Contacts of the strand formed by residues 392 - 399 (chain A) in PDB entry 2JED
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 GLY 392 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A LYS* 3.3 9.8 + - - +
389A GLY 2.8 39.2 + - - +
390A SER 3.3 1.8 + - - -
391A PHE* 1.3 80.3 - - - +
393A LYS* 1.3 62.5 + - - -
410A ALA 4.2 0.9 - - - -
411A LEU* 4.0 17.2 - - - +
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Residues in contact with LYS 393 (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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385A MET* 3.8 20.3 - - + +
387A GLY 3.6 4.3 - - - +
388A LYS* 3.7 35.0 - - + +
391A PHE 3.8 0.6 + - - -
392A GLY* 1.3 72.3 - - - +
394A VAL* 1.3 65.5 + - - +
395A PHE* 3.8 29.8 - - + -
408A ILE 3.5 0.9 - - - +
409A LYS* 3.2 4.0 - - - +
410A ALA* 2.8 43.6 + - + +
674A ARG* 2.9 22.4 + - - +
675A LEU* 5.4 2.0 - - + -
676A SEP 2.9 43.4 + - - -
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Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A MET* 3.6 2.4 - - - +
386A LEU* 2.7 35.5 + - + +
387A GLY 3.0 10.3 + - - +
391A PHE* 3.8 18.4 - - + -
393A LYS* 1.3 79.9 - - - +
395A PHE* 1.3 56.7 + - - +
407A ALA* 3.9 25.6 - - + -
408A ILE 3.2 9.2 - - - +
409A LYS* 4.2 15.0 - - + +
1701A LG8 3.6 53.4 - - + -
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Residues in contact with PHE 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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382A LEU* 4.0 31.2 - - + -
384A LYS 3.1 17.3 - - - +
385A MET* 3.9 20.4 - - + -
386A LEU* 3.9 4.4 - - - +
393A LYS* 3.8 21.3 - - + -
394A VAL* 1.3 74.1 - - - +
396A LEU* 1.3 61.9 + - - +
397A ALA 3.5 0.9 + - - -
407A ALA* 3.3 7.4 - - - -
408A ILE* 2.9 43.8 + - + +
410A ALA* 3.9 24.2 - - + -
455A PHE* 6.3 0.2 - + - -
673A PRO* 3.5 34.8 - - + -
674A ARG 3.5 25.4 - - - -
675A LEU* 4.1 10.1 - - + -
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Residues in contact with LEU 396 (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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382A LEU* 3.7 2.4 - - - -
383A HIS* 2.9 31.5 + - + +
384A LYS* 2.8 30.9 + - + +
386A LEU* 3.7 21.9 - - + +
395A PHE* 1.3 70.7 - - - +
397A ALA* 1.3 61.0 + - - +
405A PHE* 3.8 21.8 - - + -
406A PHE 3.8 7.4 - - - +
460A TYR* 3.6 35.4 - - + +
658A PRO 3.7 21.3 - - - +
659A PHE* 4.1 27.6 - - + -
661A CYS* 5.9 1.3 - - - -
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Residues in contact with ALA 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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380A PHE* 4.1 8.7 - - + -
381A GLU 3.4 4.9 - - - +
382A LEU* 3.9 15.5 - - + -
383A HIS* 4.8 0.2 - - - -
395A PHE 4.4 1.1 - - - +
396A LEU* 1.3 74.7 - - - +
398A GLU* 1.3 60.0 + - - +
399A PHE 4.2 0.2 - - - -
404A GLN 3.8 0.3 - - - +
405A PHE* 3.2 7.9 - - - -
406A PHE* 2.7 40.9 + - + +
408A ILE* 3.7 36.6 - - + -
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Residues in contact with GLU 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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380A PHE* 3.2 5.0 - - - -
381A GLU* 2.9 35.2 + - + +
383A HIS* 3.0 32.8 + - + +
397A ALA* 1.3 74.2 - - - +
399A PHE* 1.3 74.1 + - - +
400A LYS* 3.2 6.0 + - - +
403A ASN* 2.9 43.0 - - - +
404A GLN 3.3 5.6 - - - +
405A PHE* 3.7 25.0 - - + -
659A PHE* 5.2 0.3 - - - -
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Residues in contact with PHE 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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375A LEU* 4.9 11.9 - - + -
379A ASP* 3.6 25.1 - - + -
380A PHE* 3.7 30.5 - + + -
397A ALA 4.2 0.2 - - - -
398A GLU* 1.3 68.8 - - - +
400A LYS* 1.3 59.8 + - - +
401A LYS* 2.9 40.1 + - + -
402A THR* 3.7 27.4 - - + -
403A ASN* 2.9 32.1 + - - -
404A GLN* 2.8 18.8 + - + +
406A PHE* 3.9 15.0 - + + -
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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