Contacts of the strand formed by residues 75 - 83 (chain A) in PDB entry 1BQU
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 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A TRP* 3.5 18.5 - - - +
47A ALA 5.0 1.6 + - - -
74A VAL* 1.3 78.7 - - - +
76A ILE* 1.3 59.1 + - - +
95A ASN* 3.3 23.3 + - - +
96A PHE* 3.3 4.7 - - - +
97A ASP* 3.4 27.6 + - - +
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Residues in contact with ILE 76 (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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24A MET* 4.3 4.7 - - + -
44A SER* 3.9 7.9 - - - -
45A GLU 3.7 20.6 - - - +
46A TRP* 3.9 10.8 - - + +
51A PHE* 4.1 10.1 - - + -
68A TYR* 3.2 38.6 - - + +
74A VAL 4.6 1.1 - - - +
75A ASN* 1.3 76.9 - - - +
77A GLU* 1.3 64.3 + - - +
78A VAL* 3.9 4.2 + - + -
94A ILE 3.7 0.9 - - - +
95A ASN* 3.3 7.6 - - - +
96A PHE* 2.8 63.1 + - + +
98A PRO* 4.2 12.1 - - + -
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Residues in contact with GLU 77 (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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43A LYS 3.9 0.2 - - - +
44A SER* 3.0 4.9 - - - -
45A GLU* 2.8 53.8 + - + +
76A ILE* 1.3 70.6 - - - +
78A VAL* 1.3 63.4 + - - +
79A TRP* 3.5 22.9 - - + -
93A HIS* 2.9 31.4 + - + +
94A ILE 3.5 3.8 - - - +
95A ASN* 3.1 31.4 + - - +
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Residues in contact with VAL 78 (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 LEU* 3.8 7.9 - - + +
16A CYS* 4.0 15.0 - - - -
24A MET* 4.1 11.0 - - + -
26A CYS* 4.2 1.3 - - - -
42A LEU* 3.5 28.7 - - + -
43A LYS 3.3 6.1 - - - +
44A SER* 3.8 14.1 - - - -
76A ILE* 4.1 10.1 - - + -
77A GLU* 1.3 82.2 - - - +
79A TRP* 1.3 67.7 + - - +
93A HIS* 3.4 1.0 - - - -
94A ILE* 2.9 46.3 + - + +
96A PHE* 3.9 18.6 - - + -
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Residues in contact with TRP 79 (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 LEU* 3.6 9.0 - - - -
42A LEU* 3.6 5.4 - - - +
43A LYS* 2.8 80.4 + - + +
45A GLU* 3.6 35.4 - - + -
50A LYS* 6.2 0.2 - - - -
77A GLU* 3.5 25.8 - - + -
78A VAL* 1.3 83.1 - - - +
80A VAL* 1.3 65.2 + - - +
81A GLU* 4.9 1.4 + - - +
90A THR* 3.8 34.1 - - + +
91A SER* 3.8 7.4 - - - +
93A HIS* 3.5 47.2 + + + -
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Residues in contact with VAL 80 (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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11A PRO* 4.0 18.9 - - + +
14A LEU* 3.7 20.2 - - + -
28A TRP* 3.6 60.6 - - + +
40A PHE* 4.1 8.5 - - + -
41A THR 3.5 9.6 - - - +
42A LEU* 4.2 3.4 - - + -
79A TRP* 1.3 79.5 - - - +
81A GLU* 1.3 66.2 + - - +
82A ALA 4.1 0.2 + - - -
89A VAL 3.9 0.2 - - - +
90A THR* 3.1 4.9 - - - -
91A SER* 2.9 36.4 + - - +
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Residues in contact with GLU 81 (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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39A ASN 3.6 1.9 - - - +
40A PHE* 3.5 2.1 - - - -
41A THR* 2.8 47.9 + - - +
43A LYS* 4.4 25.2 - - + +
79A TRP* 4.6 0.9 + - - -
80A VAL* 1.3 74.8 - - - +
82A ALA* 1.3 60.9 + - - +
83A GLU* 5.1 4.5 - - + +
88A LYS* 3.3 47.3 + - + +
89A VAL 3.4 2.9 - - - +
90A THR* 3.9 20.6 - - + +
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Residues in contact with ALA 82 (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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8A PRO* 3.7 22.2 - - + +
9A GLU 4.3 1.1 - - - +
11A PRO* 3.9 13.4 - - + +
39A ASN 3.3 6.5 - - - +
40A PHE* 3.6 29.4 - - + -
80A VAL 4.0 1.4 - - - -
81A GLU* 1.3 72.0 - - - +
83A GLU* 1.3 64.6 + - - +
88A LYS* 3.4 1.7 - - - +
89A VAL* 2.8 38.8 + - + -
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Residues in contact with GLU 83 (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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8A PRO* 4.1 1.1 - - - -
37A GLU 4.1 0.5 - - - +
38A THR* 3.5 5.7 - - - +
39A ASN* 2.9 47.8 + - + +
81A GLU* 5.1 4.4 - - + +
82A ALA* 1.3 77.5 - - - +
84A ASN* 1.3 70.0 + - - +
87A GLY 3.4 12.8 - - - +
88A LYS* 3.7 40.2 + - + +
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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