Contacts of the strand formed by residues 190 - 197 (chain B) 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 GLU 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A HIS* 3.0 12.3 - - - -
136B ARG* 5.9 0.2 + - - -
185B PHE* 3.6 28.6 - - + -
186B ARG 2.5 43.0 + - - -
187B SER 4.2 2.4 - - - -
189B GLU* 1.3 81.6 - - - +
191B TRP* 1.3 67.9 + - + +
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Residues in contact with TRP 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A PHE* 4.7 1.6 - - - +
169A HIS* 3.5 2.5 - - - -
127B GLN* 4.7 6.8 + - - +
131B ILE* 3.5 53.9 + - + +
134B LEU* 3.5 37.9 - - + -
135B LYS 3.2 23.3 - - - -
136B ARG* 3.4 35.5 - - + +
138B SER 4.2 5.2 - - - -
140B TYR* 4.4 0.7 - + - -
183B ILE* 3.9 14.8 - - + -
184B ASN* 3.3 40.8 - - - -
185B PHE* 3.7 19.6 - + + -
189B GLU* 4.1 4.9 - - - +
190B GLU* 1.3 88.0 - - + +
192B GLY* 1.3 57.1 + - - +
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Residues in contact with GLY 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A PHE 3.2 12.8 - - - -
169A HIS* 3.1 20.7 + - - -
127B GLN* 4.7 3.6 - - - -
183B ILE* 3.3 5.3 - - - +
184B ASN 3.0 32.2 + - - +
191B TRP* 1.3 74.7 - - - +
193B TRP* 1.3 68.9 + - - -
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Residues in contact with TRP 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A TRP* 3.8 22.7 - + - -
165A VAL 4.2 4.9 - - - -
166A THR* 3.6 33.9 - - + -
167A PHE* 2.8 42.4 + + - +
168A TRP* 3.5 37.8 - + + -
169A HIS* 2.9 19.9 + - - +
172A GLU* 3.7 2.1 - - - +
121B ILE* 4.0 20.8 - - + +
127B GLN* 3.0 26.5 + - - -
142B LEU* 3.6 25.2 - - + +
144B LEU* 3.9 22.9 - - + -
181B ALA* 4.9 0.4 - - + -
182B ILE 3.0 8.1 - - - +
183B ILE* 4.1 8.2 - - + +
192B GLY* 1.3 80.4 - - - -
194B ASN* 1.3 65.4 + - - +
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Residues in contact with ASN 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A TRP* 3.6 4.6 - - - -
169A HIS* 3.1 21.2 - - - -
172A GLU* 3.4 13.3 - - - +
181B ALA* 3.3 5.5 - - - -
182B ILE* 2.8 47.9 + - + +
184B ASN* 3.1 31.9 + - - +
186B ARG* 3.1 22.6 + - - +
192B GLY 4.1 0.2 + - - -
193B TRP* 1.3 75.9 - - - +
195B ASP* 1.3 61.5 + - - +
196B ILE* 4.6 4.9 - - + -
199C HIS 5.8 1.8 + - - -
201C PRO* 5.5 1.8 - - - +
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Residues in contact with ASP 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ARG* 3.4 15.9 + - - -
153A TRP* 3.4 28.0 - - + -
168A TRP* 3.9 7.6 - - + -
172A GLU* 3.0 23.6 + - - +
173A PRO* 3.4 4.4 - - - +
174A ASN* 2.9 30.9 + - - +
179B ARG* 3.0 37.0 + - - +
180B CYS 3.4 3.1 - - - -
194B ASN* 1.3 74.5 - - - +
196B ILE* 1.3 65.3 + - - +
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Residues in contact with ILE 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B PHE* 3.8 23.3 - - + -
179B ARG* 3.4 15.2 - - - +
180B CYS 2.9 39.3 + - - +
182B ILE* 3.6 36.3 - - + -
194B ASN* 4.6 3.8 - - + -
195B ASP* 1.3 81.4 - - - +
197B HIS* 1.3 75.5 + - - +
200B VAL* 4.2 4.9 - - + -
202B GLN* 3.9 10.8 - - + -
200C VAL* 4.0 35.9 - - + -
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Residues in contact with HIS 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ASP* 3.3 31.4 + - + +
178B GLU* 3.5 28.5 + - - -
179B ARG* 3.7 15.8 - - - +
196B ILE* 1.3 90.6 - - - +
198B CYS* 1.3 63.9 + - - +
199B HIS* 3.2 60.1 + + + +
200B VAL* 3.4 23.9 + - + +
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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