Contacts of the strand formed by residues 295 - 301 (chain B) in PDB entry 1PJQ
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 ARG 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B VAL* 2.7 31.7 + - - +
185B ASN* 4.8 1.6 - - - +
186B ASP* 2.9 30.5 + - - +
215B ARG* 3.6 20.7 + - + +
217B GLU* 3.7 31.9 + - + -
219B VAL* 5.4 1.1 - - + -
238B GLN* 3.1 24.9 + - - +
241B GLN* 3.5 47.2 - - - +
242B ALA* 3.8 4.8 - - - -
243B ASP* 2.9 42.0 + - - +
244B ILE 3.5 6.2 + - - +
294B LYS* 1.3 69.1 - - - +
296B VAL* 1.3 62.9 + - - +
297B VAL* 5.3 3.5 - - + +
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Residues in contact with VAL 296 (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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217B GLU 2.9 15.0 + - - +
218B VAL* 3.5 7.1 - - + -
219B VAL* 2.8 28.8 + - - +
244B ILE* 3.7 26.0 - - + -
246B VAL* 4.3 7.2 - - + -
286B LEU* 3.8 38.6 - - + +
289B GLU* 4.2 7.2 - - + -
290B ALA* 4.0 19.3 - - - +
294B LYS 3.5 14.8 - - - +
295B ARG* 1.3 73.1 - - - +
297B VAL* 1.3 70.8 + - - +
298B ARG 4.7 0.2 - - - +
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B VAL* 3.4 17.0 - - + -
221B VAL* 3.9 25.4 - - + -
238B GLN* 3.9 20.9 - - + +
239B ILE* 4.2 15.9 - - + +
242B ALA* 3.7 28.7 - - + -
244B ILE 3.1 7.8 + - - +
245B VAL* 3.4 7.4 - - + -
246B VAL 2.9 24.9 + - - -
295B ARG* 5.0 3.6 - - + +
296B VAL* 1.3 79.7 - - - +
298B ARG* 1.3 67.6 + - - +
299B LEU* 3.5 7.4 + - + +
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Residues in contact with ARG 298 (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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218B VAL* 5.1 2.0 - - + +
219B VAL 2.9 7.6 + - - +
220B LEU* 3.6 20.7 - - + -
221B VAL 3.0 23.2 + - - +
246B VAL* 3.1 30.9 + - - +
247B TYR 4.0 1.8 - - - -
248B ASP* 3.0 27.1 + - - +
268B VAL* 3.6 25.8 - - - +
279B GLN* 5.4 0.4 + - - -
282B ILE* 4.3 7.4 - - - +
286B LEU* 3.7 32.1 - - + -
296B VAL* 4.1 1.6 + - - +
297B VAL* 1.3 73.1 - - - +
299B LEU* 1.3 59.0 + - - +
300B LYS* 2.9 32.9 + - + +
313B GLU* 2.4 48.1 + - - +
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Residues in contact with LEU 299 (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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221B VAL* 3.6 15.9 - - + +
223B ALA* 3.5 29.4 - - + -
239B ILE* 3.6 39.0 - - + -
245B VAL* 4.0 15.9 - - + -
246B VAL 2.9 9.0 + - - +
247B TYR* 3.5 22.5 - - + -
248B ASP* 3.7 5.2 - - - +
251B VAL* 3.4 21.4 - - + +
255B ILE* 4.1 6.5 - - + +
256B MET* 3.8 28.7 - - - -
259B VAL* 5.7 1.6 - - + -
297B VAL* 3.5 6.2 + - + -
298B ARG* 1.3 71.4 + - - +
300B LYS* 1.3 60.1 + - - +
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Residues in contact with LYS 300 (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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220B LEU* 4.9 2.7 - - + -
221B VAL 2.8 13.2 + - - +
222B GLY* 3.6 0.3 - - - -
223B ALA* 2.8 29.5 + - - +
248B ASP* 4.0 6.0 + - - +
251B VAL* 4.1 4.0 - - - -
279B GLN* 5.2 1.8 + - - -
298B ARG* 2.9 53.5 - - + +
299B LEU* 1.3 74.7 - - - +
301B GLY* 1.3 67.7 + - - +
302B GLY 3.6 1.7 - - - +
303B ASP 5.0 0.4 - - - +
304B PRO* 4.4 26.5 - - + -
308B GLY* 2.7 32.8 + - - -
309B ARG* 4.2 2.4 - - - +
310B GLY* 4.3 8.3 - - - -
313B GLU* 2.9 23.8 + - - +
501B SAH 5.9 0.2 - - - +
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Residues in contact with GLY 301 (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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223B ALA* 4.8 0.9 - - - -
224B GLY 4.1 1.6 - - - -
248B ASP* 3.7 13.3 + - - -
250B LEU* 3.7 34.3 - - - -
251B VAL* 3.9 2.6 - - - +
300B LYS* 1.3 75.0 - - - +
302B GLY* 1.3 64.0 + - - -
303B ASP 3.2 2.1 + - - +
501B SAH 3.2 25.8 + - - +
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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