Contacts of the strand formed by residues 355 - 362 (chain s) in PDB entry 3J7Y
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 PHE 355 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246s GLN* 4.2 9.2 - - + +
294s TYR* 4.1 23.1 - + - -
336s THR* 4.0 12.4 - - + +
339s GLN* 3.7 38.1 - - + +
340s ALA* 3.7 13.5 - - + -
343s GLN* 4.0 9.4 - - + -
345s PHE* 3.5 38.1 - + - -
351s VAL* 3.9 20.0 - - + -
353s ARG* 4.1 24.2 - - + -
354s PRO* 1.3 69.2 - - - +
356s VAL* 1.3 59.7 + - - +
374s LEU* 2.8 53.0 + - + +
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Residues in contact with VAL 356 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246s GLN* 4.8 5.6 - - - +
247s LEU* 3.4 26.9 + - + +
248s ALA 3.3 22.0 - - - +
249s GLU 3.5 22.2 - - - +
250s PHE* 3.3 34.5 - - + -
295s GLY 3.9 8.1 - - - +
336s THR* 4.5 2.0 - - - -
339s GLN* 4.3 6.6 + - - +
354s PRO 3.4 5.5 + - - +
355s PHE* 1.3 73.8 - - - +
357s SER* 1.3 71.6 + - - +
358s GLN* 5.0 0.2 - - + -
372s TYR 3.6 7.6 - - - +
373s GLN* 3.7 17.5 - - + +
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Residues in contact with SER 357 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247s LEU* 5.6 0.4 - - - -
295s GLY 4.0 13.5 - - - -
296s HIS* 4.8 0.2 - - - +
332s LEU* 3.6 17.0 + - - +
335s TRP* 3.8 20.9 - - - +
336s THR* 3.1 23.7 - - - +
339s GLN* 4.1 7.2 - - - -
356s VAL* 1.3 80.5 - - - +
358s GLN* 1.3 65.6 + - - +
371s CYS* 3.8 0.9 - - - +
372s TYR* 2.8 31.9 + - - +
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Residues in contact with GLN 358 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247s LEU* 4.3 7.0 - - + -
250s PHE* 3.3 27.7 - - + -
296s HIS 2.7 26.2 + - - +
297s THR* 3.2 6.5 + - - -
298s GLN 2.8 20.2 + - - -
332s LEU* 3.6 5.6 - - - +
335s TRP* 3.7 2.4 - - - -
357s SER* 1.3 78.9 - - - +
359s ALA* 1.3 63.3 + - - +
370s PHE 3.8 4.9 - - - +
371s CYS* 4.2 3.1 - - - +
423s HIS 5.2 0.2 - - - +
424s PHE* 2.7 61.2 + - + +
427s ASN* 3.3 29.2 - - - +
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Residues in contact with ALA 359 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297s THR* 4.6 0.9 - - - +
298s GLN* 3.1 24.2 - - + +
300s HIS* 5.0 7.4 - - + +
328s ALA* 6.1 0.9 - - - -
332s LEU* 3.3 27.6 - - + -
358s GLN* 1.3 78.9 - - - +
360s VAL* 1.3 61.7 + - - +
361s ILE* 4.1 2.7 - - + +
370s PHE* 2.8 40.9 + - + +
424s PHE* 3.7 7.9 - - - -
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Residues in contact with VAL 360 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297s THR* 4.0 9.6 - - + -
298s GLN 2.8 11.5 + - - +
299s PHE* 3.3 38.5 - - + +
300s HIS 3.4 15.2 + - - +
359s ALA* 1.3 76.8 - - - +
361s ILE* 1.3 74.1 + - - +
362s THR* 4.7 1.9 - - - +
367s PHE* 3.7 19.7 - - + -
368s SER 3.6 7.4 - - - +
369s PHE* 3.3 38.8 - - + -
370s PHE 4.8 0.2 - - - +
421s ILE* 5.0 4.7 - - + -
424s PHE* 5.5 2.7 - - + -
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Residues in contact with ILE 361 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300s HIS* 3.4 24.9 - - + +
302s LEU* 5.6 1.8 - - + -
324s PHE* 3.0 42.4 - - + +
327s ASN* 3.4 37.2 - - + +
328s ALA* 4.7 6.5 - - + +
359s ALA* 4.1 3.0 - - + +
360s VAL* 1.3 88.0 - - - +
362s THR* 1.3 64.6 + - - +
368s SER* 3.1 39.8 + - - +
370s PHE* 4.0 15.6 - - + -
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Residues in contact with THR 362 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177s LEU* 3.4 39.5 - - + -
300s HIS 2.8 22.0 + - - +
301s LEU* 3.4 2.7 - - + -
302s LEU* 3.1 29.8 + - - +
324s PHE* 4.3 4.5 - - - -
360s VAL 4.7 2.2 - - - +
361s ILE* 1.3 82.9 - - - +
363s ASP* 1.3 83.9 + - - +
366s TYR 3.1 10.7 + - - -
367s PHE* 3.2 29.1 - - + -
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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