Contacts of the helix formed by residues 104 - 121 (chain F) in PDB entry 5LN3
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 PRO 104 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267 HIS* 3.6 32.5 - - + +
1277 SER* 4.1 11.7 - - - +
101F ARG* 6.0 0.7 - - - -
103F LEU* 1.3 96.1 - - + +
105F VAL* 1.4 52.9 + - - +
106F SER* 4.2 9.2 - - - +
107F ARG* 2.9 43.1 + - + +
108F LEU* 2.9 16.3 + - - +
138F ASP* 4.9 12.3 - - + -
139F ASP* 4.2 10.3 - - - +
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Residues in contact with VAL 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ILE* 3.9 38.8 - - + -
103F LEU 3.4 4.3 + - - -
104F PRO* 1.4 68.3 - - - +
106F SER* 1.4 60.7 + - - +
108F LEU* 3.2 12.7 + - + +
109F VAL* 2.9 37.8 + - + +
134F ILE* 4.3 15.5 - - + -
135F ALA 4.8 2.0 - - - +
136F GLY* 4.7 12.6 - - - +
138F ASP* 3.4 30.6 - - + +
143F HIS* 4.9 3.1 - - + +
145F PHE* 4.7 12.6 - - + -
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Residues in contact with SER 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F PRO* 4.4 8.9 - - - +
105F VAL* 1.4 66.4 - - - +
107F ARG* 1.4 62.1 + - - +
109F VAL* 3.4 3.7 + - - +
110F SER* 3.2 26.7 + - - -
138F ASP* 4.8 2.1 + - - -
143F HIS* 4.4 14.6 + - - -
145F PHE* 3.5 32.4 - - - -
62G GLY 5.9 1.8 - - - -
63G SER* 5.4 8.4 + - - -
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Residues in contact with ARG 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197 GLU* 3.6 32.7 + - - +
1207 GLU* 3.3 32.3 + - - +
1217 LEU* 3.6 42.6 + - - +
1227 LEU 4.7 3.6 + - - -
1267 HIS* 5.8 4.0 - - - +
1277 SER* 5.7 3.3 + - - +
103F LEU* 4.0 19.1 - - + -
104F PRO* 2.9 28.8 + - + +
106F SER* 1.4 77.3 - - - +
108F LEU* 1.3 67.2 + - - +
109F VAL 3.4 0.2 + - - -
110F SER* 3.6 10.7 + - - -
111F LEU* 3.5 21.0 + - + +
86G ARG* 4.9 4.8 - - - +
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Residues in contact with LEU 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F VAL* 6.4 0.7 - - + -
70F ILE* 4.1 20.4 - - + -
88F MET* 5.0 12.1 - - + +
91F GLU* 4.1 35.2 - - + +
92F CYS* 4.1 24.5 - - - -
102F PRO 6.2 0.4 - - - +
103F LEU* 4.2 16.1 - - + +
104F PRO 2.9 11.2 + - - +
105F VAL* 3.3 15.3 - - + +
107F ARG* 1.3 77.2 - - - +
109F VAL* 1.3 65.5 + - + +
111F LEU* 3.2 23.1 + - + +
112F ILE* 3.3 20.1 + - + +
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Residues in contact with VAL 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F MET* 6.5 1.1 - - - -
105F VAL* 2.9 31.7 + - + +
106F SER* 3.4 6.7 + - - +
107F ARG 3.3 0.2 - - - -
108F LEU* 1.3 79.4 - - + +
110F SER* 1.3 66.3 - - - +
112F ILE* 3.4 15.3 + - - +
113F GLY* 3.4 10.0 + - - -
134F ILE* 3.9 25.6 - - + -
145F PHE* 4.5 22.9 - - + -
147F THR* 4.1 16.8 - - + +
153F TYR* 4.3 21.7 - - + +
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Residues in contact with SER 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F SER 3.2 11.3 + - - -
107F ARG* 3.7 11.6 - - - -
109F VAL* 1.3 79.4 - - - +
111F LEU* 1.4 64.0 + - - +
113F GLY* 3.3 10.5 + - - -
114F SER* 3.6 13.7 + - - -
153F TYR* 4.5 17.3 - - - -
63G SER* 4.3 16.6 + - - -
86G ARG* 6.0 7.2 - - - -
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Residues in contact with LEU 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1197 GLU* 6.1 1.1 - - - +
91F GLU* 4.5 12.8 - - - +
103F LEU* 4.5 13.2 - - + -
107F ARG* 3.5 20.6 - - + +
108F LEU* 3.2 20.4 + - + +
110F SER* 1.4 74.2 - - - +
112F ILE* 1.4 63.3 + - - +
114F SER* 3.2 20.9 + - - -
115F LYS* 3.9 10.2 + - - +
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Residues in contact with ILE 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F LEU* 5.4 0.9 - - + +
87F PHE* 4.7 4.5 - - + -
88F MET* 3.9 45.8 - - + -
91F GLU* 3.4 31.6 - - - +
108F LEU* 3.3 19.6 + - + +
109F VAL* 3.4 10.5 + - - +
111F LEU* 1.4 70.5 - - - +
113F GLY* 1.4 68.6 - - - +
115F LYS* 3.3 33.8 + - - +
116F THR* 3.7 14.2 + - + +
147F THR* 6.0 6.1 - - + -
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Residues in contact with GLY 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F VAL 3.4 7.0 + - - -
110F SER 3.3 7.5 + - - -
111F LEU 3.2 1.6 - - - -
112F ILE* 1.4 80.3 - - - +
114F SER* 1.4 58.6 + - - +
116F THR* 2.8 22.9 + - - -
117F GLN* 3.2 12.7 + - - +
147F THR* 6.3 2.7 - - - -
151F ALA* 4.1 14.4 - - - +
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Residues in contact with SER 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F SER 3.6 12.1 + - - -
111F LEU* 3.2 11.3 + - - -
113F GLY* 1.4 74.5 - - - +
115F LYS* 1.3 65.8 + - - +
117F GLN* 3.0 16.8 + - - +
118F ILE* 3.2 31.2 + - - +
86G ARG* 5.7 2.1 - - - +
87G SER* 4.6 11.1 + - - -
90G ASP* 4.3 13.7 + - - -
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Residues in contact with LYS 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F PHE* 3.7 29.6 - - - +
91F GLU* 3.1 29.0 + - - +
111F LEU 3.9 11.9 - - - +
112F ILE* 3.5 23.8 - - - +
113F GLY 3.2 0.2 - - - -
114F SER* 1.3 83.4 - - - +
116F THR* 1.3 58.5 + - + +
118F ILE* 4.6 3.3 - - - +
119F PRO* 2.9 24.1 - - - +
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Residues in contact with THR 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F LEU* 5.5 7.0 - - + -
112F ILE* 3.8 12.1 + - + +
113F GLY* 2.8 23.6 + - - -
115F LYS* 1.3 79.6 - - + +
117F GLN* 1.3 59.6 + - - +
118F ILE 3.3 0.7 - - - -
119F PRO* 3.2 14.4 - - - +
120F THR* 3.2 14.6 + - - -
125F ARG* 4.2 8.4 + - - -
128F TYR* 3.6 36.3 - - + +
151F ALA* 4.3 9.0 - - - +
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Residues in contact with GLN 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F GLY 3.2 13.2 + - - +
114F SER* 3.0 9.7 + - - +
116F THR* 1.3 75.4 - - - +
118F ILE* 1.3 57.1 + - - +
120F THR* 3.1 24.9 + - - +
121F GLN* 3.2 16.6 + - - +
150F SER 3.8 12.7 + - - -
151F ALA* 3.7 23.1 - - + +
81G LEU* 5.7 2.2 - - - +
83G ALA* 4.1 16.5 - - + +
84G ASP* 4.1 17.6 + - - +
87G SER* 4.0 19.3 - - - +
130G ARG* 3.5 20.4 + - - -
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Residues in contact with ILE 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F SER* 3.4 24.7 - - - +
115F LYS* 4.6 2.7 - - - +
117F GLN* 1.3 75.6 - - - +
119F PRO* 1.3 68.9 - - + +
121F GLN* 3.2 42.0 + - + +
122F ARG* 3.5 18.2 + - - +
87G SER* 4.3 19.1 - - - +
91G ILE* 5.4 9.9 - - + -
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Residues in contact with PRO 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E ASP* 4.5 13.7 - - + +
115F LYS 2.9 28.7 - - - +
116F THR* 3.2 11.2 - - - +
118F ILE* 1.3 87.9 - - + +
120F THR* 1.4 59.1 + - - +
121F GLN 3.2 1.3 - - - -
122F ARG* 3.1 41.8 - - + +
123F TYR 4.5 0.3 - - - +
124F GLY 3.2 13.2 - - - +
125F ARG* 3.6 21.5 - - + +
128F TYR* 5.1 3.8 - - - +
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Residues in contact with THR 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F VAL* 3.7 20.3 - - + +
11F THR* 5.5 0.3 - - - +
19F ILE* 6.2 0.2 - - + -
21F GLN* 5.8 7.2 - - + -
22F ILE* 6.0 6.3 - - + -
116F THR 3.2 15.4 + - - -
117F GLN* 3.1 16.5 + - - +
119F PRO* 1.4 72.3 - - - +
121F GLN* 1.3 57.6 - - - +
122F ARG 3.1 12.0 + - - +
124F GLY 5.1 0.9 - - - -
125F ARG* 3.3 34.8 + - - +
127F PRO* 6.1 1.3 - - + -
130G ARG* 3.2 39.8 + - - +
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Residues in contact with GLN 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F GLN* 3.4 13.3 + - - +
118F ILE* 3.3 40.1 - - + +
119F PRO 3.2 0.2 - - - -
120F THR* 1.3 77.4 - - - +
122F ARG* 1.3 59.2 + - - +
84G ASP* 3.6 20.7 - - - +
87G SER* 4.1 16.0 + - - -
129G VAL* 3.5 25.8 - - + +
130G ARG* 3.6 38.0 + - + +
131G PRO 5.1 0.7 - - - +
132G PHE* 3.5 35.0 - - - -
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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