Contacts of the strand formed by residues 101 - 111 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A VAL* 4.2 34.1 - - + -
103A THR* 4.6 2.5 - - + +
175A LYS* 6.1 3.4 - - - -
93C VAL* 3.7 28.5 - - + -
94C THR 3.3 4.5 - - - +
95C THR* 4.3 18.6 - - + +
99C GLY 3.5 8.3 + - - +
100C GLY* 1.3 79.2 - - - +
102C LEU* 1.3 61.2 + - - +
103C THR* 4.3 11.2 - - + -
122C ARG 3.8 1.4 - - - +
123C GLY* 3.3 1.7 - - - -
124C VAL* 2.9 39.4 + - + +
125C ASN* 5.5 0.7 - - + +
126C PHE* 3.9 2.7 - - - -
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Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C VAL* 4.3 8.7 - - + -
57C ILE* 3.8 48.0 - - + +
58C LEU* 4.3 4.5 - - + -
61C SER* 4.5 4.5 - - - +
92C ARG 4.0 0.7 - - - +
93C VAL* 3.8 0.5 - - - -
94C THR* 2.9 43.1 + - - +
96C TYR* 4.8 3.8 - - + -
100C GLY 4.2 0.4 - - - -
101C VAL* 1.3 74.1 - - - +
103C THR* 1.3 66.1 - - - +
104C ALA* 4.4 5.3 - - + +
121C ILE* 3.6 41.7 - - + -
122C ARG 3.6 2.2 - - - -
123C GLY* 4.0 4.0 - - - -
126C PHE* 4.2 12.9 - - + -
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Residues in contact with THR 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A VAL* 4.2 17.7 - - + -
103A THR* 3.4 39.6 + - + +
122A ARG* 3.8 22.0 - - - +
124A VAL* 4.5 12.6 - - + -
92C ARG 3.2 9.9 - - - +
93C VAL* 4.2 11.0 - - + -
101C VAL* 4.0 2.4 - - + -
102C LEU* 1.3 76.7 - - - +
104C ALA* 1.3 61.5 + - - +
121C ILE* 3.6 1.0 - - - -
122C ARG* 2.8 41.0 + - - +
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Residues in contact with ALA 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ARG* 4.8 0.2 - - - +
124A VAL* 4.4 0.3 - - - +
61C SER* 4.0 7.6 - - - +
90C TRP* 3.8 22.1 - - + -
91C GLU* 3.4 2.4 - - - -
92C ARG* 2.9 37.5 + - + +
102C LEU* 4.4 5.4 - - + +
103C THR* 1.3 77.1 - - - +
105C THR* 1.3 64.9 + - - +
119C VAL* 4.9 0.2 - - + -
120C LYS 3.2 5.8 - - - +
121C ILE* 3.8 23.8 - - + -
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Residues in contact with THR 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A THR* 4.1 11.4 - - + -
21A ASN* 5.8 2.7 - - - +
122A ARG* 3.4 34.6 + - + +
124A VAL* 4.0 15.5 - - + -
90C TRP 3.5 7.4 - - - -
91C GLU* 4.3 6.3 - - + +
104C ALA* 1.3 80.6 - - - +
106C GLN* 1.3 60.4 + - - +
118C ASN 3.8 1.0 - - - +
119C VAL* 3.5 2.6 - - - +
120C LYS* 2.7 72.0 + - - +
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Residues in contact with GLN 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C SER 5.2 0.2 + - - -
63C NRQ 3.0 22.4 + - - +
88C PHE 4.6 0.3 - - - +
89C THR* 3.3 9.5 - - - +
90C TRP* 2.9 74.0 + - + +
105C THR* 1.3 75.5 - - - +
107C ASP* 1.3 79.6 + - - +
108C THR* 2.5 32.3 + - - -
117C TYR* 3.5 21.0 - - - +
118C ASN 3.2 10.3 - - - +
119C VAL* 4.0 15.5 - - + +
120C LYS* 5.1 1.8 - - - +
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Residues in contact with ASP 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C PHE 4.1 2.0 - - - -
89C THR* 3.5 8.9 - - + +
106C GLN* 1.3 79.2 + - - +
108C THR* 1.3 60.9 + - - +
109C SER* 3.7 14.4 + - - -
116C ILE 3.3 6.2 - - - +
117C TYR* 3.3 2.9 - - - -
118C ASN* 3.0 45.0 + - + +
120C LYS* 6.3 0.9 - - - +
181C LYS* 3.0 34.2 + - - -
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Residues in contact with THR 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C NRQ 4.7 0.3 + - - -
68C THR* 4.4 1.6 - - - +
84C PHE* 3.8 25.4 - - + -
87C GLY* 3.4 4.0 - - - -
88C PHE* 3.0 50.9 + - + +
106C GLN* 2.5 33.5 + - - -
107C ASP* 1.3 70.2 - - - +
109C SER* 1.3 61.6 + - - +
115C LEU* 4.4 2.9 - - + -
116C ILE 3.6 2.9 - - - -
117C TYR* 3.6 21.4 - - + -
181C LYS* 3.1 15.0 + - - -
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Residues in contact with SER 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C PHE* 4.3 6.5 - - - -
86C GLU 5.3 2.5 - - - -
87C GLY* 4.9 2.5 - - - -
107C ASP* 3.7 13.4 + - - -
108C THR* 1.3 76.0 - - - +
110C LEU* 1.3 59.8 + - - +
111C GLN* 3.5 31.3 + - - -
115C LEU* 3.4 8.1 - - - +
116C ILE* 2.7 46.2 + - - +
118C ASN* 5.5 1.0 + - - -
181C LYS* 4.1 7.2 - - - +
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Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 3.6 40.8 - - + +
5C ILE* 4.6 1.3 - - + -
9C MET* 3.7 28.3 - - + -
84C PHE* 3.9 24.3 - - + -
85C PRO* 4.6 16.6 + - + +
109C SER* 1.3 74.6 - - - +
111C GLN* 1.3 69.9 + - - +
112C ASP 5.6 0.2 - - - +
113C GLY* 4.4 8.1 - - - +
114C CYS 3.4 21.8 - - - +
115C LEU* 3.9 8.5 - - + -
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Residues in contact with GLN 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C SER* 3.5 33.4 + - - -
110C LEU* 1.3 76.7 + - - +
112C ASP* 1.3 74.5 + - - +
113C GLY 3.4 0.7 - - - -
114C CYS* 3.0 27.2 + - - +
116C ILE* 4.0 22.2 - - + +
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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