Contacts of the strand formed by residues 234 - 241 (chain B) in PDB entry 6MGP
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 VAL 234 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A ARG* 3.7 31.9 - - + +
94B GLN* 3.4 38.6 - - + +
95B LEU 3.3 7.9 - - - +
96B VAL* 4.3 7.6 - - + -
109B TRP* 4.0 3.3 - - - -
144B PHE* 4.5 9.2 - - + -
145B PHE* 3.1 8.9 - - - +
146B GLN* 3.0 43.1 + - + +
163B LEU* 5.8 0.2 - - - +
231B GLY 3.8 11.7 - - - +
232B ALA 4.1 2.9 - - - +
233B THR* 1.3 80.1 - - - +
235B LEU* 1.3 65.5 + - - +
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Residues in contact with LEU 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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93B ALA 4.1 0.3 - - - +
94B GLN* 3.2 2.3 - - - -
95B LEU* 2.8 44.1 + - + +
109B TRP* 3.6 27.8 - - + +
133B LEU* 4.6 22.7 - - + +
143B VAL* 4.2 15.3 - - + -
144B PHE 3.5 16.4 - - - +
145B PHE* 4.1 11.9 - - + -
165B LEU* 4.5 17.3 - - + -
212B LEU* 4.7 14.1 - - + +
214B VAL* 4.0 19.7 - - + -
234B VAL* 1.3 75.7 - - - +
236B GLY* 1.3 65.1 + - - +
237B LEU* 6.0 0.7 - - + -
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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
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93B ALA 3.3 9.6 - - - -
94B GLN* 4.1 3.6 - - - -
143B VAL* 3.5 3.8 - - - +
144B PHE* 2.9 59.5 + - - +
235B LEU* 1.3 76.8 - - - +
237B LEU* 1.3 67.6 + - - +
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Residues in contact with LEU 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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203A LEU* 4.1 1.4 - - - +
92B PHE* 3.2 4.5 - - - +
93B ALA* 2.9 49.2 + - + +
124B LEU* 4.4 6.5 - - + -
133B LEU* 3.8 25.8 - - + -
135B VAL* 4.7 5.4 - - + -
141B TYR* 3.6 19.7 - - + -
142B TYR 3.1 14.8 - - - +
143B VAL* 3.7 14.8 - - + -
144B PHE* 3.8 4.2 - - - -
206B LEU* 3.6 31.4 - - + -
212B LEU* 4.0 11.9 - - + -
235B LEU* 6.0 1.1 - - + -
236B GLY* 1.3 77.7 - - - +
238B PHE* 1.3 64.6 + - - +
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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* 3.7 25.8 - + + -
203A LEU* 3.7 18.2 - - + -
238A PHE* 3.9 20.0 - + - -
240A VAL* 3.7 20.9 - - + -
91B MET 3.3 6.1 - - - +
92B PHE* 3.6 16.2 - - + +
141B TYR* 3.5 6.2 - - - -
142B TYR* 3.0 61.7 + + + -
144B PHE* 4.4 3.1 - + - -
237B LEU* 1.3 76.5 - - - +
239B ARG* 1.3 72.8 + - - +
240B VAL* 4.3 4.0 - - + -
238C PHE* 3.9 29.8 - + - -
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Residues in contact with ARG 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* 5.8 1.7 - - - +
90B GLY 6.0 0.2 - - - -
91B MET* 2.9 39.8 + - + +
137B LYS* 4.1 13.1 - - - +
138B ALA 4.1 16.4 + - - -
140B VAL 3.5 14.4 - - - +
141B TYR* 3.5 40.1 - - + -
238B PHE* 1.3 78.6 - - - +
240B VAL* 1.3 61.3 + - - +
241B THR* 3.5 28.0 - - - +
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Residues in contact with VAL 240 (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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140B VAL* 2.9 40.6 + - + +
142B TYR* 4.1 18.2 - - + +
203B LEU* 4.2 4.5 - - + -
238B PHE* 4.2 7.9 - - + +
239B ARG* 1.3 75.1 - - - +
241B THR* 1.3 67.4 + - - +
90C GLY* 5.1 4.2 - - - -
92C PHE* 4.0 19.9 - - + -
238C PHE* 3.7 42.0 - - + -
239C ARG 6.0 0.7 - - - +
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Residues in contact with THR 241 (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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138B ALA 5.2 0.2 - - - -
139B GLY* 3.5 6.5 - - - -
140B VAL* 2.9 25.5 + - - +
239B ARG* 3.5 34.7 - - - +
240B VAL* 1.3 86.2 - - - +
89C GLN* 4.1 11.1 + - + -
90C GLY* 3.3 31.2 + - - +
92C PHE* 3.7 22.2 - - + -
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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