Contacts of the strand formed by residues 144 - 157 (chain F) in PDB entry 3DOY
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 LYS 144 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111F ILE* 4.0 29.8 - - + +
140F GLN* 3.2 5.0 - - - -
141F VAL 3.0 31.9 + - - +
142F ASP 4.5 5.6 - - - +
143F GLY* 1.3 80.4 - - - +
145F VAL* 1.3 65.7 + - - +
146F VAL* 3.2 4.3 + - + +
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Residues in contact with VAL 145 (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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110F ARG* 3.9 24.9 - - - +
111F ILE* 3.7 13.5 - - - +
138F THR* 4.1 18.6 - - + +
139F ALA 3.6 4.7 - - - -
140F GLN* 4.0 14.6 - - + +
143F GLY 4.3 1.0 + - - +
144F LYS* 1.3 72.3 - - - +
146F VAL* 1.3 59.5 + - - +
147F ALA* 3.4 29.8 - - - +
148F GLU* 3.9 15.0 - - + +
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Residues in contact with VAL 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ILE* 4.8 2.6 - - + +
109F PHE* 3.6 3.8 - - - +
110F ARG* 2.9 23.4 + - - -
111F ILE* 3.4 41.8 + - + +
112F PRO 5.5 0.2 - - - +
113F VAL* 3.7 22.2 - - + -
119F LEU* 4.0 4.9 - - + -
139F ALA* 2.8 32.8 + - + +
141F VAL* 3.4 29.6 - - + +
144F LYS* 3.5 12.8 - - + +
145F VAL* 1.3 73.6 - - - +
147F ALA* 1.3 64.3 + - + +
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Residues in contact with ALA 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ILE* 4.2 9.0 - - + -
71F VAL* 6.5 0.2 - - + -
74F MET* 5.3 2.7 - - - -
108F LYS 3.1 14.1 - - - +
109F PHE* 3.8 20.4 - - + -
110F ARG* 4.6 1.1 - - - +
138F THR* 3.2 9.2 - - - -
139F ALA* 2.9 38.3 + - + -
145F VAL* 3.4 4.9 - - - +
146F VAL* 1.3 86.9 - - + +
148F GLU* 1.3 66.8 + - - +
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Residues in contact with GLU 148 (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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71F VAL* 5.8 0.2 - - - +
74F MET* 4.6 1.1 - - - -
106F LYS 4.1 8.1 - - - +
107F VAL* 3.2 19.6 - - - +
108F LYS* 3.0 38.0 + - - +
109F PHE* 5.8 0.7 - - - -
110F ARG* 2.6 39.3 + - - +
137F GLY 3.4 10.1 - - - +
138F THR* 4.2 7.4 - - + +
145F VAL* 3.9 12.8 - - + +
147F ALA* 1.3 79.7 - - - +
149F ALA* 1.3 67.3 + - - +
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Residues in contact with ALA 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F VAL* 4.9 13.7 - - + -
74F MET* 3.8 23.5 - - + +
105F ASP 4.2 0.7 - - - -
106F LYS 3.9 9.1 + - - -
107F VAL* 4.1 15.7 - - + +
123F LEU* 5.2 0.2 - - - +
136F GLY* 3.1 2.3 - - - -
137F GLY 2.8 37.7 + - - +
148F GLU* 1.3 78.4 - - - +
150F GLU* 1.3 69.1 + - - +
151F LEU* 5.4 4.5 - - + -
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Residues in contact with GLU 150 (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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104F ILE* 3.5 4.5 - - - +
105F ASP* 2.9 43.7 + - + +
106F LYS* 3.3 39.5 + - + +
126F LEU* 4.0 21.2 - - + +
134F GLN* 5.1 9.3 + - - +
135F VAL 3.3 9.0 - - - +
136F GLY* 3.9 5.8 - - - -
137F GLY 5.3 0.4 - - - +
149F ALA* 1.3 80.3 - - - +
151F LEU* 1.3 65.5 + - - +
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Residues in contact with LEU 151 (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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71F VAL* 4.2 14.4 - - + +
74F MET* 4.2 9.4 - - + -
75F ALA* 3.7 46.7 - - + +
101F PHE* 3.9 14.8 - - + -
103F THR* 3.3 15.7 - - - +
104F ILE* 4.4 2.9 - - + -
123F LEU* 5.0 2.2 - - + -
133F TRP 3.8 0.6 - - - +
134F GLN* 3.4 6.9 - - - +
135F VAL* 2.7 57.3 + - + +
149F ALA* 5.4 4.5 - - + -
150F GLU* 1.3 78.3 - - - +
152F LYS* 1.3 69.5 + - - +
153F ALA* 4.4 9.6 - - + +
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Residues in contact with LYS 152 (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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101F PHE* 4.2 1.9 - - - -
102F MET* 2.8 50.2 + - - +
103F THR* 3.0 41.9 + - - +
132F ILE* 3.6 26.2 - - + +
133F TRP 3.1 15.9 - - - +
134F GLN* 4.2 22.0 - - + +
151F LEU* 1.3 75.4 - - - +
153F ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 153 (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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75F ALA* 5.6 7.4 - - + +
79F GLY* 6.2 2.5 - - - -
99F VAL* 4.0 16.8 - - + -
100F TYR 3.2 14.4 - - - +
101F PHE* 4.6 5.4 - - + -
102F MET* 4.1 4.5 - - - +
131F MET 3.6 1.9 - - - +
132F ILE* 3.7 1.9 - - - +
133F TRP* 2.9 34.2 + - + +
151F LEU* 4.2 14.3 - - + +
152F LYS* 1.3 75.4 - - - +
154F MET* 1.3 62.0 + - - +
155F ILE* 4.2 1.2 + - - +
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Residues in contact with MET 154 (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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99F VAL* 3.4 4.3 - - - -
100F TYR* 2.7 66.5 + - + +
102F MET* 3.7 30.9 - - + +
131F MET* 3.5 12.3 - - + +
132F ILE* 4.5 11.9 - - + -
153F ALA* 1.3 74.5 - - - +
155F ILE* 1.3 74.6 + - - +
156F ALA* 3.8 5.9 + - + -
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Residues in contact with ILE 155 (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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79F GLY* 4.8 1.3 - - - +
82F ALA* 3.6 30.3 - - + -
83F PHE* 4.0 23.1 - - + +
86F LEU* 3.9 20.6 - - + -
87F TRP* 3.8 22.2 - - + -
97F LYS* 3.8 21.1 - - + -
98F ILE 3.5 5.2 - - - +
99F VAL* 4.4 16.6 - - + +
131F MET* 3.0 47.2 + - - +
133F TRP* 4.8 0.4 - - + -
153F ALA 5.6 1.6 - - - +
154F MET* 1.3 78.7 - - - +
156F ALA* 1.3 63.5 + - - +
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Residues in contact with ALA 156 (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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97F LYS* 2.9 13.7 - - - -
98F ILE* 2.9 34.0 + - + +
100F TYR* 4.0 30.1 - - + -
131F MET* 5.4 1.3 - - - -
154F MET* 3.8 8.5 + - + -
155F ILE* 1.3 76.5 - - - +
157F GLU* 1.3 63.7 + - - +
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Residues in contact with GLU 157 (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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62E LYS* 5.0 2.1 - - - -
96F THR* 2.7 34.1 + - - +
97F LYS* 2.6 35.5 + - - +
98F ILE* 4.8 1.4 - - - +
156F ALA* 1.3 74.8 - - - +
158F ARG* 1.3 70.4 + - - +
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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