Contacts of the strand formed by residues 83 - 96 (chain A) in PDB entry 2BQY
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 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A GLU* 5.6 4.9 - - - +
5A LYS* 6.3 1.3 - - + -
7A GLU* 4.7 20.4 - - - +
16A CYS* 3.8 30.3 - - + -
17A VAL 3.4 12.8 - - - +
18A VAL* 4.5 17.5 - - + -
81A GLY 4.5 5.6 - - - +
82A SER* 1.3 83.4 - - - +
84A VAL* 1.3 65.1 + - - +
85A LYS* 6.3 0.2 - - + -
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Residues in contact with VAL 84 (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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16A CYS* 4.3 2.5 - - - -
17A VAL* 2.9 39.8 + - + +
19A ILE* 3.9 24.7 - - + -
72A VAL* 4.1 19.3 - - + -
78A PHE* 4.4 20.4 - - + -
82A SER* 5.8 0.7 - - - +
83A VAL* 1.3 76.4 - - - +
85A LYS* 1.3 75.7 + - - +
86A ALA* 3.4 2.3 + - + -
108A PRO* 3.9 21.1 - - + -
112A ILE* 4.1 12.1 - - + -
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Residues in contact with LYS 85 (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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9A SER* 5.2 6.5 - - - -
14A SER* 3.1 34.9 + - - +
15A LEU 3.6 6.3 - - - +
16A CYS* 4.1 12.1 - - + +
83A VAL* 6.3 0.4 - - + -
84A VAL* 1.3 72.4 - - - +
86A ALA* 1.3 57.9 + - - +
108A PRO* 3.5 4.2 - - - +
109A ILE* 2.9 48.6 + - + +
111A LYS* 5.0 7.4 - - + +
112A ILE* 3.5 16.7 - - + +
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Residues in contact with ALA 86 (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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14A SER* 3.4 6.6 + - - -
15A LEU* 2.7 41.5 + - + +
17A VAL* 4.2 14.6 - - + -
72A VAL* 4.7 7.4 - - + -
84A VAL 3.4 2.4 + - - +
85A LYS* 1.3 75.1 - - - +
87A ARG* 1.3 62.2 + - - +
106A ALA* 4.0 16.4 - - + -
107A LEU 3.1 21.1 - - - +
108A PRO* 3.9 2.2 - - + -
109A ILE* 3.6 6.1 - - - -
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Residues in contact with ARG 87 (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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12A ALA 3.4 5.4 - - - -
13A ASP* 3.8 30.3 - - - +
15A LEU* 3.8 0.4 - - - -
86A ALA* 1.3 74.7 - - - +
88A LEU* 1.3 64.5 + - - +
89A VAL* 3.4 17.3 - - - +
106A ALA* 3.2 6.4 - - - -
107A LEU* 2.7 52.4 + - + +
108A PRO 4.4 6.0 + - - +
109A ILE* 4.7 10.5 - - + +
110A ASP* 4.2 16.2 + - - +
116A HIS 3.0 23.6 + - - -
117A SER* 3.6 14.6 + - - +
119A VAL 2.8 30.4 + - - -
120A LYS* 4.6 5.6 + - - +
157A LYS* 6.0 1.4 - - - +
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Residues in contact with LEU 88 (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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12A ALA* 2.9 27.8 + - + +
13A ASP* 4.7 0.2 - - - +
15A LEU* 4.2 11.9 - - + -
70A ALA* 5.6 0.7 - - + -
87A ARG* 1.3 77.0 + - - +
89A VAL* 1.3 65.7 + - - +
90A GLY 4.7 1.3 - - - +
104A LEU* 3.8 35.4 - - + -
105A ILE 3.7 9.4 - - - +
106A ALA* 4.2 10.3 - - + -
120A LYS 4.7 0.2 - - - +
157A LYS* 3.6 27.8 + - + +
160A ALA* 4.1 24.0 - - + +
161A ILE* 4.3 2.0 - - + -
164A LEU* 3.6 39.3 - - + -
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Residues in contact with VAL 89 (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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87A ARG* 3.4 29.4 - - - +
88A LEU* 1.3 79.1 - - - +
90A GLY* 1.3 59.6 + - - +
105A ILE* 3.0 34.6 + - + +
106A ALA* 4.4 5.2 - - - +
107A LEU* 4.1 9.2 - - + -
119A VAL* 4.0 17.7 - - + +
120A LYS 4.2 7.2 - - - +
121A ASP* 3.1 19.0 - - - +
122A ILE* 2.7 28.2 + - - +
125A LEU* 4.5 12.8 - - + -
157A LYS* 3.4 12.1 + - - -
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Residues in contact with GLY 90 (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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88A LEU* 4.7 0.3 - - - +
89A VAL* 1.3 81.9 - - - +
91A VAL* 1.3 60.4 + - - +
104A LEU* 3.9 1.6 - - - +
105A ILE* 2.9 27.7 + - - +
122A ILE* 4.2 9.0 - - - -
155A GLU 3.2 14.1 - - - -
156A ASN 3.5 7.0 - - - -
157A LYS* 4.0 2.0 - - - +
160A ALA* 3.1 16.8 - - - +
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Residues in contact with VAL 91 (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 GLY* 1.3 75.9 - - - +
92A LEU* 1.3 63.4 + - - +
93A ASN* 4.0 17.6 + - - +
102A GLU* 4.6 4.0 - - + -
103A LYS 3.5 27.6 - - - +
104A LEU* 3.9 13.0 - - + -
105A ILE* 3.9 7.2 - - - +
122A ILE* 4.7 1.0 - - - +
154A PHE* 3.3 4.5 - - - -
155A GLU* 2.9 55.1 + - + +
159A SER* 3.9 11.7 - - - +
160A ALA* 4.0 13.7 - - + -
163A VAL* 4.5 12.6 - - + -
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Residues in contact with LEU 92 (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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91A VAL* 1.3 71.8 - - - +
93A ASN* 1.3 62.4 + - - +
94A MET* 3.4 30.0 + - + +
101A ASP 3.8 1.4 - - - +
102A GLU* 3.8 2.6 - - - -
103A LYS* 2.8 41.5 + - + +
105A ILE* 4.0 4.9 - - + +
133A ILE* 4.0 8.1 - - + -
134A LYS* 4.8 5.8 - - + -
137A PHE* 3.8 20.2 - - + -
151A VAL* 3.8 19.7 - - + -
153A GLY* 3.3 25.4 - - - +
154A PHE* 3.6 37.5 - - + -
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Residues in contact with ASN 93 (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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91A VAL* 4.2 11.9 - - - +
92A LEU* 1.3 75.4 - - - +
94A MET* 1.3 63.0 + - - +
100A MET* 5.7 5.2 - - + -
101A ASP 3.8 3.4 - - - +
102A GLU* 3.5 23.4 - - - +
151A VAL* 3.9 2.6 - - - +
152A LYS* 2.8 35.3 + - + -
153A GLY 2.8 18.3 + - - +
155A GLU* 3.0 45.4 + - - +
163A VAL* 5.5 0.2 - - - +
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Residues in contact with MET 94 (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 LEU* 3.4 38.8 - - + +
93A ASN* 1.3 75.7 - - - +
95A GLU* 1.3 62.2 + - - +
96A ASP* 6.0 1.3 - - + +
100A MET* 3.2 11.4 - - - +
101A ASP* 2.8 47.5 + - + +
103A LYS* 3.8 30.5 - - + -
137A PHE* 3.7 24.5 - - + -
140A TYR* 5.7 0.7 - - - -
149A VAL* 3.9 24.7 - - + -
150A LYS 3.7 6.3 - - - -
151A VAL* 3.8 16.2 - - + -
152A LYS* 4.0 2.9 - - - +
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Residues in contact with GLU 95 (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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94A MET* 1.3 78.9 - - - +
96A ASP* 1.3 62.9 + - - +
99A GLY* 3.6 11.8 - - - +
100A MET* 3.4 22.3 - - + +
148A TRP* 3.0 33.5 - - - -
149A VAL* 3.2 3.1 - - - -
150A LYS* 2.7 48.0 + - + +
152A LYS* 3.3 30.4 + - - -
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Residues in contact with ASP 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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94A MET* 4.4 1.7 - - + +
95A GLU* 1.3 77.0 - - - +
97A GLU* 1.3 76.5 + - - +
98A SER* 2.8 22.3 + - - -
99A GLY* 2.9 35.8 + - - +
101A ASP* 4.0 20.5 - - + +
141A LYS* 3.9 5.2 - - - +
148A TRP* 3.1 33.9 - - - +
149A VAL* 4.2 6.5 - - + -
1174A POP 3.7 18.4 + - - -
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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