Contacts of the strand formed by residues 66 - 72 (chain D) in PDB entry 5BOU
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 66 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61D GLU* 4.0 0.9 - - - +
62D ILE* 3.0 39.5 + - + -
63D ASP* 2.9 24.1 + - + +
64D ARG 3.5 0.8 + - - -
65D HIS* 1.3 101.8 - - + +
67D GLY* 1.3 68.0 + - - +
99D ILE* 3.3 34.1 - - + -
101D VAL* 4.1 21.3 - - + -
104D LEU* 3.9 15.7 - - + -
136D ILE* 3.8 18.4 - - + -
137D ALA 3.4 10.1 - - - +
138D GLY* 4.4 0.4 - - - -
220D PHE* 4.6 4.0 - - - -
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Residues in contact with GLY 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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40D LEU* 4.1 4.7 - - - -
60D VAL 3.6 6.5 - - - -
62D ILE* 4.5 0.4 - - - -
66D ILE* 1.3 79.0 - - - +
68D CYS* 1.3 63.0 + - - +
136D ILE* 3.7 2.6 - - - -
137D ALA* 2.7 32.9 + - - +
214D ILE* 5.2 2.2 - - - +
220D PHE* 3.6 29.2 - - - +
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Residues in contact with CYS 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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40D LEU* 3.8 8.2 - - - +
58D LYS 4.0 0.5 - - - +
59D ILE* 3.4 3.1 - - - +
60D VAL* 2.8 43.9 + - - +
62D ILE* 3.5 22.2 - - + -
67D GLY* 1.3 75.7 - - - +
69D ALA* 1.3 64.5 + - - +
70D MET* 5.3 2.8 - - - +
81D ILE* 3.7 25.8 - - + -
134D LEU* 3.9 31.9 - - - -
135D LEU 3.3 9.2 - - - +
136D ILE* 4.5 3.8 - - + -
220D PHE* 4.5 1.6 - - - -
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Residues in contact with ALA 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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29D ALA* 4.3 10.1 - - + -
40D LEU* 3.7 22.2 - - + +
41D GLY 5.1 1.6 - - - +
42D VAL* 3.9 22.7 - - + -
58D LYS 3.4 5.2 - - - +
59D ILE* 4.4 4.5 - - + -
68D CYS* 1.3 77.6 - - - +
70D MET* 1.3 59.9 + - - +
134D LEU* 3.4 4.5 - - - -
135D LEU* 2.8 39.9 + - + +
164D ILE* 4.6 0.3 - - - +
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Residues in contact with MET 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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27D SER* 4.6 2.6 + - - +
29D ALA* 4.0 9.3 - - - +
42D VAL* 4.6 1.6 - - - +
57D GLU 4.1 7.6 - - - +
58D LYS* 3.2 35.8 + - + +
60D VAL* 4.3 13.5 - - + -
68D CYS* 5.3 1.3 - - - +
69D ALA* 1.3 76.3 - - - +
71D SER* 1.3 64.3 + - - +
74D THR* 3.8 32.0 - - + +
77D ALA* 3.7 24.2 - - + -
78D ARG* 3.9 27.4 - - - +
81D ILE* 4.5 13.0 - - + -
132D VAL* 4.0 5.8 - - + -
133D ALA 3.5 4.3 - - - -
134D LEU* 3.8 15.9 - - + -
164D ILE* 4.5 2.0 - - - -
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Residues in contact with SER 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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23D ILE* 3.8 9.7 + - - +
26D GLY* 3.7 3.1 - - - -
27D SER* 2.6 30.2 + - - +
29D ALA* 4.5 1.3 - - - -
70D MET* 1.3 77.2 - - - +
72D GLY* 1.3 59.7 + - - +
74D THR* 5.0 2.2 - - - -
132D VAL* 3.3 4.1 - - - +
133D ALA 3.0 31.3 + - - -
164D ILE* 3.7 26.5 - - - -
165D GLY* 3.2 19.1 - - - -
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Residues in contact with GLY 72 (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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22D ALA 4.2 3.6 - - - -
23D ILE* 4.1 11.4 - - - -
26D GLY* 3.8 22.5 - - - -
27D SER* 4.7 1.2 + - - +
71D SER* 1.3 76.8 + - - +
73D LEU* 1.3 63.7 + - - +
74D THR* 3.0 16.9 + - - +
131D GLY 3.7 6.3 - - - -
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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