Contacts of the strand formed by residues 95 - 106 (chain A) in PDB entry 1BV1
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 LEU 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A PRO* 3.6 32.8 - - + +
91A ILE* 3.8 4.5 - - + +
92A GLY* 3.0 25.5 + - - +
93A ASP 3.6 0.6 - - - -
94A THR* 1.3 79.6 + - - +
96A GLU* 1.3 63.2 + - - +
97A LYS 3.4 22.2 - - - +
98A ILE* 4.1 17.9 - - + -
120A TYR* 4.0 28.9 - - + -
121A HIS 3.4 24.7 - - - +
122A THR* 4.2 8.1 - - + -
128A VAL* 5.1 3.4 - - + -
132A GLN* 5.5 2.5 - - + -
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Residues in contact with GLU 96 (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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86A ILE 4.3 4.0 - - - +
91A ILE* 3.4 19.8 - - - +
94A THR 4.1 1.6 - - - -
95A LEU* 1.3 73.2 - - - +
97A LYS* 1.3 82.8 + - - +
121A HIS* 2.9 33.8 + - + +
122A THR 5.4 1.1 - - - -
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Residues in contact with LYS 97 (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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70A ARG* 5.0 10.8 - - - +
84A SER* 4.2 17.9 - - - -
85A VAL 3.3 14.6 - - - +
86A ILE* 4.5 11.2 - - + -
91A ILE* 3.5 5.4 - - - -
95A LEU* 3.4 6.4 - - - +
96A GLU* 1.3 102.7 + - - +
98A ILE* 1.3 65.4 + - - +
99A SER* 3.3 23.3 - - - +
121A HIS* 3.1 56.0 + - + +
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Residues in contact with ILE 98 (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 SER* 3.0 5.7 - - - -
85A VAL* 2.7 54.0 + - + -
90A PRO* 3.9 28.7 - - + -
91A ILE* 4.1 2.7 - - + -
95A LEU* 4.1 7.6 - - + -
97A LYS* 1.3 81.1 - - - +
99A SER* 1.3 62.6 + - - +
100A ASN* 3.3 27.9 - - - +
118A ASN* 4.7 0.4 - - + -
119A LYS 3.4 10.5 - - - +
120A TYR* 4.0 40.2 - - + +
132A GLN* 4.6 4.7 - - - +
136A SER* 5.7 2.2 - - - +
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Residues in contact with SER 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP* 5.5 0.7 - - - -
83A TYR 3.8 3.8 - - - -
84A SER* 3.6 8.0 + - - -
97A LYS* 3.3 17.0 - - - -
98A ILE* 1.3 71.8 - - - +
100A ASN* 1.3 60.9 + - - +
117A SER 3.7 1.4 - - - +
118A ASN 3.7 0.2 - - - -
119A LYS* 2.7 50.0 + - - +
121A HIS* 3.3 24.3 - - - -
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Residues in contact with ASN 100 (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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81A TYR 4.5 0.4 - - - -
82A ASN* 3.3 7.2 - - - +
83A TYR* 2.8 82.4 + - + +
85A VAL* 3.9 14.7 - - - +
98A ILE* 3.3 26.4 - - - +
99A SER* 1.3 77.1 + - - +
101A GLU* 1.3 62.3 - - - +
102A ILE* 5.4 2.2 - - + -
116A ILE* 5.6 0.7 - - + -
117A SER 3.2 4.7 - - - +
118A ASN* 2.7 29.6 + - - +
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Residues in contact with GLU 101 (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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80A LYS* 3.4 34.3 + - + +
81A TYR 3.5 3.6 - - - -
82A ASN* 3.2 29.3 - - - +
100A ASN* 1.3 73.5 - - - +
102A ILE* 1.3 67.0 + - - +
103A LYS* 4.3 16.3 + - + +
115A LYS 3.5 2.9 - - - +
116A ILE* 3.4 4.5 - - - +
117A SER* 2.8 47.1 + - - -
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Residues in contact with ILE 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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22A PHE* 4.7 10.8 - - + -
23A ILE* 4.5 22.2 - - + -
79A PHE 3.9 0.7 - - - +
80A LYS* 3.4 2.4 - - - +
81A TYR* 2.8 46.3 + - + +
83A TYR* 4.4 25.6 - - + +
100A ASN* 5.4 0.7 - - + -
101A GLU* 1.3 78.8 - - - +
103A LYS* 1.3 65.6 + - - +
104A ILE* 4.6 4.0 - - + -
114A LEU* 4.3 30.3 - - + -
115A LYS 3.5 4.5 - - - +
116A ILE* 4.2 22.9 - - + -
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Residues in contact with LYS 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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78A ASN* 4.2 13.0 - - + +
79A PHE 3.4 9.2 - - - +
80A LYS* 4.0 25.7 - - + +
101A GLU* 4.3 16.2 + - + +
102A ILE* 1.3 76.2 - - - +
104A ILE* 1.3 66.1 - - - +
105A VAL* 3.8 10.3 + - + +
113A ILE 3.6 1.2 - - - +
114A LEU* 3.5 1.8 - - - -
115A LYS* 2.9 58.5 + - + +
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Residues in contact with ILE 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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15A ALA* 3.7 31.6 - - + +
18A LEU* 4.2 16.6 - - + +
19A PHE* 3.8 33.9 - - + +
22A PHE* 5.0 1.6 - - + -
23A ILE* 4.1 16.6 - - + -
78A ASN 4.2 3.6 - - - +
79A PHE* 2.9 41.4 + - + +
102A ILE* 4.6 5.8 - - + -
103A LYS* 1.3 74.4 - - - +
105A VAL* 1.3 64.0 + - - +
112A SER* 3.8 14.1 - - - +
113A ILE 3.6 4.0 - - - +
114A LEU* 4.0 19.3 - - + -
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Residues in contact with VAL 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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15A ALA* 4.5 0.7 - - - -
103A LYS* 4.2 15.5 - - + +
104A ILE* 1.3 77.8 - - - +
106A ALA* 1.3 75.0 + - - +
112A SER* 3.2 5.8 - - - -
113A ILE* 3.0 45.6 + - + +
115A LYS* 3.6 34.8 - - + +
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Residues in contact with ALA 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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15A ALA* 4.1 21.1 - - + +
79A PHE* 6.0 0.2 - - - -
104A ILE 4.3 0.2 + - - -
105A VAL* 1.3 86.3 - - - +
107A THR* 1.3 64.1 + - - +
108A PRO* 4.6 0.9 - - - +
110A GLY 6.2 0.2 - - - -
111A GLY 3.6 9.6 - - - +
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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