Contacts of the strand formed by residues 88 - 93 (chain D) in PDB entry 5WBY
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 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D ASN* 3.3 20.1 + - - +
60D ALA* 3.5 21.3 - - + +
61D GLY 2.9 12.2 + - - +
63D GLN* 4.2 5.4 - - - -
64D HIS* 3.6 28.7 - - - +
65D ILE* 3.6 28.3 - - + -
81D TYR 4.8 1.3 - - - +
84D VAL* 4.6 22.0 - - + -
86D LYS 4.6 2.5 - - - +
87D ASN* 1.3 75.6 - - - +
89D ALA* 1.3 61.9 + - - +
90D SER 3.8 17.9 - - - +
102D THR* 3.9 19.7 - - - +
103D GLY 3.7 4.7 - - - +
104D GLY* 5.0 3.6 - - - -
106D ASP* 5.2 0.4 - - - +
112D TRP* 5.5 0.7 - - + -
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Residues in contact with ALA 89 (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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2279B THR* 5.1 12.3 - - + -
46D ASN* 4.1 14.1 - - - +
47D ALA* 3.5 19.4 - - - +
87D ASN* 3.9 2.9 - - + -
88D ILE* 1.3 73.7 - - - +
90D SER* 1.3 59.5 + - - +
103D GLY 2.9 9.4 + - - +
104D GLY* 4.4 1.1 - - - -
105D GLU* 5.4 3.8 - - + +
131D ILE 3.8 17.0 - - - +
132D ASN* 3.4 24.7 - - - +
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Residues in contact with SER 90 (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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47D ALA* 4.5 2.7 - - - -
60D ALA* 4.8 0.4 - - - -
88D ILE* 3.8 5.6 - - - +
89D ALA* 1.3 77.6 + - - +
91D VAL* 1.3 65.9 + - - +
102D THR* 3.3 24.7 - - - -
103D GLY* 3.3 8.4 + - - -
132D ASN 3.8 2.9 + - - -
133D CYS* 3.5 15.2 - - - +
134D VAL* 3.4 41.2 + - - -
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Residues in contact with VAL 91 (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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47D ALA* 4.1 24.1 - - + +
49D GLU* 3.8 40.4 - - + +
58D ALA* 4.4 7.9 - - + -
60D ALA* 4.1 11.2 - - + -
65D ILE* 4.1 22.9 - - + -
90D SER* 1.3 80.4 + - - +
92D GLY* 1.3 57.8 + - - +
93D PHE* 5.2 1.3 - - + -
100D MET* 4.3 10.3 - - + -
101D TYR 3.2 5.2 - - - +
102D THR* 3.8 19.1 - - + -
134D VAL* 4.3 10.9 - - - +
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Residues in contact with GLY 92 (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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49D GLU* 5.2 2.5 - - - -
91D VAL* 1.3 76.6 - - - +
93D PHE* 1.3 66.9 + - - -
100D MET* 3.4 5.9 - - - +
101D TYR* 2.7 46.7 + - - -
134D VAL* 5.2 5.4 - - - -
135D CYS* 6.0 2.9 - - - -
136D LEU* 5.7 3.6 - - - -
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Residues in contact with PHE 93 (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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49D GLU* 3.7 35.0 - - + -
50D VAL 4.1 5.8 - - - -
51D THR* 3.6 37.0 - - + -
52D PRO* 3.7 23.7 - - + +
58D ALA* 3.8 22.0 - - + -
67D MET* 3.8 5.2 - - + -
91D VAL* 5.2 2.2 - - + -
92D GLY* 1.3 77.4 - - - -
94D HIS* 1.3 62.8 + - - +
95D GLU* 3.6 1.6 + - - -
97D GLY* 6.1 1.8 - - - -
99D TRP 3.7 7.0 - - - -
100D MET* 3.4 33.4 - - + -
101D TYR* 4.1 0.6 - - - -
114D LEU* 3.9 13.7 - - + -
136D LEU* 3.3 19.2 - - - +
140D GLN* 4.5 0.2 + - - -
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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