Contacts of the strand formed by residues 101 - 111 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B VAL* 4.0 37.5 - - + -
101B VAL* 4.5 0.9 - - + -
103B THR* 4.2 10.8 - - + -
175B LYS* 6.5 0.4 - - - -
93D VAL* 3.9 26.0 - - + -
94D THR 3.3 4.0 - - - +
95D THR* 4.3 19.3 - - + +
99D GLY 4.0 7.6 - - - +
100D GLY* 1.3 79.1 - - - +
102D LEU* 1.3 63.3 + - - +
103D THR* 4.3 1.1 - - + -
122D ARG 3.7 2.1 - - - +
123D GLY* 3.2 2.8 - - - -
124D VAL* 3.1 36.8 + - + +
125D ASN* 5.2 0.9 - - - +
126D PHE* 3.8 3.8 - - - -
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Residues in contact with LEU 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL* 4.4 5.8 - - + -
57D ILE* 3.7 52.5 - - + +
58D LEU* 4.3 4.7 - - + -
60D THR* 5.9 1.1 - - - +
61D SER* 4.3 15.5 - - - +
92D ARG* 3.9 1.2 - - - +
93D VAL* 3.7 0.9 - - - -
94D THR* 2.8 46.6 + - - +
96D TYR* 4.9 3.1 - - + -
100D GLY 4.4 0.2 - - - -
101D VAL* 1.3 73.7 - - - +
103D THR* 1.3 67.3 + - - +
104D ALA* 4.2 3.5 + - + -
121D ILE* 3.6 33.2 - - + -
122D ARG 3.8 2.7 - - - -
123D GLY* 4.1 2.0 - - - -
126D PHE* 4.4 10.2 - - + -
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Residues in contact with THR 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B VAL* 4.3 5.2 - - + -
103B THR* 3.3 38.8 + - + +
122B ARG* 3.6 25.4 - - - +
124B VAL* 4.0 24.5 - - + -
92D ARG 3.2 6.5 - - - -
93D VAL* 4.1 14.4 - - + -
101D VAL* 4.3 1.3 - - + -
102D LEU* 1.3 76.6 - - - +
104D ALA* 1.3 59.7 + - - +
120D LYS 4.1 0.2 - - - +
121D ILE* 3.5 5.4 - - - +
122D ARG* 2.8 34.6 + - - +
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Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ARG* 4.6 0.4 - - - +
124B VAL* 4.3 0.7 - - - +
61D SER* 3.8 18.6 - - - +
90D TRP* 3.7 23.1 - - + +
91D GLU* 3.4 0.5 - - - -
92D ARG* 2.9 36.5 + - + +
102D LEU* 4.2 5.4 + - + +
103D THR* 1.3 76.1 - - - +
105D THR* 1.3 68.8 + - - +
119D VAL* 4.8 0.9 - - + -
120D LYS 3.4 6.1 - - - +
121D ILE* 4.0 11.7 - - + -
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Residues in contact with THR 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B THR* 3.9 22.7 - - + -
21B ASN* 5.2 9.4 - - - +
122B ARG* 2.7 31.2 + - - +
124B VAL* 4.0 10.5 - - + -
90D TRP 3.3 5.2 - - - -
91D GLU* 3.9 22.7 - - + -
104D ALA* 1.3 78.9 - - - +
106D GLN* 1.3 61.5 + - - +
118D ASN 3.7 1.4 - - - +
119D VAL* 3.4 3.2 - - - +
120D LYS* 2.9 35.5 + - - +
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Residues in contact with GLN 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ASN* 4.8 3.6 - - - +
13D LEU* 5.6 0.2 - - - +
61D SER 5.0 0.6 + - - +
63D NRQ 3.4 13.3 + - - -
88D PHE 4.4 0.5 - - - +
89D THR* 3.1 9.7 - - - -
90D TRP* 2.7 71.6 + - + +
105D THR* 1.3 76.2 - - - +
107D ASP* 1.3 77.3 + - - +
108D THR* 2.7 31.6 + - - -
117D TYR* 3.3 29.7 - - - +
118D ASN 3.2 11.0 - - - +
119D VAL* 3.7 19.9 - - + +
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Residues in contact with ASP 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ASN* 5.6 1.1 - - - +
88D PHE 4.0 2.7 - - - -
89D THR* 3.3 15.7 - - + +
106D GLN* 1.3 81.9 + - - +
108D THR* 1.3 62.9 + - - +
109D SER* 4.4 6.2 + - - -
116D ILE 3.7 1.4 - - - +
117D TYR* 3.5 2.4 - - - -
118D ASN* 3.0 44.3 + - + +
181D LYS* 3.3 28.9 + - - +
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Residues in contact with THR 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D NRQ 4.7 0.7 + - - -
68D THR* 4.2 1.1 - - - +
84D PHE* 3.9 13.4 - - + -
87D GLY* 3.2 7.6 - - - -
88D PHE* 2.7 72.7 + - + +
106D GLN* 2.7 31.0 + - - -
107D ASP* 1.3 73.0 - - - +
109D SER* 1.3 64.1 + - - +
115D LEU* 4.5 2.9 - - + -
116D ILE 3.6 2.9 - - - -
117D TYR* 3.5 22.9 - - + -
181D LYS* 3.8 2.6 + - - -
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Residues in contact with SER 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D PHE* 4.4 7.0 - - - -
86D GLU 5.1 3.4 - - - -
87D GLY* 4.8 3.1 - - - -
107D ASP* 4.2 6.1 + - - -
108D THR* 1.3 75.4 - - - +
110D LEU* 1.3 62.9 + - - +
111D GLN* 5.0 5.1 - - - +
115D LEU* 3.4 5.9 - - - +
116D ILE* 2.8 55.7 + - - +
181D LYS* 4.3 12.8 - - - -
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Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 3.8 42.8 - - + +
5D ILE* 4.1 9.0 - - + -
9D MET* 4.0 13.2 - - + -
84D PHE* 3.8 30.9 - - + -
85D PRO* 4.6 14.7 + - + +
109D SER* 1.3 78.0 - - - +
111D GLN* 1.3 60.9 + - - +
112D ASP 4.3 0.4 - - - -
113D GLY* 3.7 29.2 - - - +
114D CYS 3.4 18.8 - - - +
115D LEU* 4.3 3.8 - - + +
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Residues in contact with GLN 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D SER* 4.1 6.6 + - - +
110D LEU* 1.3 74.5 - - - +
112D ASP* 1.3 77.2 + - + +
113D GLY 3.1 1.8 - - - -
114D CYS* 2.7 41.9 + - - +
116D ILE* 3.9 24.2 - - + +
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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