Contacts of the strand formed by residues 101 - 111 (chain F) in PDB entry 3BXB
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 VAL 101 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93F VAL* 3.6 28.7 - - + -
94F THR 3.3 4.9 - - - +
95F THR* 4.4 17.3 - - + +
99F GLY 4.1 8.7 - - - +
100F GLY* 1.3 78.8 - - - +
102F LEU* 1.3 64.7 + - - +
122F ARG 3.7 1.9 - - - +
123F GLY* 3.0 2.8 - - - -
124F VAL* 2.9 41.8 + - + +
126F PHE* 3.8 2.6 - - - -
93G VAL* 4.2 38.6 - - + -
101G VAL* 4.5 1.3 - - + -
103G THR* 4.5 8.5 - - + -
175G LYS* 6.3 0.9 - - + -
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Residues in contact with LEU 102 (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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19F VAL* 4.2 4.7 - - + -
57F ILE* 3.9 47.6 - - + +
58F LEU* 4.5 1.6 - - + -
60F THR* 6.1 0.7 - - - +
61F SER* 4.4 7.0 - - - +
92F ARG* 3.8 1.7 - - - +
93F VAL* 3.6 1.2 - - - -
94F THR* 2.9 48.6 + - - +
96F TYR* 4.9 3.4 - - + -
100F GLY 4.3 0.2 - - - -
101F VAL* 1.3 73.6 - - - +
103F THR* 1.3 69.6 + - - +
104F ALA* 4.5 2.9 - - + +
121F ILE* 3.9 40.6 - - + -
122F ARG 3.7 1.6 - - - -
123F GLY* 4.2 10.1 - - - -
126F PHE* 4.2 11.9 - - + -
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Residues in contact with THR 103 (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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92F ARG 3.3 5.2 - - - -
93F VAL* 4.1 13.2 - - + -
101F VAL* 4.1 0.6 - - + -
102F LEU* 1.3 77.5 - - - +
104F ALA* 1.3 60.2 + - - +
121F ILE* 3.5 2.4 - - - -
122F ARG* 2.8 39.9 + - - +
101G VAL* 4.4 4.9 - - + -
103G THR* 2.9 38.9 + - + +
122G ARG* 3.7 14.2 - - - +
124G VAL* 3.7 33.2 - - + -
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Residues in contact with ALA 104 (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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61F SER* 4.1 14.1 - - - +
90F TRP* 3.6 25.8 - - + -
91F GLU* 3.4 0.9 - - - -
92F ARG* 2.9 36.6 + - + +
102F LEU* 4.5 5.2 - - + +
103F THR* 1.3 75.7 - - - +
105F THR* 1.3 67.9 + - - +
119F VAL* 4.9 1.3 - - + -
120F LYS 3.2 9.6 - - - +
121F ILE* 4.2 7.6 - - + -
122G ARG* 4.5 0.4 - - - +
124G VAL* 4.1 0.7 - - - +
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Residues in contact with THR 105 (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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90F TRP 3.4 6.5 - - - -
91F GLU* 4.5 7.9 - - + -
104F ALA* 1.3 81.5 - - - +
106F GLN* 1.3 60.5 + - - +
118F ASN 3.7 1.2 - - - +
119F VAL* 3.5 2.8 - - - -
120F LYS* 2.8 42.9 + - - +
18G THR* 4.5 13.2 + - + +
21G ASN* 4.3 11.0 - - - +
122G ARG* 2.9 45.4 + - + +
123G GLY 4.9 2.5 - - - +
124G VAL* 4.0 13.2 - - + -
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Residues in contact with GLN 106 (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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61F SER 5.3 0.8 + - - -
63F NRQ 3.5 12.5 + - - -
88F PHE 4.4 0.2 - - - +
89F THR* 3.3 9.4 - - - +
90F TRP* 2.7 79.8 + - + +
105F THR* 1.3 74.9 - - - +
107F ASP* 1.3 68.4 + - - +
108F THR* 2.5 31.8 + - - -
117F TYR* 3.4 30.9 - - - +
118F ASN 3.3 4.3 - - - +
119F VAL* 3.8 20.4 - - + +
21G ASN* 4.4 2.4 + - - +
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Residues in contact with ASP 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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88F PHE 4.1 1.8 - - - -
89F THR* 3.6 15.1 - - + +
106F GLN* 1.3 78.1 + - - +
108F THR* 1.3 60.6 + - - +
109F SER* 3.8 14.0 + - - -
116F ILE 3.4 4.0 - - - +
117F TYR* 3.5 2.3 - - - -
118F ASN* 2.9 47.4 + - + +
181F LYS* 3.1 27.4 + - - +
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Residues in contact with THR 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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63F NRQ 4.8 0.9 + - - -
68F THR* 4.6 0.9 - - - +
84F PHE* 4.1 11.2 - - + -
87F GLY* 3.4 4.2 - - - -
88F PHE* 2.8 74.7 + - + +
90F TRP* 4.7 0.2 - - - -
106F GLN* 2.5 32.6 + - - -
107F ASP* 1.3 74.2 + - - +
109F SER* 1.3 65.5 + - - +
115F LEU* 4.4 2.0 - - + -
116F ILE 3.5 2.7 - - - -
117F TYR* 3.7 22.5 - - + -
181F LYS* 3.8 3.8 + - - -
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Residues in contact with SER 109 (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 PHE* 4.4 5.2 - - - -
86F GLU 4.8 4.5 - - - -
87F GLY* 4.7 2.7 - - - -
107F ASP* 3.8 14.1 + - - -
108F THR* 1.3 74.6 - - - +
110F LEU* 1.3 64.2 + - - +
111F GLN 4.3 0.2 - - - -
115F LEU* 3.2 15.1 - - - +
116F ILE* 3.0 42.3 + - - +
118F ASN* 5.6 1.6 + - - -
181F LYS* 4.2 9.0 - - - -
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Residues in contact with LEU 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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4F LEU* 4.4 19.1 - - + +
5F ILE* 4.3 9.4 - - + -
9F MET* 4.3 9.4 - - + -
84F PHE* 3.9 37.0 - - + -
85F PRO* 4.4 21.9 + - + +
109F SER* 1.3 82.6 + - - +
111F GLN* 1.3 64.2 + - - +
112F ASP 4.3 0.3 + - - -
113F GLY* 3.7 16.4 - - - +
114F CYS 3.6 33.2 - - - +
115F LEU* 4.1 10.8 - - + +
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Residues in contact with GLN 111 (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 SER 4.3 0.2 - - - -
110F LEU* 1.3 75.3 - - - +
112F ASP* 1.3 105.7 + - - +
113F GLY 3.1 2.7 - - - -
114F CYS* 2.9 25.9 + - - +
116F ILE* 4.3 15.3 - - + +
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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