Contacts of the strand formed by residues 101 - 111 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A VAL* 3.7 27.1 - - + -
94A THR 3.4 2.9 - - - +
95A THR* 4.5 17.7 - - + +
99A GLY 3.9 8.7 - - - +
100A GLY* 1.3 79.4 - - - +
102A LEU* 1.3 62.7 + - - +
122A ARG 3.8 1.0 - - - +
123A GLY* 3.0 2.6 - - - -
124A VAL* 2.8 44.7 + - + +
125A ASN* 5.6 0.2 - - + -
126A PHE* 3.5 3.5 - - - -
93C VAL* 4.0 36.6 - - + -
101C VAL* 4.7 0.4 - - + -
103C THR* 4.2 13.0 - - + -
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A VAL* 4.1 4.0 - - + -
57A ILE* 3.9 47.6 - - + +
58A LEU* 4.7 1.3 - - + -
60A THR* 6.2 0.2 - - - +
61A SER* 4.1 6.7 - - - +
92A ARG* 3.9 0.9 - - - +
93A VAL* 3.3 2.4 - - - +
94A THR* 2.7 50.3 + - - +
96A TYR* 4.9 3.6 - - + -
101A VAL* 1.3 74.3 - - - +
103A THR* 1.3 67.3 + - - +
104A ALA* 4.7 2.2 - - + -
121A ILE* 3.8 42.0 - - + -
122A ARG 3.6 1.6 - - - -
123A GLY* 3.9 16.4 - - - -
126A PHE* 4.2 9.1 - - + -
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Residues in contact with THR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ARG 3.1 11.7 - - - +
93A VAL* 4.0 18.6 - - + -
101A VAL* 4.5 0.4 - - + -
102A LEU* 1.3 81.1 - - - +
104A ALA* 1.3 62.7 + - - +
120A LYS 3.9 0.2 - - - +
121A ILE* 3.5 1.9 - - - -
122A ARG* 2.9 38.6 + - - +
101C VAL* 4.6 3.6 - - + +
103C THR* 3.4 34.4 + - + -
122C ARG* 3.7 25.0 - - - +
124C VAL* 4.2 13.5 - - + -
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A SER* 3.9 15.3 - - - +
90A TRP* 3.5 28.2 - - + -
91A GLU* 3.1 3.6 - - - -
92A ARG* 2.8 35.9 + - + +
102A LEU* 4.7 3.4 - - + -
103A THR* 1.3 76.4 - - - +
105A THR* 1.3 64.6 + - - +
119A VAL* 4.6 1.6 - - + -
120A LYS 3.2 9.6 - - - +
121A ILE* 4.1 7.9 - - + -
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Residues in contact with THR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A TRP 3.5 4.3 - - - -
91A GLU* 3.8 18.8 - - + +
104A ALA* 1.3 80.1 - - - +
106A GLN* 1.3 61.0 + - - +
118A ASN 3.8 1.0 - - - +
119A VAL* 3.5 2.2 - - - +
120A LYS* 2.9 35.6 + - - +
18C THR* 4.6 14.1 - - + +
21C ASN* 5.7 4.3 - - - +
122C ARG* 2.5 42.8 + - + +
123C GLY 5.2 0.9 - - - +
124C VAL* 4.0 13.9 - - + -
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Residues in contact with GLN 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A SER 5.5 0.4 + - - -
63A NRQ 3.5 14.3 + - - -
88A PHE 4.4 0.2 - - - +
89A THR* 3.3 9.7 - - - +
90A TRP* 2.7 72.2 + - + +
105A THR* 1.3 76.4 - - - +
107A ASP* 1.3 70.3 + - - +
108A THR* 2.7 30.1 + - - -
117A TYR* 3.4 28.5 - - - +
118A ASN 3.2 10.3 - - - +
119A VAL* 3.5 19.7 - - + +
21C ASN* 5.3 0.3 + - - +
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Residues in contact with ASP 107 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A THR* 3.5 15.2 - - + +
106A GLN* 1.3 77.8 + - - +
108A THR* 1.3 63.4 + - - +
109A SER* 4.1 9.9 + - - -
116A ILE 3.5 1.7 - - - +
117A TYR* 3.4 5.5 - - - -
118A ASN* 2.9 48.8 + - + +
181A LYS* 3.2 26.5 + - - +
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Residues in contact with THR 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A NRQ 4.8 0.9 + - - -
68A THR* 4.6 1.6 - - - +
84A PHE* 3.9 14.1 - - + -
87A GLY* 3.5 2.6 - - - -
88A PHE* 3.0 72.5 + - + +
106A GLN* 2.7 30.6 + - - +
107A ASP* 1.3 74.0 + - - +
109A SER* 1.3 64.3 + - - +
115A LEU* 4.8 1.3 - - + -
116A ILE 3.6 2.7 - - - -
117A TYR* 3.7 22.2 - - + -
181A LYS* 3.4 8.0 + - - -
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Residues in contact with SER 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A PHE* 4.2 6.7 - - - -
86A GLU 5.3 2.2 - - - -
87A GLY* 4.7 3.4 - - - -
107A ASP* 4.0 11.3 + - - -
108A THR* 1.3 76.4 - - - +
110A LEU* 1.3 61.4 + - - +
111A GLN* 3.1 29.6 + - - -
115A LEU* 3.4 8.3 - - - +
116A ILE* 2.9 41.5 + - - +
181A LYS* 4.5 6.3 - - - -
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 3.7 42.4 - - + +
5A ILE* 4.2 7.0 - - + -
9A MET* 5.0 4.5 - - + -
84A PHE* 3.8 34.3 - - + -
85A PRO* 4.4 16.4 + - + +
109A SER* 1.3 73.8 - - - +
111A GLN* 1.3 63.4 + - - +
112A ASP 4.0 1.6 + - - -
113A GLY* 3.7 28.9 - - - +
114A CYS 3.5 19.1 - - - +
115A LEU* 3.8 11.0 - - + -
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Residues in contact with GLN 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A SER* 3.1 29.0 + - - +
110A LEU* 1.3 75.6 - - - +
112A ASP* 1.3 77.1 + - + +
113A GLY 3.3 1.3 - - - -
114A CYS* 3.0 23.1 + - - +
116A ILE* 3.6 27.3 - - + +
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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