Contacts of the strand formed by residues 93 - 102 (chain D) in PDB entry 3WBR
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 SER 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D CYS* 4.0 0.4 - - - -
89D SER* 3.3 6.4 - - - -
90D PHE 2.8 32.5 + - - -
91D GLN 3.3 1.4 + - - -
92D SER* 1.3 86.8 + - - +
94D CYS* 1.3 64.6 + - - +
95D TYR* 3.6 28.1 + - - -
207D LYS* 3.8 21.2 - - - -
208D MET 3.4 10.0 + - - -
209D LYS* 4.8 4.3 - - - +
210D LYS* 4.0 2.6 - - - +
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Residues in contact with CYS 94 (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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83D CYS* 2.0 53.2 - - + -
84D PRO* 4.9 0.2 - - - -
87D TRP* 3.7 17.7 - - + -
88D THR 3.2 4.7 - - - -
93D SER* 1.3 70.6 - - - +
95D TYR* 1.3 64.2 + - - +
207D LYS* 3.3 5.7 - - - +
208D MET* 2.7 50.3 + - + +
209D LYS 4.8 0.4 - - - -
210D LYS* 3.8 24.2 - - - -
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Residues in contact with TYR 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D PRO 4.7 0.3 - - - +
87D TRP* 3.4 7.8 - - - -
88D THR* 2.6 49.3 + - - +
90D PHE* 3.6 25.4 + - + -
93D SER* 3.6 32.3 + - - -
94D CYS* 1.3 75.6 - - - +
96D PHE* 1.3 60.7 + - - +
97D ILE* 4.3 6.2 - - + +
119D VAL* 4.0 9.9 - - + -
126D GLU* 2.5 40.3 + - + +
129D PHE* 3.4 24.5 - + + -
130D ILE* 4.2 20.0 - - + -
133D ASN* 6.0 1.6 - - - +
205D ILE* 4.8 6.5 - - + -
206D CYS 3.4 12.6 - - - +
207D LYS* 3.7 16.3 - - + -
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Residues in contact with PHE 96 (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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86D PRO* 4.4 21.8 - - + -
87D TRP* 3.6 48.4 - + + -
95D TYR* 1.3 74.1 - - - +
97D ILE* 1.3 70.9 + - - +
98D SER* 3.6 32.2 + - - -
110D ASN* 5.4 1.6 - - - -
114D MET* 4.1 26.7 - - + -
205D ILE* 3.5 5.5 - - - +
206D CYS* 2.9 42.1 + - + -
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Residues in contact with ILE 97 (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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88D THR* 6.0 1.6 - - - +
95D TYR* 5.5 5.4 - - + +
96D PHE* 1.3 86.6 - - - +
98D SER* 1.3 62.7 + - - +
99D THR* 3.6 10.3 + - + +
130D ILE* 5.0 2.0 - - + +
133D ASN* 3.7 33.4 - - + +
134D LEU* 3.7 21.5 - - + -
135D LYS* 3.9 15.0 - - - +
140D TYR* 3.5 31.6 - - + +
204D SER 3.9 1.6 - - - -
205D ILE* 4.0 18.6 - - + -
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Residues in contact with SER 98 (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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96D PHE* 3.6 21.5 + - - -
97D ILE* 1.3 71.5 - - - +
99D THR* 1.3 59.7 + - - +
100D GLY* 3.3 11.8 + - - +
102D GLN* 5.1 1.4 + - - -
110D ASN* 3.1 25.2 + - - -
140D TYR* 4.7 0.9 - - - -
203D LYS* 3.3 8.7 - - - +
204D SER* 2.9 50.8 + - - +
206D CYS* 5.1 3.1 - - - -
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Residues in contact with THR 99 (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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97D ILE* 3.6 12.0 + - + +
98D SER* 1.3 71.4 + - - +
100D GLY* 1.3 62.1 + - - +
101D MET* 3.9 1.2 + - - +
135D LYS* 4.2 24.9 - - - +
203D LYS* 3.2 29.8 - - - +
137F ASN* 4.0 13.0 + - - -
203F LYS* 4.6 5.9 + - - -
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Residues in contact with GLY 100 (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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98D SER* 3.3 11.2 + - - +
99D THR* 1.3 80.7 + - - +
101D MET* 1.3 61.1 + - - -
102D GLN* 3.9 12.4 + - - +
107D SER* 5.6 0.2 + - - -
202D GLN 3.4 1.9 - - - +
203D LYS* 3.4 20.3 - - - -
204D SER* 4.4 2.3 + - - -
137F ASN* 3.8 21.9 - - - +
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Residues in contact with MET 101 (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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99D THR 4.6 2.7 - - - +
100D GLY* 1.3 70.5 - - - -
102D GLN* 1.3 65.4 + - - +
201D PRO* 3.7 21.2 - - + +
202D GLN 3.2 14.4 - - - +
203D LYS* 4.1 12.1 - - + +
101F MET* 3.8 17.0 - - + -
137F ASN* 2.7 25.5 + - - +
138F SER* 4.0 10.1 - - - -
139F SER* 3.5 38.4 - - - +
202F GLN* 3.4 26.2 - - - +
203F LYS* 4.0 27.4 - - - +
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Residues in contact with GLN 102 (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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98D SER* 5.1 1.4 + - - -
100D GLY* 4.4 8.6 - - - +
101D MET* 1.3 84.1 - - - +
103D SER* 1.3 72.5 + - - +
106D LYS* 3.5 35.4 + - + +
107D SER* 3.5 7.4 + - - +
110D ASN* 3.8 28.9 + - - +
141D PHE* 3.3 4.0 - - - -
201D PRO* 3.6 10.5 - - - -
202D GLN 2.9 26.7 + - - +
204D SER* 5.6 1.0 + - - -
137F ASN* 6.5 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