Contacts of the strand formed by residues 114 - 124 (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 CYS 114 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F HIS* 3.7 25.8 - - + -
11F MET 3.9 0.9 - - - -
12F LYS* 3.3 49.1 - - + +
110F LEU* 3.6 3.7 - - - +
111F GLN 2.9 29.1 + - - +
112F ASP* 4.5 4.0 - - + +
113F GLY* 1.3 80.5 - - - +
115F LEU* 1.3 71.5 + - - +
116F ILE* 3.4 5.5 - - + +
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Residues in contact with LEU 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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5F ILE* 4.7 3.8 - - + -
9F MET* 4.8 11.2 - - + -
10F HIS 3.1 13.4 + - - +
11F MET* 3.3 2.5 - - + -
12F LYS 2.8 27.6 + - - +
68F THR* 4.1 16.2 - - + +
69F PHE* 3.6 36.6 - - + -
84F PHE* 3.5 36.3 - - + -
108F THR* 4.4 4.0 - - + -
109F SER 3.2 16.6 - - - +
110F LEU* 4.2 12.8 - - + -
114F CYS* 1.3 72.2 - - - +
116F ILE* 1.3 62.2 + - - +
117F TYR* 3.8 19.3 - - + +
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Residues in contact with ILE 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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12F LYS* 3.4 35.0 - - + +
14F TYR* 3.9 26.7 - - + -
107F ASP 3.4 4.7 - - - +
109F SER* 3.0 42.0 + - - +
111F GLN* 4.3 20.9 - - + +
114F CYS* 3.4 18.4 - - + +
115F LEU* 1.3 71.6 - - - +
117F TYR* 1.3 65.3 + - - +
118F ASN* 4.0 17.3 + - - +
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Residues in contact with TYR 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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11F MET* 4.0 6.3 - - + -
12F LYS 2.9 13.0 + - - +
13F LEU* 3.4 15.7 - - + -
14F TYR* 2.9 32.3 + - - -
41F MET* 3.5 30.3 - - + -
62F PHE 3.7 11.7 - - - -
66F SER* 2.7 39.9 + - - -
68F THR* 4.8 2.8 + - - -
69F PHE* 3.3 20.8 - - - -
88F PHE* 6.0 0.2 - + - -
106F GLN* 3.4 22.0 - - - +
107F ASP 3.5 2.9 - - - -
108F THR* 3.7 23.6 - - + -
115F LEU* 3.8 19.7 - - + +
116F ILE* 1.3 80.9 - - - +
118F ASN* 1.3 61.2 + - - +
119F VAL* 4.1 1.3 - - + -
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Residues in contact with ASN 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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14F TYR* 3.6 24.2 - - - +
105F THR 3.7 1.7 - - - +
106F GLN* 3.3 2.8 - - - +
107F ASP* 2.9 51.3 + - + +
109F SER* 5.6 1.6 + - - -
116F ILE* 4.0 21.2 - - - +
117F TYR* 1.3 73.6 - - - +
119F VAL* 1.3 60.9 + - - +
120F LYS* 4.1 4.5 + - + +
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Residues in contact with VAL 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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13F LEU* 3.9 19.7 - - + -
14F TYR 2.9 16.0 + - - +
15F MET* 3.3 13.4 - - + +
16F GLU 3.0 25.0 + - - +
61F SER* 3.6 40.6 - - - +
90F TRP* 4.3 5.6 - - + -
104F ALA* 4.9 0.7 - - + -
105F THR 3.5 8.3 - - - +
106F GLN* 3.8 18.8 - - + -
117F TYR* 4.6 0.7 - - + -
118F ASN* 1.3 78.7 + - - +
120F LYS* 1.3 72.2 + - - +
121F ILE* 4.5 3.8 - - + -
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Residues in contact with LYS 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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16F GLU* 3.4 24.9 - - + +
104F ALA* 3.2 4.7 - - - +
105F THR* 2.8 43.0 + - - +
118F ASN* 5.5 3.8 - - + +
119F VAL* 1.3 78.9 - - - +
121F ILE* 1.3 62.6 + - - +
122F ARG* 6.3 0.2 - - - +
16G GLU* 5.4 3.8 + - - +
18G THR* 5.0 2.8 + - - -
23G HIS* 4.4 21.8 + - - -
122G ARG* 3.5 40.2 - - - +
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Residues in contact with ILE 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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15F MET* 4.1 20.0 - - + -
16F GLU 2.9 15.2 + - - +
17F GLY* 3.1 18.9 - - - -
18F THR 3.2 7.8 + - - +
24F PHE* 3.9 22.4 - - + -
58F LEU* 4.2 10.8 - - + -
61F SER* 3.3 36.1 - - - +
102F LEU* 3.9 33.0 - - + -
103F THR 3.5 2.5 - - - -
104F ALA* 4.2 6.3 - - + -
119F VAL* 4.5 2.9 - - + -
120F LYS* 1.3 78.6 - - - +
122F ARG* 1.3 75.5 + - - +
122G ARG* 4.3 3.3 - - - +
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Residues in contact with ARG 122 (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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17F GLY* 4.8 4.2 - - - -
18F THR* 2.6 45.4 + - - +
101F VAL 3.7 1.7 - - - +
102F LEU* 3.7 1.0 - - - -
103F THR* 2.8 41.1 + - - +
120F LYS* 6.3 0.4 - - - +
121F ILE* 1.3 82.1 + - - +
123F GLY* 1.3 58.9 + - - +
124F VAL* 4.1 2.7 + - + -
103G THR* 3.4 34.3 + - - +
104G ALA* 4.3 0.7 - - - +
105G THR* 3.2 28.6 + - + +
120G LYS* 3.4 52.9 + - - +
121G ILE 4.6 0.6 - - - +
122G ARG* 4.2 24.9 - - + +
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Residues in contact with GLY 123 (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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18F THR 2.8 15.1 + - - +
19F VAL* 3.4 4.1 - - - +
20F ASN 3.0 25.0 + - - -
101F VAL 3.0 10.8 - - - -
102F LEU* 3.9 13.0 - - - +
122F ARG* 1.3 74.3 - - - +
124F VAL* 1.3 66.3 + - - +
126F PHE* 4.0 13.7 - - - -
105G THR* 5.2 1.7 - - - +
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Residues in contact with VAL 124 (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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20F ASN* 3.8 3.4 - - - -
100F GLY* 3.6 0.5 - - - -
101F VAL* 2.9 34.3 + - + +
122F ARG* 4.1 1.8 + - + -
123F GLY* 1.3 78.3 - - - +
125F ASN* 1.3 66.9 + - + +
126F PHE* 3.3 5.1 + - - -
91G GLU* 3.9 28.3 - - + -
92G ARG 3.6 19.3 - - - +
93G VAL* 3.5 36.6 - - + -
103G THR* 3.9 16.6 - - + -
104G ALA 3.9 7.0 - - - +
105G THR* 4.0 9.4 - - + -
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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