Contacts of the strand formed by residues 202 - 209 (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 GLN 202 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100D GLY 3.4 1.6 - - - +
101D MET* 3.2 7.2 - - - -
102D GLN 2.9 27.1 + - - +
107D SER* 4.2 2.9 + - - -
139D SER* 2.7 36.1 + - - +
141D PHE* 3.7 20.9 - - + +
182D ILE* 3.6 20.4 - - + +
196D ILE* 3.8 24.5 - - + -
200D VAL 3.4 1.5 + - - +
201D PRO* 1.3 86.1 - - - +
203D LYS* 1.3 72.0 + - - +
101F MET* 3.9 8.0 - - - +
200F VAL* 3.5 6.2 - - - +
201F PRO* 2.9 27.5 - - - +
202F GLN* 3.3 1.7 - - - +
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Residues in contact with LYS 203 (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 8.7 - - - +
99D THR* 3.2 41.4 - - - +
100D GLY 3.4 7.6 - - - +
101D MET* 4.1 8.3 - - + +
135D LYS* 4.0 12.9 - - - +
138D SER* 3.3 27.7 + - - +
139D SER 3.2 13.5 + - - +
140D TYR* 3.2 17.9 - - + -
141D PHE* 2.8 22.7 + - - +
202D GLN* 1.3 78.9 - - - +
204D SER* 1.3 63.6 + - - +
99F THR* 4.8 4.2 + - - -
101F MET* 4.0 20.5 - - - +
203F LYS* 4.2 23.9 - - - +
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Residues in contact with SER 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ILE* 3.8 1.0 - - - -
98D SER* 2.9 45.5 + - - +
100D GLY 4.9 2.3 + - - -
102D GLN* 5.6 0.7 + - - -
107D SER* 3.7 24.2 + - - -
110D ASN* 4.9 3.3 + - - -
111D CYS* 5.0 3.1 - - - -
118D LEU* 3.7 23.5 - - - +
140D TYR* 3.9 3.2 - - - -
141D PHE* 3.9 8.7 - - - +
203D LYS* 1.3 79.9 - - - +
205D ILE* 1.3 67.2 + - - +
206D CYS 4.3 0.2 - - - -
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Residues in contact with ILE 205 (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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95D TYR* 4.8 7.4 - - + -
96D PHE 3.5 9.6 - - - +
97D ILE* 4.0 13.2 - - + -
111D CYS* 4.3 0.4 - - - -
118D LEU* 3.4 9.4 - - - +
119D VAL* 2.9 55.0 + - + +
130D ILE* 3.9 17.0 - - + -
134D LEU* 3.7 26.0 - - + -
140D TYR* 3.8 25.1 - - + -
141D PHE 3.5 6.3 + - - +
142D LEU* 4.6 0.4 - - + -
183D ILE* 3.8 17.0 - - + -
204D SER* 1.3 80.1 - - - +
206D CYS* 1.3 69.9 + - - +
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Residues in contact with CYS 206 (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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87D TRP* 4.1 21.8 - - + -
95D TYR* 3.4 7.4 - - - +
96D PHE* 2.9 45.9 + - + +
98D SER* 5.1 1.8 - - - -
110D ASN* 4.9 6.5 - - - -
111D CYS* 2.0 53.8 - - + -
114D MET* 5.2 3.1 - - - -
116D ALA* 4.2 1.1 - - + -
117D ASP 3.2 4.3 - - - -
204D SER* 5.0 5.2 - - - -
205D ILE* 1.3 79.6 - - - +
207D LYS* 1.3 62.2 + - - +
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Residues in contact with LYS 207 (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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93D SER* 3.8 21.1 - - - -
94D CYS 3.3 5.8 - - - +
95D TYR* 3.7 15.9 - - + -
116D ALA* 3.4 1.8 - - - +
117D ASP* 2.8 32.7 + - + +
118D LEU 5.1 0.4 - - - +
119D VAL* 3.9 19.5 - - + -
120D VAL* 2.8 29.3 + - + +
122D ASN* 3.4 20.0 - - - +
126D GLU* 2.7 30.0 + - - +
205D ILE 4.4 0.2 + - - -
206D CYS* 1.3 74.8 - - - +
208D MET* 1.3 66.2 + - - +
157E ASP* 6.1 1.1 - - - -
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Residues in contact with MET 208 (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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84D PRO* 4.3 20.2 - - + -
87D TRP* 3.7 42.0 - - + -
93D SER* 3.4 5.4 - - - -
94D CYS* 2.7 48.4 + - + +
114D MET 3.5 24.5 - - - +
115D GLY 3.8 17.5 - - - +
116D ALA* 3.8 3.1 - - + +
207D LYS* 1.3 78.3 - - - +
209D LYS* 1.3 71.4 + - - +
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Residues in contact with LYS 209 (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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92D SER* 4.0 15.7 - - - +
93D SER* 4.7 3.6 - - - +
94D CYS* 4.8 1.4 - - - -
208D MET* 1.3 83.8 - - - +
210D LYS* 1.3 87.7 + - - +
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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