Contacts of the strand formed by residues 191 - 196 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D PHE* 4.8 1.9 - - - +
169D HIS* 3.4 3.3 + - - -
127E GLN* 5.0 5.7 + - - +
131E ILE* 4.0 47.9 + - + -
134E LEU* 3.5 38.8 - - + -
135E LYS 3.4 21.8 - - - -
136E ARG* 3.8 33.7 - - + +
138E SER 4.4 2.7 - - - -
140E TYR* 4.3 1.6 - + - -
183E ILE* 3.8 17.0 - - + -
184E ASN* 3.2 41.1 - - - -
185E PHE* 3.3 29.1 - + + -
190E GLU* 1.3 85.4 + - + +
192E GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D PHE 3.3 11.4 - - - -
169D HIS* 3.1 22.1 + - - -
127E GLN* 4.7 4.3 - - - -
183E ILE* 3.3 6.4 - - - +
184E ASN 3.0 32.4 + - - -
191E TRP* 1.3 76.7 - - - +
193E TRP* 1.3 66.6 + - - -
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Residues in contact with TRP 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D TRP* 3.7 24.7 - + - -
161D TYR* 4.7 0.7 - + - -
165D VAL 4.1 5.8 - - - -
166D THR* 3.9 30.5 - - + -
167D PHE* 2.8 42.0 + + + +
168D TRP* 3.5 31.1 - + + -
169D HIS* 2.9 26.2 + - - +
172D GLU* 4.0 1.7 - - - +
121E ILE* 3.9 25.1 - - + +
127E GLN* 3.4 22.6 + - - +
142E LEU* 3.6 24.0 - - + +
144E LEU* 3.7 26.7 - - + -
181E ALA* 5.5 0.4 - - + -
182E ILE 3.2 5.2 - - - +
183E ILE* 4.4 6.4 - - + +
192E GLY* 1.3 81.0 - - - -
194E ASN* 1.3 64.2 + - - +
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Residues in contact with ASN 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D TRP* 3.6 8.7 - - - -
169D HIS* 4.6 7.8 - - + -
172D GLU* 2.9 32.1 + - - +
181E ALA* 3.2 4.7 - - - -
182E ILE* 2.8 51.4 + - + +
184E ASN* 4.7 6.8 + - - +
186E ARG* 3.5 19.4 - - - +
193E TRP* 1.3 73.8 - - - +
195E ASP* 1.3 84.4 + - - +
196E ILE* 5.3 3.4 - - - +
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Residues in contact with ASP 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D ARG* 5.3 0.2 + - - -
153D TRP* 3.5 31.0 - - + -
168D TRP* 3.9 1.5 - - + -
172D GLU* 3.9 2.1 - - - +
173D PRO* 3.3 11.2 - - + +
174D ASN* 3.0 42.1 + - - +
179E ARG* 3.1 35.3 + - + -
180E CYS 3.3 4.3 - - - -
194E ASN* 1.3 90.8 + - - +
196E ILE* 1.3 69.0 - - - +
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Residues in contact with ILE 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E PHE* 3.8 6.7 - - + -
179E ARG* 3.5 15.3 + - - +
180E CYS 2.8 38.2 + - - +
182E ILE* 3.7 43.3 - - + -
194E ASN* 5.3 4.5 - - - +
195E ASP* 1.3 79.7 - - - +
197E HIS* 1.3 66.5 + - - +
200E VAL* 3.1 31.0 - - + -
202E GLN* 3.7 15.0 - - + +
200H VAL* 3.8 26.5 - - + -
201H PRO* 5.4 0.2 - - + -
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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