Contacts of the strand formed by residues 101 - 111 (chain B) in PDB entry 3BX9
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A VAL* 4.1 36.3 - - + -
175A LYS* 5.6 7.6 - - + +
93B VAL* 3.9 25.8 - - + -
94B THR 3.4 3.1 - - - +
95B THR* 4.5 15.3 - - + +
99B GLY* 3.4 16.2 - - - +
100B GLY* 1.3 76.0 - - - +
102B LEU* 1.3 62.5 + - - +
103B THR* 4.3 9.4 - - + -
122B ARG 3.8 1.6 - - - +
123B GLY* 3.2 1.9 - - - -
124B VAL* 2.8 37.2 + - + +
125B ASN* 5.4 2.0 - - + +
126B PHE* 3.6 3.6 - - - -
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 4.3 6.5 - - + -
57B ILE* 3.7 48.7 - - + +
58B LEU* 4.3 2.2 - - + -
60B THR* 6.0 1.1 - - - +
61B SER* 4.3 9.9 - - - +
92B ARG* 3.9 1.9 - - - +
93B VAL* 3.6 0.5 - - - -
94B THR* 2.8 52.4 + - - +
96B TYR* 4.8 3.1 - - + -
100B GLY 4.3 0.4 - - - -
101B VAL* 1.3 74.5 - - - +
103B THR* 1.3 73.9 + - - +
104B ALA* 4.2 11.6 + - + -
121B ILE* 3.8 28.7 - - + -
122B ARG 3.4 4.3 - - - +
123B GLY* 4.4 2.5 - - - -
126B PHE* 4.1 9.4 - - + -
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Residues in contact with THR 103 (chain B).
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* 4.9 1.8 - - + -
103A THR* 3.2 42.2 + - + +
122A ARG* 5.2 11.6 - - + +
124A VAL* 5.7 3.8 - - + -
92B ARG 3.2 6.5 - - - -
93B VAL* 4.0 24.2 - - + -
101B VAL* 4.3 4.7 - - + -
102B LEU* 1.3 77.0 - - - +
104B ALA* 1.3 61.2 + - - +
105B THR* 5.7 0.7 - - - -
120B LYS 4.0 0.2 - - - +
121B ILE* 3.5 2.8 - - - -
122B ARG* 2.8 50.4 + - - +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B SER* 3.7 8.3 - - - +
90B TRP* 3.5 23.4 - - + -
91B GLU* 3.3 2.4 - - - -
92B ARG* 2.9 38.1 + - + +
102B LEU* 4.2 6.7 - - + -
103B THR* 1.3 74.2 - - - +
105B THR* 1.3 66.7 + - - +
119B VAL* 4.8 0.4 - - + -
120B LYS 3.4 6.1 - - - -
121B ILE* 3.5 23.1 - - + -
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Residues in contact with THR 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG* 3.2 56.0 + - + +
124A VAL* 5.4 0.2 - - + -
90B TRP 3.4 6.5 - - - -
91B GLU* 3.7 8.5 - - + -
103B THR 5.7 0.2 - - - -
104B ALA* 1.3 81.3 - - - +
106B GLN* 1.3 63.0 + - - +
118B ASN 3.9 0.6 - - - +
119B VAL* 3.4 5.1 - - - +
120B LYS* 3.0 47.5 + - - +
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Residues in contact with GLN 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B SER 4.8 0.8 + - - +
63B NRQ 3.3 19.2 + - - +
88B PHE 4.3 0.3 - - - +
89B THR* 3.1 11.1 - - - +
90B TRP* 2.8 72.4 + - + +
91B GLU* 4.3 0.3 - - - +
105B THR* 1.3 79.3 - - - +
107B ASP* 1.3 78.0 + - - +
108B THR* 2.7 30.6 + - - -
117B TYR* 3.4 22.8 - - - +
118B ASN 3.2 11.9 - - - +
119B VAL* 3.9 14.6 - - + -
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Residues in contact with ASP 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B PHE 4.0 1.8 - - - -
89B THR* 3.4 10.9 - - + +
106B GLN* 1.3 81.5 - - - +
108B THR* 1.3 59.1 + - - +
109B SER* 3.9 14.2 + - - -
116B ILE 3.6 1.0 - - - +
117B TYR* 3.4 3.3 - - - -
118B ASN* 3.0 47.1 + - + +
181B LYS* 3.1 34.9 + - - +
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Residues in contact with THR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B NRQ 4.7 0.7 + - - -
68B THR* 4.5 1.6 - - - +
84B PHE* 3.8 16.4 - - + -
87B GLY* 3.5 2.1 - - - -
88B PHE* 2.9 68.0 + - + -
106B GLN* 2.7 30.3 + - - -
107B ASP* 1.3 70.8 - - - +
109B SER* 1.3 64.0 + - - +
115B LEU* 4.7 0.4 - - + -
116B ILE 3.6 4.0 - - - -
117B TYR* 3.6 19.8 - - + -
181B LYS* 3.1 17.1 + - - -
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Residues in contact with SER 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B PHE* 4.3 5.8 - - - -
86B GLU 4.5 4.9 - - - -
107B ASP* 3.9 14.0 + - - -
108B THR* 1.3 75.0 - - - +
110B LEU* 1.3 59.0 + - - +
111B GLN* 3.0 30.6 + - - -
115B LEU* 3.5 7.1 - - - +
116B ILE* 2.8 43.7 + - - +
118B ASN* 5.3 0.5 + - - -
181B LYS* 4.0 8.5 - - - +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 4.1 33.4 - - + +
5B ILE* 4.5 1.8 - - + -
9B MET* 4.8 4.9 - - + -
84B PHE* 3.7 29.2 - - + -
85B PRO* 3.9 15.3 + - + +
109B SER* 1.3 73.1 - - - +
111B GLN* 1.3 64.9 + - - +
113B GLY 4.0 7.4 - - - +
114B CYS 3.5 28.7 - - - +
115B LEU* 4.0 14.8 - - + +
236B CIT 3.2 47.9 + - + +
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Residues in contact with GLN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B SER* 3.0 28.3 + - - +
110B LEU* 1.3 77.4 - - - +
112B ASP* 1.3 79.8 + - - +
113B GLY 3.1 2.1 + - - -
114B CYS* 2.8 25.2 + - - +
116B ILE* 3.8 26.8 - - + +
118B ASN* 5.6 2.0 - - - +
236B CIT 4.1 1.6 - - - -
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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