Contacts of the strand formed by residues 234 - 241 (chain B) in PDB entry 6Q2J
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 GLU 234 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ARG* 2.5 49.9 + - + +
218B ALA 3.6 16.2 - - - +
219B SER* 4.8 3.4 - - - +
232B PRO* 3.2 13.9 - - - +
233B ARG* 1.3 81.6 - - + +
235B VAL* 1.3 63.0 + - - +
236B GLN* 4.1 10.2 + - - +
140D GLY* 5.5 4.2 - - - +
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Residues in contact with VAL 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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216B VAL 3.8 1.0 - - - +
217B ARG* 3.6 2.8 - - - -
218B ALA* 2.9 40.5 + - + +
219B SER 5.4 0.7 - - - -
220B LEU* 4.0 27.4 - - + -
223B LEU* 4.8 14.8 - - + -
225B TRP* 5.6 4.3 - - + -
232B PRO* 4.0 15.3 - - + -
234B GLU* 1.3 77.8 - - - +
236B GLN* 1.3 65.4 + - - +
237B VAL* 3.7 22.7 + - + +
282B MET* 3.8 26.0 - - + -
284B LEU* 6.3 2.0 - - + -
300B LEU* 5.2 4.0 - - + -
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Residues in contact with GLN 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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215B THR* 3.4 25.3 - - + +
216B VAL 3.8 1.3 - - - -
217B ARG* 3.4 41.4 - - - +
234B GLU* 4.1 11.0 + - - +
235B VAL* 1.3 76.2 - - - +
237B VAL* 1.3 61.9 + - - +
238B THR* 5.2 2.9 - - + +
282B MET* 4.7 4.9 - - - +
301B LEU* 3.7 17.3 - - - +
142D VAL* 4.5 23.8 - - + -
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Residues in contact with VAL 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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254A HIS* 4.6 5.2 - - + -
257A ILE* 4.4 23.3 - - + -
261A LEU* 4.8 7.0 - - + -
214B HIS 3.5 1.0 - - - +
215B THR* 3.3 4.4 - - - -
216B VAL* 2.9 40.7 + - - +
218B ALA* 5.4 4.5 - - + -
223B LEU* 5.5 2.9 - - + -
235B VAL* 3.7 23.6 - - + +
236B GLN* 1.3 76.2 - - - +
238B THR* 1.3 69.7 + - - +
239B MET* 3.7 27.7 + - + +
300B LEU* 4.5 9.9 - - + +
301B LEU* 3.7 13.0 - - + -
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Residues in contact with THR 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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254A HIS* 3.7 6.4 - - - -
213B LEU* 4.5 15.3 - - + -
214B HIS 3.3 7.6 - - - +
215B THR* 4.1 17.0 - - + +
236B GLN* 5.2 2.0 - - + +
237B VAL* 1.3 75.1 - - - +
239B MET* 1.3 60.0 + - - +
301B LEU* 3.5 19.0 - - + +
302B ALA* 2.7 51.5 + - - +
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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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254A HIS* 3.8 21.8 - - + +
257A ILE* 5.1 2.5 - - + -
258A LYS* 5.0 12.6 - - - -
261A LEU* 3.8 30.1 - - + -
269A VAL* 3.6 39.5 - - + -
270A PRO* 5.0 4.3 - - - -
213B LEU* 4.8 0.2 - - - -
214B HIS* 2.8 34.0 + - - +
216B VAL* 4.3 21.8 - - + -
237B VAL* 3.7 20.4 + - + +
238B THR* 1.3 73.7 - - - +
240B CYS* 1.3 67.0 + - - +
241B ILE* 4.7 8.5 - - + -
302B ALA* 4.6 1.6 - - - -
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Residues in contact with CYS 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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254A HIS* 5.3 1.0 + - - -
258A LYS* 4.4 9.8 + - - +
270A PRO* 4.1 14.6 - - - +
212B ARG 3.5 17.5 - - - +
213B LEU* 4.0 15.0 - - - -
239B MET* 1.3 83.1 - - - +
241B ILE* 1.3 64.5 + - - +
274B CYS* 3.7 19.3 - - - +
276B PRO* 5.4 2.6 - - + +
302B ALA* 4.7 3.1 - - - +
305B CYS* 2.0 52.9 - - + -
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Residues in contact with ILE 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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268A THR* 3.6 41.1 - - + +
270A PRO* 4.4 12.3 - - + -
210B CYS 3.4 16.1 - - - +
211B CYS* 4.3 2.1 - - - -
212B ARG 3.7 4.5 + - - +
214B HIS* 3.5 52.4 + - + +
216B VAL* 4.6 10.1 - - + -
239B MET* 4.7 7.0 - - + -
240B CYS* 1.3 79.9 - - - +
242B GLY* 1.3 64.6 + - - +
274B CYS* 5.2 2.0 - - - -
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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