Contacts of the strand formed by residues 286 - 292 (chain B) in PDB entry 6CAJ
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 GLN 286 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B GLU* 4.1 26.9 + - - +
178B VAL* 3.2 13.0 + - + +
179B SER* 3.9 1.0 - - - -
180B VAL* 2.9 28.6 + - - +
211B ARG* 2.7 52.2 + - - +
276B LEU* 5.1 0.9 - - - -
277B LEU* 6.0 1.8 - - - -
285B ASN* 1.3 74.7 - - - +
287B ILE* 1.3 63.1 + - - +
288B HIS* 3.3 32.5 + - + -
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Residues in contact with ILE 287 (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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180B VAL* 4.5 0.4 - - + -
181B MET* 3.3 39.5 - - + +
183B MET* 3.7 27.6 - - + -
211B ARG* 3.6 5.7 - - - +
212B VAL* 2.9 33.4 + - + +
272B PHE* 4.6 4.5 - - + -
273B VAL* 3.7 33.0 - - + +
276B LEU* 3.7 28.9 - - + -
277B LEU* 5.2 10.4 - - + +
286B GLN* 1.3 79.1 - - - +
288B HIS* 1.3 68.3 + - - +
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Residues in contact with HIS 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ARG* 3.3 45.1 - - + +
175B GLU* 6.0 0.9 - - + -
179B SER* 2.9 36.2 + - - -
181B MET 2.6 13.5 + - - +
182B THR* 3.4 1.7 - - - +
183B MET* 2.8 28.4 + - - +
209B THR* 3.6 13.9 - - - -
210B ASN 3.6 4.9 - - - +
211B ARG* 3.5 21.1 - - + +
212B VAL* 4.0 1.5 - - - +
286B GLN* 3.3 42.2 + - + -
287B ILE* 1.3 80.4 - - - +
289B MET* 1.3 59.9 + - - +
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Residues in contact with MET 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU* 5.2 0.2 - - - +
171B ARG* 4.9 2.3 + - - -
182B THR* 4.2 4.6 - - - +
183B MET 3.3 18.4 - - - +
185B PHE* 3.7 13.7 - - + -
203B VAL* 4.8 0.2 - - - -
205B VAL* 3.7 40.2 - - + -
210B ASN* 2.7 54.9 + - + +
212B VAL* 3.7 10.8 - - + -
241B ARG* 4.7 5.8 - - - +
244B LEU* 3.7 28.5 - - + -
288B HIS* 1.3 77.5 - - - +
290B HIS* 1.3 64.5 + - - +
291B VAL* 3.8 20.6 - - + +
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Residues in contact with HIS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE* 5.5 0.7 - - + -
160B ASN 5.1 7.2 - - - -
163B ARG* 3.9 29.4 - - + +
164B ALA* 3.6 36.1 + - + +
167B GLU* 3.2 27.5 + - - +
171B ARG* 5.8 0.4 - - - +
182B THR* 4.0 7.2 - - + +
183B MET 3.2 6.2 + - - +
184B ILE* 3.4 15.1 - - + +
185B PHE* 2.9 27.2 + - - +
210B ASN* 5.3 1.6 - - - +
289B MET* 1.3 76.1 - - - +
291B VAL* 1.3 88.3 + - - +
292B THR* 3.7 18.3 + - + -
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Residues in contact with VAL 291 (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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185B PHE 3.8 2.2 - - - +
187B GLU* 3.7 35.7 - - + +
210B ASN* 6.1 2.0 - - + -
241B ARG* 4.1 20.4 - - - +
244B LEU* 4.6 10.8 - - + -
289B MET* 3.8 30.3 - - + -
290B HIS* 1.3 92.3 + - - +
292B THR* 1.3 64.3 + - - +
293B ALA* 4.2 2.1 + - + +
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Residues in contact with THR 292 (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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159B ILE* 3.4 30.4 - - + +
184B ILE* 3.9 3.3 - - - +
185B PHE 3.0 17.4 + - - -
186B LYS* 3.3 6.7 - - - +
187B GLU* 3.0 25.5 + - - +
290B HIS* 3.7 14.5 + - + -
291B VAL* 1.3 74.4 - - - +
293B ALA* 1.3 62.8 + - - +
294B LYS 4.2 0.7 - - - +
295B GLU* 3.4 45.5 - - + +
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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