Contacts of the strand formed by residues 234 - 239 (chain B) in PDB entry 4KG8
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 TYR 234 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LEU 5.3 1.3 - - - -
180A LEU* 3.7 31.8 - - + +
181A VAL 5.0 0.7 - - - -
203A LEU* 4.2 3.8 - - - +
204A GLY 3.0 40.0 + - - -
97B HIS* 3.4 29.8 - + + +
98B LEU 3.0 14.8 - - - +
99B THR* 4.3 3.1 - - + -
114B TRP* 3.5 6.7 - - - -
144B TYR* 3.6 18.2 - + - -
145B SER* 3.1 8.7 + - - -
146B LYS* 2.8 71.6 + - + +
202B PHE* 3.8 2.7 - + - -
232B ARG* 4.4 6.1 - - - -
233B SER* 1.3 81.4 - - - +
235B PHE* 1.3 61.6 + - - +
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Residues in contact with PHE 235 (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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97B HIS* 4.5 0.2 - - - -
98B LEU* 2.6 53.2 + - + +
114B TRP* 3.6 40.6 - + + -
131B GLY 3.9 12.1 - - - -
133B LEU* 3.6 33.2 - - + -
143B ILE* 5.3 3.1 - - + -
144B TYR* 3.4 16.2 - - - -
145B SER* 4.5 0.4 - - - -
166B LEU* 3.5 21.1 - - + -
215B VAL* 3.4 37.0 - - + -
216B VAL* 4.6 0.2 - - - -
217B VAL* 3.6 16.8 - - + -
234B TYR* 1.3 78.3 - - - +
236B GLY* 1.3 67.5 - - - +
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Residues in contact with GLY 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ALA 3.1 14.4 - - - -
133B LEU* 4.2 6.3 - - - -
143B ILE* 3.5 2.6 - - - +
144B TYR* 2.9 50.5 + - - +
235B PHE* 1.3 82.2 - - - +
237B ALA* 1.3 64.3 + - - +
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Residues in contact with ALA 237 (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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206A VAL* 4.9 0.7 - - - +
95B ALA* 3.2 2.9 - - - +
96B ALA 2.8 32.1 + - - +
126B LEU* 4.5 12.1 - - + -
133B LEU* 3.8 18.8 - - + +
141B TYR* 4.6 8.1 - - + -
142B TYR 3.2 12.6 - - - +
143B ILE* 4.2 14.1 - - + -
144B TYR* 3.6 3.3 - - - -
209B LEU* 6.3 0.2 - - + -
236B GLY* 1.3 77.4 - - - +
238B PHE* 1.3 67.4 + - - +
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Residues in contact with PHE 238 (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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142A TYR* 3.6 21.3 - + + -
206A VAL* 3.6 18.4 - - + -
238A PHE* 3.9 20.6 - + - -
240A VAL* 3.4 37.9 - - + -
94B PRO 3.3 11.7 - - - +
95B ALA* 3.9 4.9 - - + +
141B TYR* 3.4 7.6 - - - -
142B TYR* 2.8 65.0 + + + -
144B TYR* 4.6 2.0 - + - -
237B ALA* 1.3 76.5 - - - +
239B MET* 1.3 67.7 - - - +
240B VAL* 3.6 18.8 - - + -
238C PHE* 3.9 14.4 - + - -
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Residues in contact with MET 239 (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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240A VAL* 4.8 3.8 - - - +
93B ASN 5.5 1.5 + - - +
94B PRO* 3.1 25.7 + - + +
137B LYS* 3.4 43.5 - - - +
138B ALA 4.2 13.2 - - - +
139B GLY* 4.8 3.4 - - - -
140B TYR 3.3 17.3 - - - +
141B TYR* 3.9 28.9 - - + -
238B PHE* 1.3 85.9 - - - +
240B VAL* 1.3 70.7 + - - +
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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