Contacts of the strand formed by residues 409 - 416 (chain A) in PDB entry 1JEY
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 TYR 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A LEU* 3.4 27.4 - - + -
399A ARG* 3.7 1.5 - - - -
400A TYR* 2.8 38.9 + - + +
407A PRO* 4.0 6.5 + - + +
408A PRO* 1.3 80.4 - - - +
410A PHE* 1.3 64.2 + - - +
411A VAL* 4.8 0.4 - - + -
436A PHE* 4.4 25.1 - + + -
437A LEU 3.4 22.0 - - - -
439A PHE* 3.6 22.7 - + - -
442A ASP* 2.9 27.9 + - - -
269B GLN* 3.6 27.1 + - - +
484B ASN* 3.8 18.6 + - - -
486B ARG* 6.3 1.1 - - - -
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Residues in contact with PHE 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A MET* 3.9 20.0 - - + -
397A LEU* 4.4 3.1 - - + -
398A CYS 3.4 13.2 - - - -
399A ARG* 4.2 14.4 - - + -
408A PRO* 6.5 0.4 - - + -
409A TYR* 1.3 77.3 - - - +
411A VAL* 1.3 60.7 + - - +
436A PHE* 4.1 0.2 - - - -
437A LEU* 2.9 36.3 + - + +
439A PHE* 3.6 33.9 - + - -
477B PHE* 3.9 13.2 - + - -
479B THR* 3.7 39.5 - - + +
482B ILE* 4.5 8.7 - - + -
516B LEU* 3.5 46.7 - - + -
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Residues in contact with VAL 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A LEU* 4.0 15.9 - - + -
397A LEU* 3.1 5.9 - - - +
398A CYS* 2.9 43.9 + - + +
400A TYR* 3.8 28.7 - - + -
409A TYR 3.9 2.2 - - - +
410A PHE* 1.3 80.1 - - - +
412A ALA* 1.3 59.3 + - - +
413A LEU* 4.4 5.4 - - + -
434A LEU* 3.7 30.7 - - + -
435A VAL 3.2 10.3 - - - +
436A PHE* 3.9 20.2 - - + -
437A LEU* 3.9 4.7 - - - -
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Residues in contact with ALA 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A LEU* 3.7 32.5 - - + -
395A ALA* 4.4 5.4 - - + -
396A ALA 3.7 4.9 - - - -
397A LEU* 4.6 3.1 - - + +
411A VAL* 1.3 73.6 - - - +
413A LEU* 1.3 61.9 + - - +
414A VAL* 3.2 5.4 + - + +
433A GLN 3.0 3.8 - - - +
435A VAL* 2.8 39.5 + - + +
437A LEU* 4.0 16.8 - - + +
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Residues in contact with LEU 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A LEU* 4.1 26.9 - - + -
345A LEU* 4.8 6.7 - - + -
368A VAL* 4.1 16.6 - - + -
395A ALA* 3.5 5.4 - - - +
396A ALA* 2.8 47.3 + - + +
398A CYS* 4.2 15.5 - - - -
411A VAL* 4.1 7.8 - - + -
412A ALA* 1.3 70.6 - - - +
414A VAL* 1.3 62.5 + - - +
415A PRO* 3.5 2.8 - - - +
432A PHE* 3.7 29.2 - - + -
433A GLN 3.4 2.0 - - - -
434A LEU* 3.9 36.3 - - + +
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Residues in contact with VAL 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A LEU* 4.2 13.0 - - + -
356A LEU* 4.2 24.9 - - + -
395A ALA* 4.5 2.2 - - + -
412A ALA 3.7 4.9 - - - +
413A LEU* 1.3 73.1 - - - +
415A PRO* 1.3 81.8 - - + +
416A GLN* 3.3 0.6 + - + +
432A PHE* 3.3 2.3 - - - -
433A GLN* 2.6 55.9 + - + +
435A VAL* 3.7 24.2 - - + -
353B ARG* 6.0 2.5 - - - +
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Residues in contact with PRO 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A LEU* 4.2 16.7 - - + +
386A LEU* 4.0 5.2 - - + -
389A CYS* 4.0 21.5 - - + +
390A LEU* 3.7 32.5 - - + +
394A VAL 3.3 27.4 - - - +
395A ALA* 4.2 0.2 - - - -
413A LEU 3.5 6.7 - - - +
414A VAL* 1.3 97.0 - - + +
416A GLN* 1.3 58.8 + - - +
431A GLY 3.8 1.3 - - - +
432A PHE* 3.7 14.5 - - + -
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Residues in contact with GLN 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A PHE* 3.6 14.5 - - - -
386A LEU* 4.0 8.1 - - - +
414A VAL* 4.0 5.6 - - + +
415A PRO* 1.3 75.0 - - - +
417A GLU* 1.3 61.5 + - - +
428A THR* 3.4 27.4 - - + +
429A PRO* 2.8 35.1 + - - +
430A PRO* 3.3 3.1 - - - +
431A GLY 2.7 44.8 + - - +
433A GLN* 4.1 19.5 - - + +
354B ARG* 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