Contacts of the strand formed by residues 191 - 196 (chain H) 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 TRP 191 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F PHE* 4.6 1.9 - - - +
169F HIS* 3.6 2.9 + - - -
127H GLN* 4.9 3.6 + - - +
131H ILE* 3.5 52.9 + - + +
134H LEU* 3.6 40.6 - - + -
135H LYS 3.3 24.5 - - - -
136H ARG* 3.8 33.3 - - + +
138H SER 4.3 4.3 - - - -
140H TYR* 4.5 0.9 - + - -
183H ILE* 4.1 11.2 - - + -
184H ASN* 3.4 29.8 - - - -
185H PHE* 3.4 37.1 - + + -
190H GLU* 1.3 87.3 + - + +
192H GLY* 1.3 59.3 + - - +
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Residues in contact with GLY 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F PHE* 3.1 13.9 - - - -
169F HIS* 3.2 21.9 + - - -
127H GLN* 4.7 4.2 - - - +
183H ILE* 3.4 5.5 - - - +
184H ASN 3.0 30.7 + - - -
191H TRP* 1.3 76.7 - - - +
193H TRP* 1.3 65.9 + - - -
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Residues in contact with TRP 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F TRP* 3.8 23.1 - + - -
161F TYR* 4.6 0.4 - + - -
165F VAL 4.0 6.5 - - - -
166F THR* 3.7 33.2 - - + -
167F PHE* 2.7 47.4 + + + +
168F TRP* 3.5 40.1 - + + -
169F HIS* 2.9 25.0 + - - +
172F GLU* 4.0 1.9 - - - +
121H ILE* 4.0 24.6 - - + +
127H GLN* 3.1 22.1 + - - -
142H LEU* 3.7 23.5 - - + +
144H LEU* 4.0 20.4 - - + -
182H ILE 3.1 6.3 - - - +
183H ILE* 4.3 7.1 - - + +
192H GLY* 1.3 79.1 - - - -
194H ASN* 1.3 62.0 + - - +
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Residues in contact with ASN 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E HIS* 6.2 2.0 - - - +
168F TRP* 3.8 8.7 - - - -
169F HIS* 4.4 9.0 - - + -
172F GLU* 2.9 32.3 + - - +
181H ALA* 3.2 4.7 - - - +
182H ILE* 2.8 50.6 + - + +
184H ASN* 4.8 4.9 + - - +
186H ARG* 3.4 17.6 - - - +
193H TRP* 1.3 76.0 - - - +
195H ASP* 1.3 85.7 + - - +
196H ILE* 4.9 6.3 - - - +
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Residues in contact with ASP 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F ARG* 5.2 1.6 + - - -
153F TRP* 3.5 31.0 - - + -
168F TRP* 4.0 1.7 - - + -
172F GLU* 3.8 2.4 - - - +
173F PRO* 3.2 10.8 - - + +
174F ASN* 2.9 47.4 + - - +
179H ARG* 2.9 32.1 + - + +
180H CYS 3.3 4.5 - - - -
181H ALA* 4.5 0.4 - - - +
194H ASN* 1.3 91.2 + - - +
196H ILE* 1.3 69.4 + - - +
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Residues in contact with ILE 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E VAL* 3.7 26.7 - - + -
141H PHE* 3.6 22.7 - - + -
179H ARG* 3.6 16.7 - - - +
180H CYS 2.8 38.2 + - - +
182H ILE* 3.8 35.9 - - + -
194H ASN* 4.9 6.1 - - - +
195H ASP* 1.3 81.0 - - - +
197H HIS* 1.3 74.6 + - - +
200H VAL* 4.1 11.4 - - + -
202H GLN* 3.8 17.0 - - + +
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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