Contacts of the strand formed by residues 77 - 84 (chain A) in PDB entry 4BPU
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 LYS 77 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TYR* 5.4 0.2 - - - -
47A PHE* 3.4 6.6 - - - -
48A THR* 3.0 59.5 + - + +
52A ASP* 4.4 11.5 + - - -
75A PRO* 3.7 3.1 - - - +
76A TYR* 1.3 86.8 - - + +
78A ILE* 1.3 66.6 - - - +
79A ASP* 4.3 12.8 - - - +
318A LYS* 6.2 5.2 - - - -
322A SER* 5.5 3.1 - - - -
325A PRO* 4.4 22.7 - - + -
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Residues in contact with ILE 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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17A TYR* 3.5 24.7 - - + +
21A PHE* 4.7 9.0 - - + -
26A TYR* 4.2 9.4 - - - +
45A PHE* 4.4 11.7 - - + -
46A SER 3.5 3.8 - - - +
47A PHE* 3.9 17.0 - - + -
70A MET* 3.6 33.0 - - + -
75A PRO* 3.7 16.2 - - + -
77A LYS* 1.3 78.3 - - - +
79A ASP* 1.3 62.8 + - - +
318A LYS* 3.7 1.6 - - - +
319A SER* 2.8 43.2 + - - -
322A SER* 3.4 21.4 + - - +
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Residues in contact with ASP 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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45A PHE* 3.3 9.0 - - - +
46A SER* 2.9 52.5 + - - +
48A THR* 5.1 3.5 + - - -
54A TYR* 4.6 10.6 + - - -
77A LYS* 5.0 10.3 - - - +
78A ILE* 1.3 86.4 + - - +
80A ILE* 1.3 62.5 + - - +
316A LEU* 4.0 18.9 - - + +
317A LEU 3.4 7.9 - - - +
318A LYS* 3.3 21.7 + - - +
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Residues in contact with ILE 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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26A TYR* 3.3 28.5 - - + +
29A TRP* 3.7 30.3 - - + -
30A LEU* 4.4 8.7 - - + -
43A ARG* 3.8 24.7 - - + +
44A GLU 4.0 3.4 - - - +
45A PHE* 4.3 6.3 - - + -
79A ASP* 1.3 74.1 - - - +
81A GLY* 1.3 71.7 + - - +
104A LYS* 5.0 1.3 + - - +
168A TRP* 3.8 22.6 - - + -
315A HIS 3.6 2.4 - - - +
316A LEU* 3.3 3.1 - - - -
317A LEU* 2.8 28.4 + - - +
319A SER* 3.5 20.4 - - - +
320A PRO* 3.9 6.5 - - + -
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Residues in contact with GLY 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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43A ARG* 2.7 34.8 + - - -
44A GLU* 2.9 18.6 + - - -
80A ILE* 1.3 75.5 - - - +
82A ALA* 1.3 57.0 + - - -
104A LYS* 3.6 9.4 - - - +
314A ASN 5.5 0.2 - - - -
315A HIS 3.8 9.0 - - - -
316A LEU* 3.5 19.1 - - - +
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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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43A ARG* 3.5 1.6 - - - +
44A GLU* 2.9 26.4 + - - +
81A GLY* 1.3 72.9 - - - -
83A VAL* 1.3 64.5 + - - +
84A TYR* 3.5 19.1 - - + -
101A ALA* 3.7 25.4 - - + -
103A GLU 3.5 10.8 - - - +
104A LYS* 3.8 5.6 - - - +
313A ILE* 3.2 22.9 - - + +
314A ASN* 4.2 4.7 - - - +
315A HIS 4.8 0.2 + - - -
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Residues in contact with VAL 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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39A TYR* 3.5 57.0 - - + +
42A HIS* 3.6 15.3 - - + +
43A ARG* 3.6 34.5 - - - +
82A ALA* 1.3 71.6 - - - +
84A TYR* 1.3 64.4 + - - +
102A GLN* 2.9 27.4 + - + +
103A GLU* 2.7 27.6 + - + +
104A LYS* 5.5 0.4 - - - -
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Residues in contact with TYR 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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42A HIS* 2.9 35.8 + - - +
44A GLU* 2.7 43.0 + - + -
56A ARG* 3.4 2.6 + - - -
57A TYR* 4.7 0.2 - + - -
82A ALA* 3.5 21.1 - - + -
83A VAL* 1.3 78.2 - - - +
85A SER* 1.3 60.5 + - - +
86A HIS 3.2 17.3 - - - +
88A PRO* 4.2 4.9 - - + -
99A PHE* 3.6 34.3 - + + -
100A GLN 3.3 23.6 - - - -
101A ALA* 3.5 12.3 - - + -
102A GLN* 3.9 8.2 - - - +
314A ASN* 3.9 8.8 - - - +
244D GLU* 3.3 40.5 + - + +
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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