Contacts of the strand formed by residues 139 - 146 (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 139 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138D SER* 1.3 77.1 - - - +
140D TYR* 1.3 62.8 + - - +
182D ILE* 3.5 4.2 - - - +
183D ILE 3.6 4.8 + - - -
184D ASN* 3.2 27.3 + - - +
202D GLN* 2.7 30.3 + - - +
203D LYS* 3.2 26.5 + - - +
101F MET* 3.5 12.3 - - - +
201F PRO* 3.8 20.1 - - - +
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Residues in contact with TYR 140 (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* 3.5 22.2 - - + -
134D LEU* 3.6 31.8 - - + -
135D LYS* 2.8 45.1 + - - -
138D SER* 3.2 27.5 - - - -
139D SER* 1.3 76.4 + - - +
141D PHE* 1.3 60.8 + - - +
182D ILE* 3.1 7.5 - - - -
183D ILE* 2.7 47.2 + - + +
191D TRP* 4.7 1.1 - + - -
202D GLN* 4.7 0.4 - - - -
203D LYS* 3.2 32.1 - - + +
204D SER* 3.9 12.8 - - - -
205D ILE* 3.8 25.4 - - + -
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Residues in contact with PHE 141 (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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102D GLN 3.3 12.8 - - - -
104D TRP* 3.3 46.7 - + + -
107D SER* 3.9 7.0 - - - -
118D LEU* 4.2 8.4 - - + +
140D TYR* 1.3 73.8 - - - +
142D LEU* 1.3 62.2 + - - +
180D CYS* 3.9 18.2 - - + -
181D ALA 3.6 5.6 - - - -
182D ILE* 3.6 12.1 - - + +
196D ILE* 3.8 23.3 - - + -
197D HIS 4.3 1.1 - - - -
198D CYS 3.7 12.8 - - - -
200D VAL 3.3 26.0 - - - -
202D GLN* 3.7 19.5 - - + +
203D LYS 2.8 12.7 + - - +
204D SER* 3.9 7.6 - - - -
205D ILE* 3.5 24.3 + - - +
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Residues in contact with LEU 142 (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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104D TRP* 2.7 31.5 + - - -
118D LEU* 3.9 5.6 - - - +
119D VAL* 3.8 19.5 - - + +
121D ILE* 3.8 23.1 - - + -
141D PHE* 1.3 76.4 - - - +
143D GLY* 1.3 53.4 + - - +
144D LEU* 3.0 15.2 + - + +
181D ALA* 3.0 28.3 + - + +
182D ILE 4.3 3.1 - - - +
183D ILE* 3.6 31.9 - - + +
193D TRP* 3.6 45.1 - - + +
205D ILE* 4.6 2.5 - - + -
155E TRP* 4.6 2.9 - - + -
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Residues in contact with GLY 143 (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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104D TRP* 4.0 10.9 - - - -
118D LEU* 3.5 27.9 - - - +
119D VAL 2.8 20.0 + - - +
142D LEU* 1.3 68.9 - - - +
144D LEU* 1.3 57.3 + - - +
154E GLN 3.7 0.3 - - - +
155E TRP* 3.3 12.2 - - - -
156E VAL* 2.8 31.4 + - - +
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Residues in contact with LEU 144 (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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104D TRP* 3.8 5.2 + - - -
142D LEU* 3.0 5.7 + - + +
143D GLY* 1.3 78.1 - - - +
145D SER* 1.3 64.5 + - - +
180D CYS* 3.7 0.9 - - - -
181D ALA* 2.9 41.8 + - + +
193D TRP* 4.1 13.7 - - + -
153E TRP* 3.9 11.4 - - + -
154E GLN 3.3 20.9 - - - +
155E TRP* 3.6 36.1 - - + -
161E TYR* 3.8 24.9 - - + -
168E TRP* 3.7 31.0 - - + -
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Residues in contact with SER 145 (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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104D TRP* 3.9 21.7 - - - -
144D LEU* 1.3 77.5 - - - +
146D ASP* 1.3 63.6 + - - +
147D PRO* 4.0 5.1 - - - +
179D ARG 3.2 14.4 - - - -
180D CYS* 3.9 14.8 - - - -
198D CYS* 5.1 0.2 - - - -
153E TRP* 3.6 9.6 - - - -
154E GLN* 2.8 40.7 + - - +
156E VAL* 5.9 0.7 + - - -
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Residues in contact with ASP 146 (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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145D SER* 1.3 75.5 - - - +
147D PRO* 1.3 70.1 - - - +
148D GLY* 2.8 18.8 + - - +
176D LEU* 5.1 4.2 - - - +
178D GLU* 3.2 3.6 - - - +
179D ARG* 2.8 34.6 + - + +
198D CYS* 5.2 0.2 - - - -
151E ARG* 2.8 57.4 + - + +
152E HIS* 3.8 19.0 + - - +
153E TRP* 3.7 7.0 - - + -
176E LEU* 5.1 3.5 - - - +
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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