Contacts of the strand formed by residues 403 - 409 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A THR 4.6 2.4 - - - +
305A ARG* 4.2 16.5 + - - +
352A TYR* 3.7 33.4 - - + +
355A ALA* 3.8 17.0 - - + -
356A ILE* 3.8 11.9 - - + +
383A THR* 3.5 11.4 - - + -
385A ILE* 3.7 22.0 - - + -
401A VAL* 2.7 38.2 + - + +
402A PRO* 1.3 78.8 - - - +
404A LEU* 1.3 62.9 + - - +
405A TYR* 3.7 38.8 + - + +
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Residues in contact with LEU 404 (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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289A ALA* 5.0 3.4 - - + +
293A SER* 3.4 28.7 - - - +
304A THR* 3.8 16.8 - - + +
305A ARG 3.8 17.0 - - - +
307A LEU* 3.9 39.5 - - + -
321A ILE* 5.0 9.6 - - + -
325A TYR* 4.0 16.8 - - + +
383A THR 2.9 15.5 + - - +
384A ILE* 3.6 13.0 - - + +
385A ILE* 2.9 28.6 + - - +
403A ILE* 1.3 75.3 - - - +
405A TYR* 1.3 61.7 + - - +
406A VAL* 3.7 6.6 + - + -
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Residues in contact with TYR 405 (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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271A ASN* 5.9 0.2 - - - -
305A ARG* 3.0 34.2 + - + +
306A ARG* 3.5 3.7 - - + -
307A LEU 2.9 25.6 + - - -
355A ALA* 4.1 8.2 - - - +
359A ALA* 4.6 2.9 - - + -
385A ILE* 3.6 14.1 - - + +
388A LEU* 3.6 26.9 - - + -
394A ILE* 3.4 42.2 + - + +
395A VAL* 4.3 32.3 - - + -
397A THR 5.0 5.8 - - - -
399A THR* 4.0 16.1 + - - -
403A ILE* 3.7 36.5 - - + +
404A LEU* 1.3 70.3 - - - +
406A VAL* 1.3 62.6 + - - +
407A LEU* 3.8 5.7 + - + +
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Residues in contact with VAL 406 (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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307A LEU* 3.3 26.9 - - + +
309A LEU* 3.8 20.2 - - + -
314A HIS* 3.6 25.9 + - + +
318A VAL* 3.8 9.0 - - + -
384A ILE* 3.8 28.5 - - + -
385A ILE 2.8 17.6 + - - +
386A THR* 3.9 8.6 - - + -
387A GLY 3.9 15.6 + - - -
388A LEU* 4.6 4.5 + - - +
404A LEU* 4.3 6.3 - - + +
405A TYR* 1.3 74.8 - - - +
407A LEU* 1.3 67.3 + - - +
408A LYS 4.4 0.2 + - - -
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Residues in contact with LEU 407 (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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306A ARG* 4.8 8.3 - - + +
307A LEU 2.9 6.1 + - - +
308A MET* 4.0 40.2 - - + -
309A LEU* 2.7 34.8 + - - +
314A HIS* 4.1 3.7 - - - -
388A LEU* 4.1 17.7 - - + +
389A ALA 4.6 1.3 - - - +
390A HIS* 4.0 35.7 - - + +
395A VAL* 4.3 26.7 - - + -
405A TYR* 3.8 12.1 + - + +
406A VAL* 1.3 82.6 - - - +
408A LYS* 1.3 55.8 + - - +
418A TRP* 4.3 10.1 - - + -
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Residues in contact with LYS 408 (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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309A LEU 3.4 3.4 - - - +
311A GLU* 3.9 32.5 - - + +
314A HIS* 3.6 40.4 + - + +
315A ASP* 5.0 5.0 + - - -
388A LEU 5.7 0.2 + - - -
406A VAL 4.4 0.2 + - - -
407A LEU* 1.3 73.5 - - - +
409A PHE* 1.3 62.6 + - - +
418A TRP* 3.3 18.0 - - - -
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Residues in contact with PHE 409 (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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275A ILE* 3.7 19.1 - - + -
276A VAL 3.3 27.1 - - - -
277A PHE* 3.7 29.4 - + - -
308A MET* 3.7 17.9 - - + -
309A LEU 3.0 22.1 + - - -
310A HIS* 3.3 28.8 - + + -
311A GLU* 2.9 29.8 + - - +
408A LYS* 1.3 73.9 - - - +
410A LYS* 1.3 62.2 + - - +
411A THR 3.3 21.3 - - - -
414A GLU* 4.2 4.5 - - + +
415A ALA* 3.8 11.7 - - + -
418A TRP* 3.6 25.1 - - + -
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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