Contacts of the strand formed by residues 403 - 409 (chain H) in PDB entry 2JG7
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 ILE 403 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293H SER* 6.4 0.4 - - - -
304H THR 4.6 2.8 - - - +
305H ARG* 4.2 16.3 + - - +
352H TYR* 3.8 25.1 - - + +
355H ALA* 3.8 24.7 - - + -
356H ILE* 3.8 13.5 - - + +
383H THR* 3.4 11.9 - - + +
385H ILE* 3.7 20.4 - - + -
401H VAL* 2.7 36.8 + - + +
402H PRO* 1.3 79.0 - - - +
404H LEU* 1.3 63.3 + - - +
405H TYR* 3.7 39.5 + - + +
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Residues in contact with LEU 404 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289H ALA* 5.1 3.6 - - + +
293H SER* 3.4 29.6 - - - +
304H THR* 3.9 12.1 - - + +
305H ARG 3.8 20.6 - - - +
307H LEU* 3.9 40.6 - - + +
321H ILE* 5.0 10.5 - - + -
325H TYR* 4.0 17.0 - - + +
383H THR 2.8 15.4 + - - +
384H ILE* 3.6 12.9 - - + +
385H ILE* 2.9 28.6 + - - +
403H ILE* 1.3 74.3 - - - +
405H TYR* 1.3 61.4 + - - +
406H VAL* 3.7 5.7 + - + -
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Residues in contact with TYR 405 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305H ARG* 3.0 33.5 + - + +
306H ARG* 3.5 3.8 - - + -
307H LEU 2.9 24.8 + - - -
355H ALA* 4.0 11.5 - - - +
359H ALA* 4.6 2.7 - - + -
385H ILE* 3.6 13.9 - - + +
388H LEU* 3.6 26.0 - - + -
394H ILE* 3.4 44.4 - - + +
395H VAL* 4.3 34.3 - - + -
397H THR 5.0 6.1 - - - -
399H THR* 4.1 10.4 + - - -
403H ILE* 3.7 38.3 - - + +
404H LEU* 1.3 71.4 - - - +
406H VAL* 1.3 61.9 + - - +
407H LEU* 3.9 5.2 + - + +
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Residues in contact with VAL 406 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307H LEU* 3.3 26.2 - - + +
309H LEU* 3.8 20.0 - - + -
314H HIS* 3.6 26.3 + - + +
318H VAL* 3.8 9.2 - - + -
384H ILE* 3.8 28.5 - - + -
385H ILE 2.7 19.3 + - - +
386H THR* 3.9 8.1 - - + -
387H GLY 4.0 15.4 + - - -
388H LEU* 4.5 4.2 + - - +
404H LEU* 4.3 5.8 - - + +
405H TYR* 1.3 75.1 - - - +
407H LEU* 1.3 68.0 + - - +
408H LYS 4.4 0.2 + - - -
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Residues in contact with LEU 407 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306H ARG* 4.8 8.1 - - + +
307H LEU 2.8 6.9 + - - +
308H MET* 4.0 39.3 - - + -
309H LEU* 2.7 34.7 + - - +
314H HIS* 4.0 4.2 - - - -
388H LEU* 4.0 17.7 - - + +
389H ALA 4.5 1.1 - - - +
390H HIS* 3.9 37.5 - - + +
395H VAL* 4.3 24.0 - - + -
405H TYR* 3.9 11.4 + - + +
406H VAL* 1.3 83.4 - - - +
408H LYS* 1.3 55.4 + - - +
409H PHE 4.2 0.2 - - - -
418H TRP* 4.2 9.9 - - + -
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Residues in contact with LYS 408 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309H LEU 3.4 3.8 - - - +
311H GLU* 3.9 32.1 - - + +
314H HIS* 3.7 39.9 + - + +
315H ASP* 5.0 5.1 + - - -
388H LEU 5.7 0.4 + - - -
406H VAL 4.4 0.2 + - - -
407H LEU* 1.3 73.1 - - - +
409H PHE* 1.3 62.1 + - - +
418H TRP* 3.3 17.6 - - - -
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Residues in contact with PHE 409 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275H ILE* 3.6 24.5 - - + -
276H VAL 3.3 17.7 - - - -
277H PHE* 3.7 29.4 - + - -
308H MET* 3.7 13.5 - - + -
309H LEU 3.0 22.1 + - - -
310H HIS* 3.3 31.0 - + + -
311H GLU* 2.9 30.1 + - - +
408H LYS* 1.3 74.3 - - - +
410H LYS* 1.3 68.8 + - - +
411H THR 3.4 21.3 - - - -
414H GLU* 4.2 5.2 - - + +
415H ALA* 3.8 11.0 - - + -
418H TRP* 3.6 24.9 - - + -
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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