Contacts of the strand formed by residues 65 - 71 (chain D) in PDB entry 5BUG
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 TYR 65 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D VAL* 4.5 2.6 + - - +
57D LEU* 3.6 51.4 - - + +
58D ASP* 3.2 34.0 + - - -
61D HIS* 3.1 22.7 - - + +
62D LYS 3.7 7.2 - - - -
63D ASN* 3.7 2.1 - - - -
64D HIS* 1.3 82.5 - - - +
66D LYS* 1.3 61.6 + - - +
67D ILE* 4.0 4.5 - - + -
81D PHE* 3.8 11.5 - + - -
82D ASN 3.6 21.0 + - - -
83D CYS* 3.3 49.7 - - + +
84D ARG 4.6 0.7 + - - -
111D TRP* 3.5 11.6 - - - -
119D VAL* 3.2 20.6 - - + +
121D ALA 5.7 1.1 - - - +
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Residues in contact with LYS 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ASP* 5.2 2.2 + - - -
65D TYR* 1.3 76.2 - - - +
67D ILE* 1.3 64.9 + - - +
68D TYR* 3.6 26.8 + - + +
83D CYS* 4.5 0.7 - - - -
84D ARG* 3.4 59.5 - - + +
86D ALA* 3.9 19.2 - - - +
107D ASP* 3.0 26.5 + - - -
111D TRP* 3.5 36.3 - - + +
119D VAL 3.1 4.6 + - - -
120D ALA* 3.4 4.9 - - - -
121D ALA 3.0 23.2 + - - -
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Residues in contact with ILE 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D MET* 4.2 4.9 - - + -
57D LEU* 3.7 23.3 - - + -
65D TYR* 4.0 6.7 - - + -
66D LYS* 1.3 75.8 - - - +
68D TYR* 1.3 68.9 + - - +
76D TYR* 3.4 23.6 - - - +
81D PHE* 4.0 18.8 - - + -
83D CYS* 3.6 18.4 - - - -
84D ARG 3.0 9.1 + - - +
85D VAL* 3.4 10.1 - - + -
86D ALA 2.8 25.2 + - - -
121D ALA* 3.3 26.7 - - + +
123D HIS* 3.6 21.1 - - + +
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Residues in contact with TYR 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D LYS* 3.6 33.9 - - + +
67D ILE* 1.3 77.6 - - - +
69D ASN* 1.3 60.3 + - - +
70D LEU* 3.8 2.8 + - + -
86D ALA* 3.4 17.7 - - + -
88D TYR* 3.9 9.9 - + + -
104D PHE* 3.6 32.5 - + + -
107D ASP* 2.6 43.8 + - + -
108D LEU* 3.4 34.0 - - + -
111D TRP* 3.7 5.3 - + - +
120D ALA* 4.0 12.8 - - + -
121D ALA 2.8 14.0 + - - +
122D ILE* 3.6 13.9 - - + +
123D HIS* 3.2 26.3 + - - +
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Residues in contact with ASN 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 5.1 0.2 - - - -
67D ILE* 4.1 1.2 - - - +
68D TYR* 1.3 71.2 - - - +
70D LEU* 1.3 60.8 + - - +
71D CYS* 2.8 42.5 + - - +
74D ARG 3.6 20.0 + - - -
75D HIS* 4.6 3.2 - - - +
76D TYR* 3.7 25.2 - - - +
85D VAL* 4.2 8.4 - - + +
86D ALA 2.7 14.7 + - - +
87D GLN* 3.4 22.3 + - - +
88D TYR 3.0 26.2 + - - -
89D PRO* 4.2 0.5 - - - +
123D HIS* 3.7 21.5 - - - +
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Residues in contact with LEU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D TYR* 4.2 7.9 - - + +
69D ASN* 1.3 74.5 + - - +
71D CYS* 1.3 61.6 + - - +
88D TYR* 3.2 35.0 - - + +
89D PRO* 3.8 2.5 - - - -
90D PHE* 3.3 19.4 + - + +
104D PHE* 4.2 13.9 - - + -
122D ILE* 3.9 11.7 - - + -
123D HIS 3.1 12.1 + - - +
124D CYS* 4.0 7.2 - - + -
130D ARG* 3.2 29.9 + - + +
131D THR* 3.7 35.7 - - - +
134D MET* 3.8 22.0 - - + -
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Residues in contact with CYS 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 4.0 18.4 - - - -
69D ASN* 2.8 20.0 + - - +
70D LEU* 1.3 77.6 - - - +
72D ALA* 1.3 58.7 + - - +
73D GLU* 3.1 15.4 + - + -
74D ARG* 3.8 18.3 - - - +
87D GLN* 4.9 5.9 - - - +
89D PRO* 3.1 13.0 - - - +
123D HIS* 4.7 0.2 - - - -
124D CYS* 2.0 61.7 - - - -
125D LYS* 5.0 1.6 - - - -
130D ARG* 3.8 0.4 - - - +
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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