Contacts of the strand formed by residues 98 - 115 (chain A) in PDB entry 1BND
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 ILE 98 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 4.0 16.6 - - + -
90A LEU* 3.7 23.3 - - + -
91A THR 3.2 6.7 - - - +
92A MET* 4.0 23.3 - - + -
96A LYS 3.9 4.2 + - - +
97A ARG* 1.3 76.5 - - - +
99A GLY* 1.3 62.1 + - - +
101A ARG* 4.1 1.8 - - - -
44B GLN* 5.1 9.1 - - - +
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Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 3.7 11.2 - - - -
91A THR* 2.7 42.6 + - - -
98A ILE* 1.3 77.6 - - - +
100A TRP* 1.3 60.5 + - - -
101A ARG* 3.3 11.1 - - - +
44B GLN* 5.2 4.7 - - - -
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Residues in contact with TRP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 4.1 30.7 - - + -
51A GLN* 4.3 4.3 - - - -
88A ARG* 3.9 46.0 + - + +
89A ALA* 3.3 28.7 - - - -
90A LEU* 3.7 33.9 - - + +
99A GLY* 1.3 69.8 - - - -
101A ARG* 1.3 65.5 + - - +
41B ILE* 5.4 12.4 - - + +
43B THR 5.8 0.8 + - - -
44B GLN* 4.3 23.0 + - - +
48B VAL* 4.6 20.3 - - + +
99B TRP* 4.5 27.1 - + - -
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Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP* 3.7 25.4 + - + +
36A VAL* 4.0 9.9 - - - -
87A VAL 3.4 0.5 - - - +
88A ARG* 3.2 6.9 - - - +
89A ALA* 2.9 32.3 + - - +
91A THR* 2.7 57.0 + - + +
92A MET* 3.8 1.4 - - - +
93A ASP* 2.9 34.9 + - - +
97A ARG* 3.2 23.9 + - - +
98A ILE 4.5 0.6 - - - -
99A GLY* 3.2 15.8 + - - +
100A TRP* 1.3 79.5 - - - +
102A PHE* 1.3 69.2 + - - +
103A ILE* 3.7 1.6 + - + +
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Residues in contact with PHE 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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30A ASP* 3.1 7.1 - - - +
31A MET* 3.0 47.5 + - + +
86A TYR* 3.9 26.7 - - + -
87A VAL* 3.3 15.0 - - - -
88A ARG* 3.7 37.0 - - + -
101A ARG* 1.3 76.0 - - - +
103A ILE* 1.3 60.0 + - - +
20B TRP* 3.4 32.5 - + - -
51B TYR* 3.5 52.7 - + - -
52B PHE* 5.2 0.2 - - - -
53B TYR 4.9 2.7 - - - -
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Residues in contact with ILE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 4.6 3.1 - - - +
28A ALA* 4.0 20.2 - - + -
29A VAL 3.3 13.0 - - - +
30A ASP* 4.4 4.9 - - + -
36A VAL* 3.9 27.8 - - + -
38A VAL* 4.2 7.0 - - + -
53A PHE* 4.0 17.3 - - + -
86A TYR* 3.4 6.3 - - - -
87A VAL* 2.9 44.0 + - + +
89A ALA* 3.8 19.3 - - + -
91A THR* 4.0 11.4 - - + -
101A ARG* 4.5 3.4 - - + +
102A PHE* 1.3 77.3 - - - +
104A ARG* 1.3 60.3 + - - +
105A ILE* 3.8 15.2 + - + -
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Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 5.2 0.9 + - - -
28A ALA* 4.8 8.3 - - - +
29A VAL* 3.1 21.2 + - + +
84A GLN* 3.4 39.0 + - + +
85A SER 3.2 7.4 - - - +
86A TYR* 3.0 38.9 + - + -
103A ILE* 1.3 74.9 - - - +
105A ILE* 1.3 65.3 + - - +
500A IPA 2.8 43.1 + - + +
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 3.1 28.9 - - - +
53A PHE* 4.4 8.5 - - + -
54A TYR 3.6 24.2 - - - +
55A GLU* 3.9 12.3 - - + +
84A GLN* 3.3 4.2 - - - +
85A SER 2.8 30.7 + - - +
87A VAL* 3.7 46.9 - - + -
103A ILE* 4.1 7.4 - - + -
104A ARG* 1.3 80.4 - - - +
106A ASP* 1.3 65.8 + - - +
107A THR* 3.4 15.4 + - + +
84B THR* 6.3 0.7 - - + -
85B TYR 6.0 1.3 - - - +
86B VAL* 6.2 0.2 - - + -
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Residues in contact with ASP 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 3.4 27.8 + - + +
56A THR 3.1 31.6 + - - +
57A LYS* 3.9 17.9 + - + +
82A THR* 3.6 20.8 - - + +
83A THR 3.7 6.7 - - - -
84A GLN* 3.0 26.7 + - - +
105A ILE* 1.3 71.6 - - - +
107A THR* 1.3 62.2 + - - +
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Residues in contact with THR 107 (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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54A TYR 5.0 0.4 - - - +
56A THR* 3.4 22.0 + - - +
83A THR* 3.1 8.0 + - - -
84A GLN 4.2 0.9 - - - -
85A SER* 3.3 26.3 + - - -
87A VAL* 5.4 2.0 - - + -
105A ILE* 3.4 27.3 + - + +
106A ASP* 1.3 80.0 - - - +
108A SER* 1.3 64.6 + - - +
82B SER* 5.3 0.5 + - - -
84B THR* 4.3 16.0 + - + +
106B THR* 3.0 41.2 + - - +
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Residues in contact with SER 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 3.4 15.5 + - - -
57A LYS* 4.2 2.1 - - - -
82A THR* 3.1 11.4 - - - +
83A THR* 2.8 40.4 + - - -
107A THR* 1.3 84.3 + - - +
109A CYS* 1.3 70.3 + - - +
110A VAL* 4.0 4.5 - - - +
82B SER* 4.6 2.3 + - - -
107B SER* 2.8 33.1 + - - -
109B VAL* 4.1 5.7 - - - +
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Residues in contact with CYS 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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13A CYS* 3.5 33.1 - - + +
14A ASP 3.7 6.3 - - - -
15A SER* 3.8 18.0 - - - -
58A CYS* 2.0 58.3 - - - +
80A CYS* 3.7 5.2 - - - -
81A ARG 3.1 4.5 - - - -
108A SER* 1.3 76.6 + - - +
110A VAL* 1.3 61.5 + - - +
109B VAL* 4.0 13.3 - - - +
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Residues in contact with VAL 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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13A CYS* 3.8 4.3 - - - -
80A CYS* 3.4 0.7 - - - -
81A ARG* 2.7 45.8 + - + +
83A THR* 3.4 37.9 - - + +
108A SER* 4.0 10.3 - - - +
109A CYS* 1.3 79.0 - - - +
111A CYS* 1.3 62.6 + - - +
112A THR* 4.5 7.9 - - - +
12B SER* 6.4 1.6 - - - -
13B VAL* 6.2 0.7 - - + -
107B SER* 4.7 4.5 - - - +
108B CYS 4.1 20.2 - - - +
109B VAL* 4.4 5.4 - - + -
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Residues in contact with CYS 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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12A VAL* 3.4 23.5 - - + +
13A CYS* 3.6 1.9 - - - -
68A CYS* 2.0 48.2 - - - -
71A ILE* 4.2 2.9 - - - -
78A SER* 3.9 10.8 - - - -
79A GLN 3.5 3.1 - - - -
110A VAL* 1.3 78.7 - - - +
112A THR* 1.3 64.8 + - - +
12B SER* 4.0 4.7 - - - -
13B VAL* 3.5 48.5 + - + +
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Residues in contact with THR 112 (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 SER* 3.1 5.4 - - - -
79A GLN* 2.9 34.8 + - - +
81A ARG* 3.3 35.7 + - - +
110A VAL* 3.9 5.7 + - - +
111A CYS* 1.3 77.0 + - - +
113A LEU* 1.3 72.6 + - - +
114A THR* 5.0 2.6 - - + +
10B GLU* 3.4 30.7 - - + +
11B VAL 3.9 8.7 - - - +
12B SER* 4.8 3.9 - - - +
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Residues in contact with LEU 113 (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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71A ILE* 3.6 31.6 - - + -
76A TRP* 3.5 30.3 - - + -
77A ASN 3.2 8.3 - - - +
78A SER* 4.0 12.6 - - - -
112A THR* 1.3 76.3 - - - +
114A THR* 1.3 63.3 + - - +
10B GLU* 3.4 4.7 - - - -
11B VAL 2.8 43.2 + - - +
12B SER 4.3 0.2 - - - -
13B VAL* 3.9 16.6 - - + +
68B ARG* 3.6 40.8 - - + +
69B GLY* 3.8 11.4 - - - -
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Residues in contact with THR 114 (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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76A TRP* 3.3 7.1 - - - -
77A ASN* 3.1 49.3 + - - +
112A THR* 5.0 2.7 - - + +
113A LEU* 1.3 79.3 - - - +
115A ILE* 1.3 67.5 + - - +
116A LYS 3.3 0.3 + - - -
9B GLY* 3.7 9.2 - - - +
10B GLU* 3.6 30.1 - - + +
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Residues in contact with ILE 115 (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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75A HIS* 3.9 14.6 - - + +
76A TRP* 3.6 18.8 - - + -
77A ASN* 5.1 0.9 + - - -
114A THR* 1.3 74.0 + - - +
116A LYS* 1.3 74.5 + - - +
9B GLY* 2.9 39.0 + - - +
11B VAL* 4.1 11.2 - - + -
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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
------------------------------------------------------------
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