Contacts of the strand formed by residues 76 - 90 (chain B) 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 ASN 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B ASN* 4.6 16.5 + - - +
72B ASP 5.5 0.4 + - - -
75B TRP* 1.3 81.8 + - - +
77B SER* 1.3 62.0 + - - +
111B ALA 3.4 0.7 - - - +
112B LEU* 3.4 5.0 - - - +
113B SER* 2.7 54.6 + - - +
114B ARG 4.4 2.0 - - - +
116B LYS* 3.7 26.5 - - - +
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Residues in contact with SER 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASN* 3.9 10.5 + - - +
66B GLY* 3.3 18.4 - - - -
67B CYS* 2.8 38.8 + - - -
70B ILE* 3.8 15.4 - - - +
75B TRP 4.1 0.8 + - - -
76B ASN* 1.3 77.0 - - - +
78B GLN* 1.3 65.9 + - - +
110B CYS* 3.6 9.2 - - - -
111B ALA 3.1 7.6 - - - -
112B LEU* 4.0 8.7 - - - -
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Residues in contact with GLN 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 4.3 12.1 + - - -
60B ALA* 3.8 31.8 - - + +
66B GLY* 4.4 1.6 - - - -
67B CYS* 3.3 8.3 - - - -
77B SER* 1.3 80.3 - - - +
79B CYS* 1.3 65.0 + - - +
80B LYS* 3.5 41.5 + - - +
111B ALA* 2.8 33.4 + - + +
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Residues in contact with CYS 79 (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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14B CYS* 2.0 53.4 - - + -
57B CYS* 3.6 8.0 - - - +
59B GLU 3.8 12.8 - - - +
60B ALA* 3.1 28.3 + - - +
62B PRO* 3.9 16.8 - - - -
67B CYS* 3.5 17.5 - - - -
78B GLN* 1.3 75.7 + - - +
80B LYS* 1.3 59.5 + - - +
108B CYS* 3.8 8.5 - - - -
109B VAL 3.3 4.9 - - - -
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Residues in contact with LYS 80 (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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9A GLN* 5.0 10.1 - - - +
57B CYS* 3.3 5.2 - - - -
78B GLN* 3.5 37.5 + - - +
79B CYS* 1.3 72.1 - - - +
81B THR* 1.3 72.5 + - - +
82B SER* 3.5 0.9 + - - -
109B VAL* 2.8 38.1 + - + +
111B ALA* 5.1 8.5 - - + -
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Residues in contact with THR 81 (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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56B ARG* 3.4 13.5 - - + +
57B CYS* 3.0 29.1 + - - +
80B LYS* 1.3 83.6 - - - +
82B SER* 1.3 64.4 + - - +
83B GLN* 5.0 2.6 - - - +
105B ASP* 3.3 44.4 - - + +
107B SER 3.3 13.0 - - - +
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Residues in contact with SER 82 (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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107A THR 5.3 0.5 + - - -
108A SER* 4.6 2.9 + - - -
80B LYS 3.5 1.0 + - - -
81B THR* 1.3 79.2 - - - +
83B GLN* 1.3 64.8 + - - +
105B ASP* 3.7 0.2 - - - -
106B THR* 2.9 28.9 + - - +
107B SER* 2.8 30.3 + - - +
109B VAL* 4.6 19.4 - - - +
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Residues in contact with GLN 83 (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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54A TYR* 5.7 1.0 - - - -
56A THR* 5.8 0.3 + - - -
107A THR 5.6 0.2 - - - +
81B THR* 5.0 3.1 - - + +
82B SER* 1.3 83.5 + - - +
84B THR* 1.3 65.5 + - - +
103B ARG* 3.6 54.0 + - + +
104B ILE 3.1 11.2 - - - +
105B ASP* 3.2 33.8 + - - +
106B THR* 3.9 5.1 - - - +
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Residues in contact with THR 84 (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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54A TYR* 3.6 29.6 + - - +
56A THR* 4.4 5.9 + - - -
87A VAL* 6.1 0.2 - - + -
105A ILE* 6.3 0.7 - - + -
107A THR* 4.3 16.0 - - + +
83B GLN* 1.3 75.8 - - - +
85B TYR* 1.3 67.6 + - - +
86B VAL* 3.8 23.6 - - + -
103B ARG* 3.3 8.2 - - - +
104B ILE* 3.0 33.4 + - + -
106B THR* 3.7 30.9 - - - +
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Residues in contact with TYR 85 (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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19A TRP* 4.5 1.1 - + + -
54A TYR* 3.7 58.1 + + + +
30B ILE* 3.7 42.9 + - + +
84B THR* 1.3 78.3 + - - +
86B VAL* 1.3 69.1 + - - +
101B TRP* 3.8 32.1 - - + -
102B ILE 3.2 16.8 - - - +
103B ARG* 3.3 37.9 + - + -
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Residues in contact with VAL 86 (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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87A VAL* 4.3 24.0 - - + -
105A ILE* 6.2 0.4 - - + -
52B PHE* 4.0 20.4 - - + -
84B THR* 3.8 9.2 - - + -
85B TYR* 1.3 82.7 - - - +
87B ARG* 1.3 64.5 + - - +
101B TRP* 3.5 7.2 - - - -
102B ILE* 2.9 34.9 + - + +
104B ILE* 3.5 50.5 - - + -
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Residues in contact with ARG 87 (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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49A LEU* 4.1 27.5 - - - +
50A LYS* 2.7 30.5 + - - +
51A GLN* 4.8 0.8 - - - +
52A TYR* 2.9 40.6 + - - +
50B GLN* 4.9 0.5 - - - +
52B PHE* 4.8 3.3 - - - -
86B VAL* 1.3 78.0 - - - +
88B ALA* 1.3 57.2 - - - +
99B TRP* 3.9 48.4 + - + +
100B ARG 3.3 6.3 - - - +
101B TRP* 3.3 41.5 - - + +
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Residues in contact with ALA 88 (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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37B VAL* 4.4 1.8 - - + -
50B GLN* 3.4 14.1 - - - +
52B PHE* 3.8 13.7 - - + -
87B ARG* 1.3 73.0 - - - +
89B LEU* 1.3 62.9 + - - +
90B THR* 3.5 12.1 + - + +
99B TRP* 3.3 6.5 - - - -
100B ARG 2.9 30.3 + - - +
102B ILE* 3.5 31.9 - - + -
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Residues in contact with LEU 89 (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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37B VAL* 3.9 0.2 - - - -
38B LEU* 3.2 30.7 + - + +
40B GLU 3.7 11.4 - - - +
41B ILE* 4.2 18.2 - - + -
42B LYS* 3.2 29.6 - - + +
50B GLN* 2.9 23.8 + - - +
88B ALA* 1.3 69.9 - - - +
90B THR* 1.3 62.5 + - - +
97B VAL* 4.3 6.7 - - + -
98B GLY* 3.5 25.4 - - - +
99B TRP* 3.7 36.1 - - + +
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Residues in contact with THR 90 (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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35B VAL* 3.9 21.8 - - + -
36B THR 3.0 16.6 - - - +
37B VAL* 4.1 9.9 - - + -
38B LEU* 4.2 5.8 - - - -
88B ALA* 3.7 21.3 - - + +
89B LEU* 1.3 81.4 - - - +
91B SER* 1.3 61.1 + - - +
97B VAL* 3.2 5.7 - - - +
98B GLY 2.7 38.9 + - - +
100B ARG* 2.9 30.8 + - + +
102B ILE* 4.2 7.2 - - + -
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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
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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