Contacts of the strand formed by residues 394 - 401 (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 VAL 394 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A PHE* 3.3 43.3 - - + +
351A LYS 3.7 3.6 - - - -
352A PRO* 3.8 28.0 - - + -
353A LEU* 3.7 3.4 - - - -
389A CYS* 3.0 16.3 + - - +
392A LYS* 3.8 23.8 - - + +
393A GLU* 1.3 75.3 - - - +
395A ALA* 1.3 62.2 + - - +
415A PRO* 3.3 22.5 - - - +
458B ILE* 4.0 11.2 - - + -
462B SER* 6.2 0.4 - - - +
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Residues in contact with ALA 395 (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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350A PHE* 3.0 6.1 - - - +
351A LYS* 2.7 40.7 + - + +
353A LEU* 3.4 21.1 - - + -
356A LEU* 3.9 17.0 - - + -
389A CYS* 4.9 0.2 - - - -
394A VAL* 1.3 77.2 - - - +
396A ALA* 1.3 61.9 + - - +
397A LEU 3.5 0.7 + - - -
412A ALA* 4.4 6.5 - - + -
413A LEU 3.5 19.1 - - - +
414A VAL* 4.5 0.4 - - + -
415A PRO* 4.2 0.2 - - - -
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Residues in contact with ALA 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU* 4.0 12.3 - - + -
349A GLY 3.5 5.2 - - - -
350A PHE* 3.9 21.5 - - + -
385A LEU* 6.3 0.7 - - + -
389A CYS* 4.7 6.5 - - - -
395A ALA* 1.3 71.4 - - - +
397A LEU* 1.3 62.9 + - - +
398A CYS* 3.6 3.1 + - - -
412A ALA* 4.6 0.4 - - - -
413A LEU* 2.8 55.9 + - + +
432A PHE* 5.2 3.4 - - + -
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Residues in contact with LEU 397 (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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347A LEU* 3.5 1.9 - - - +
348A MET* 2.7 37.1 + - + -
349A GLY 2.7 17.5 + - - +
351A LYS* 4.2 20.9 - - + +
356A LEU* 6.2 0.2 - - + -
395A ALA 3.5 2.6 + - - -
396A ALA* 1.3 70.8 - - - +
398A CYS* 1.3 59.0 + - - +
410A PHE* 4.4 7.9 - - + -
411A VAL 3.1 22.2 - - - +
412A ALA* 4.6 4.3 - - + +
437A LEU* 3.5 25.8 - - + -
463B LEU* 3.5 18.4 - - + -
477B PHE* 3.5 33.4 - - + -
479B THR* 3.7 13.9 - - + -
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Residues in contact with CYS 398 (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* 5.2 5.6 - - - -
345A LEU* 3.9 27.1 - - + -
346A MET 3.1 11.2 - - - +
347A LEU* 4.0 22.7 - - - -
348A MET* 4.0 6.5 - - - -
396A ALA* 3.9 10.8 - - - -
397A LEU* 1.3 81.4 - - - +
399A ARG* 1.3 61.2 + - - +
400A TYR 3.8 0.2 - - - -
410A PHE* 3.4 6.4 - - - -
411A VAL* 2.9 38.4 + - + +
413A LEU* 4.2 19.7 - - - -
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Residues in contact with ARG 399 (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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341A ASP* 2.7 40.6 + - - +
344A GLY 3.7 2.3 - - - +
345A LEU* 3.6 2.9 - - - -
346A MET* 2.9 66.6 + - + +
348A MET* 3.9 15.5 - - - +
398A CYS* 1.3 71.4 - - - +
400A TYR* 1.3 60.1 + - - +
401A THR* 4.2 0.3 + - - -
408A PRO* 3.6 23.5 - - + +
409A TYR 3.8 3.6 - - - +
410A PHE* 4.2 15.7 - - + -
513B TRP* 3.8 15.0 - - - -
516B LEU* 2.8 45.9 + - - +
517B ASN* 2.7 28.5 + - - +
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Residues in contact with TYR 400 (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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256A LEU* 5.9 1.0 - - - +
257A SER* 4.9 2.9 + - - -
259A LEU* 3.8 24.3 - - + +
273A ILE* 4.5 7.1 - - + +
344A GLY 3.6 6.7 - - - -
345A LEU* 3.7 27.6 - - + -
366A LEU* 3.9 15.8 - - + +
399A ARG* 1.3 73.9 - - - +
401A THR* 1.3 70.4 + - - +
402A PRO* 3.3 36.8 - - + +
407A PRO 4.4 0.5 - - - +
408A PRO* 3.4 3.5 - - - +
409A TYR* 2.8 39.6 + - + +
411A VAL* 3.8 13.9 - - + -
434A LEU* 4.4 14.8 - - + -
436A PHE* 3.5 38.1 - + - -
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Residues in contact with THR 401 (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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259A LEU* 4.4 2.1 - - - +
341A ASP* 3.5 41.7 + - - +
342A ASP 3.7 11.7 - - - -
343A PRO* 3.1 12.0 - - + +
344A GLY* 2.7 36.5 + - - +
399A ARG 4.2 0.4 + - - -
400A TYR* 1.3 76.6 + - - +
402A PRO* 1.3 60.6 - - - +
403A ARG 3.2 22.0 - - - +
406A ILE* 3.3 19.2 + - + +
408A PRO* 4.0 8.5 - - - +
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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