Contacts of the strand formed by residues 390 - 398 (chain A) in PDB entry 1EQR
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 ASP 390 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A ARG* 3.3 24.4 + - + +
323A VAL 4.1 4.0 - - - +
324A PRO* 4.1 10.3 - - - +
325A GLY 3.9 5.7 + - - -
327A ALA* 3.9 3.6 - - - +
352A ILE 3.7 0.3 - - - +
353A LYS* 3.9 1.4 - - - -
354A VAL* 2.9 32.0 + - + +
386A ALA* 4.6 4.0 - - + -
387A GLN* 2.8 60.7 + - - +
388A ASP 3.7 1.7 - - - +
389A GLY* 1.3 85.0 - - - +
391A MET* 1.3 64.1 + - - +
392A ILE* 5.4 0.4 - - + -
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Residues in contact with MET 391 (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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322A ARG* 3.5 3.8 - - - -
323A VAL* 2.9 37.1 + - + +
326A GLY* 3.2 40.4 - - - +
327A ALA* 3.7 1.7 - - - +
329A LEU* 4.5 3.1 - - + -
334A ILE* 4.0 15.7 - - + -
351A TYR* 3.5 29.4 - - + -
352A ILE 3.3 16.8 - - - +
353A LYS* 3.5 33.7 - - + +
390A ASP* 1.3 75.0 - - - +
392A ILE* 1.3 64.2 + - - +
393A PHE* 3.7 28.7 - - + -
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Residues in contact with ILE 392 (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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320A ALA* 3.9 13.5 - - + -
321A LEU 3.7 8.7 - - - +
322A ARG* 4.6 7.2 - - + +
351A TYR* 2.9 26.6 - - - -
352A ILE* 2.9 23.9 + - + +
354A VAL* 3.9 10.8 - - + -
380A ILE* 4.7 5.6 - - + -
381A LEU* 3.4 33.0 - - + -
384A THR* 3.8 18.2 - - + +
386A ALA* 4.0 6.3 - - + -
390A ASP* 4.8 1.1 - - + +
391A MET* 1.3 79.9 - - - +
393A PHE* 1.3 68.9 + - - +
394A PHE* 3.5 26.6 - - + -
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Residues in contact with PHE 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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320A ALA* 3.2 4.7 - - - -
321A LEU* 2.9 36.1 + - + +
323A VAL* 3.7 20.4 - - + -
329A LEU* 3.5 31.6 - - + -
334A ILE* 4.1 18.4 - - + -
337A TYR* 3.8 17.7 - + - -
349A LEU* 3.5 34.1 - - + -
350A ALA 3.3 4.3 - - - -
351A TYR* 3.7 23.1 - - + -
391A MET* 3.7 17.9 - - + -
392A ILE* 1.3 76.9 - - - +
394A PHE* 1.3 61.9 + - - +
406A MET* 4.1 7.6 - - + -
409A LEU* 4.3 15.9 - - + -
413A VAL* 4.8 4.0 - - + -
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Residues in contact with PHE 394 (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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295A VAL* 4.1 20.6 - - + -
299A LEU* 5.2 1.1 - - + -
307A PHE* 4.2 22.7 - + + -
318A VAL* 4.2 9.4 - - + -
319A ALA 3.3 3.8 - - - -
320A ALA* 3.7 22.4 - - + -
349A LEU* 3.6 12.5 - - - +
350A ALA* 3.0 45.0 + - + +
351A TYR* 4.2 0.7 - - - -
352A ILE* 3.9 23.6 - - + -
368A VAL* 5.8 1.3 - - + -
372A LEU* 6.3 0.9 - - + -
380A ILE* 3.7 34.8 - - + -
392A ILE* 3.5 30.7 - - + -
393A PHE* 1.3 77.1 - - - +
395A GLY* 1.3 59.9 + - - +
396A ALA 4.0 1.3 + - - -
406A MET* 3.6 3.6 - - - -
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Residues in contact with GLY 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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317A ARG 3.6 2.1 - - - +
318A VAL* 3.2 2.2 - - - -
319A ALA* 2.8 34.9 + - - -
348A GLY 5.7 1.3 - - - -
349A LEU* 5.0 1.8 - - - -
394A PHE* 1.3 72.9 - - - +
396A ALA* 1.3 59.8 + - - -
402A VAL* 3.7 10.4 - - - +
406A MET* 3.2 24.9 - - - +
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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
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306A VAL* 3.2 28.7 - - + +
307A PHE* 4.0 8.3 - - + -
310A PRO* 3.5 11.0 - - + -
317A ARG 3.7 4.9 - - - -
318A VAL* 3.6 20.4 - - + -
347A LYS* 3.4 22.1 - - - +
394A PHE 4.0 1.4 + - - -
395A GLY* 1.3 73.4 - - - -
397A ASP* 1.3 72.5 + - - +
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Residues in contact with ASP 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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310A PRO* 3.4 15.0 - - - +
313A ASP* 5.4 1.1 - - - -
316A GLY* 3.2 19.9 - - - -
317A ARG 3.3 7.7 + - - -
345A GLY 4.4 2.7 - - - +
346A ALA* 4.0 5.2 - - + -
347A LYS* 3.6 34.7 + - - +
396A ALA* 1.3 78.2 - - - +
398A ASN* 1.3 78.1 + - - +
401A ILE* 4.1 19.3 - - + +
402A VAL* 3.4 14.7 - - + +
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Residues in contact with ASN 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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313A ASP* 4.9 5.2 - - - +
315A LYS* 3.4 18.6 - - - +
316A GLY* 4.3 0.7 - - - -
397A ASP* 1.3 86.2 + - - +
399A LYS* 1.3 73.3 + - - +
400A LYS* 3.4 18.5 + - - +
401A ILE* 2.9 53.2 + - + +
402A VAL* 2.9 11.2 + - - +
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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