Contacts of the strand formed by residues 190 - 196 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A PHE* 3.6 29.4 - - + -
186A ARG 2.5 44.1 + - - -
187A SER 5.3 2.5 - - - -
189A GLU* 1.3 78.4 - - - +
191A TRP* 1.3 64.4 + - + +
169B HIS* 3.1 12.0 - - - -
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Residues in contact with TRP 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLN* 4.6 6.5 + - - +
131A ILE* 3.7 55.3 + - + -
134A LEU* 3.6 33.7 - - + -
135A LYS 3.2 26.7 - - - -
136A ARG* 3.5 31.5 - - + +
138A SER 4.2 4.3 - - - -
140A TYR* 4.5 0.7 - + - -
183A ILE* 4.1 8.7 - - + -
184A ASN* 3.3 43.7 - - - -
185A PHE* 3.7 21.7 - + + -
189A GLU* 4.1 4.9 - - - +
190A GLU* 1.3 85.4 - - + +
192A GLY* 1.3 59.2 + - - +
167B PHE* 4.7 1.7 - - - +
169B HIS* 3.5 2.5 + - - -
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Residues in contact with GLY 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLN* 4.7 3.4 - - - -
183A ILE* 3.4 3.7 - - - +
184A ASN* 3.0 31.5 + - - +
191A TRP* 1.3 76.8 - - - +
193A TRP* 1.3 69.0 + - - -
167B PHE 3.2 13.2 - - - -
169B HIS* 3.1 22.1 + - - -
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Residues in contact with TRP 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 4.0 20.2 - - + +
127A GLN* 3.1 23.4 + - - -
142A LEU* 3.7 23.9 - - + +
144A LEU* 3.8 21.8 - - + -
181A ALA* 4.9 0.4 - - + -
182A ILE 3.1 9.6 - - - +
183A ILE* 4.0 12.5 - - + +
192A GLY* 1.3 79.1 - - - -
194A ASN* 1.3 61.4 + - - +
155B TRP* 3.9 22.0 - + - -
165B VAL 4.0 4.7 - - - -
166B THR* 3.6 36.3 - - + -
167B PHE* 2.8 43.5 + + + +
168B TRP* 3.5 35.8 - + + -
169B HIS* 2.9 25.7 + - - +
172B GLU* 3.8 1.9 - - - +
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Residues in contact with ASN 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ALA* 3.2 3.3 - - - -
182A ILE* 2.8 50.7 + - + +
184A ASN* 4.7 6.3 - - - +
186A ARG* 3.0 26.3 - - - +
192A GLY 4.2 0.2 + - - -
193A TRP* 1.3 74.2 - - - +
195A ASP* 1.3 72.3 + - - +
196A ILE* 4.8 0.6 - - - +
168B TRP* 3.7 7.9 - - - -
169B HIS* 4.6 6.2 - - + -
172B GLU* 2.7 32.3 + - - +
199G HIS* 3.5 29.7 + - - -
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Residues in contact with ASP 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ARG* 3.0 38.6 + - - +
180A CYS 3.4 3.8 - - - -
194A ASN* 1.3 82.7 + - - +
196A ILE* 1.3 68.8 + - - +
151B ARG* 5.0 1.2 + - - -
153B TRP* 3.4 32.3 - - + -
168B TRP* 3.8 6.5 - - + -
172B GLU* 3.7 7.5 + - - +
173B PRO* 3.3 7.8 - - - +
174B ASN* 3.0 40.2 + - - +
199G HIS* 4.5 4.3 + - - -
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Residues in contact with ILE 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A PHE* 3.8 12.3 - - + -
179A ARG* 3.6 17.9 + - - +
180A CYS 2.9 39.5 + - - +
182A ILE* 3.7 44.9 - - + -
194A ASN* 4.6 1.6 - - + -
195A ASP* 1.3 82.4 - - - +
197A HIS* 1.3 74.4 + - - +
200A VAL* 4.1 4.9 - - + -
202A GLN* 4.0 7.4 - - + -
199G HIS* 4.3 11.7 - - + +
200G VAL* 3.9 40.6 - - + -
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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