.8 11.7 - - + -
304B VAL* 3.5 42.2 - - + +
305B LYS* 3.9 32.8 - - + +
308B LYS* 5.2 3.5 + - - -
352B TYR* 4.4 4.2 - - - -
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LEU* 3.0 38.2 + - + +
115B VAL* 1.3 82.9 - - + +
117B GLY* 1.3 60.5 + - - +
118B ASN* 4.0 26.9 - - + +
230B TRP* 4.0 15.7 - - + -
231B PRO* 4.2 13.5 - - + -
236B ILE* 4.4 5.8 - - + +
304B VAL* 4.3 3.4 - - + -
315B ASN* 4.0 19.1 - - - +
351B ASN* 5.6 0.9 - - - +
352B TYR* 3.6 34.3 + - + +
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Residues in contact with GLY 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B HIS 2.8 13.0 + - - -
114B GLU 3.8 8.1 - - - -
115B VAL 3.4 2.2 - - - -
116B VAL* 1.3 77.9 - - - +
118B ASN* 1.3 59.9 + - - +
119B ALA 3.4 2.2 - - - -
236B ILE* 3.7 10.2 - - - +
238B TYR 3.8 0.7 - - - +
239B LYS* 3.4 35.6 + - - +
351B ASN* 5.6 2.9 + - - +
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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