Contacts of the strand formed by residues 391 - 398 (chain B) 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 MET 391 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B LEU 3.3 1.0 - - - +
322B ARG* 3.3 3.5 - - - +
323B VAL* 2.8 38.3 + - + +
326B GLY* 3.3 33.6 - - - +
329B LEU* 4.6 1.3 - - + -
334B ILE* 3.4 35.9 - - + -
351B TYR* 3.4 31.2 - - + -
352B ILE 3.4 18.2 - - - +
353B LYS* 3.7 19.7 - - + -
390B ASP* 1.3 74.5 - - - +
392B ILE* 1.3 63.5 + - - +
393B PHE* 3.9 27.4 - - + -
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Residues in contact with ILE 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B ALA* 4.1 17.9 - - + -
321B LEU 3.2 6.5 - - - +
322B ARG* 3.8 18.4 - - + -
351B TYR* 3.0 7.9 - - - +
352B ILE* 2.9 50.9 + - + +
354B VAL* 4.6 3.1 - - + -
380B ILE* 4.8 2.2 - - + -
381B LEU* 4.1 16.8 - - + -
384B THR* 3.7 23.8 - - + +
386B ALA* 3.7 20.2 - - + -
390B ASP* 4.9 1.1 - - + -
391B MET* 1.3 76.5 - - - +
393B PHE* 1.3 61.4 + - - +
394B PHE* 3.5 30.8 - - + -
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Residues in contact with PHE 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B ALA 3.6 0.5 - - - +
320B ALA* 3.3 3.6 - - - -
321B LEU* 2.6 45.7 + - + +
323B VAL* 3.8 25.6 - - + -
329B LEU* 3.7 28.3 - - + -
334B ILE* 4.0 20.0 - - + -
337B TYR* 4.2 18.4 - + - -
349B LEU* 3.7 26.9 - - + -
350B ALA 3.6 0.9 - - - -
351B TYR* 3.7 24.7 - + + -
391B MET* 3.9 18.2 - - + -
392B ILE* 1.3 73.8 - - - +
394B PHE* 1.3 61.1 + - - +
406B MET* 4.0 16.6 - - + -
409B LEU* 4.2 12.3 - - + -
413B VAL* 4.7 6.7 - - + -
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Residues in contact with PHE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B VAL* 4.1 15.0 - - + -
299B LEU* 5.3 1.6 - - + -
307B PHE* 4.1 29.4 - + + -
318B VAL* 4.4 7.6 - - + -
319B ALA 3.2 6.5 - - - +
320B ALA* 3.9 23.1 - - + -
348B GLY 4.5 0.7 - - - +
349B LEU* 3.8 10.8 - - - +
350B ALA* 3.1 36.6 + - + +
351B TYR* 4.1 4.0 - - - -
352B ILE* 3.8 29.6 - - + -
368B VAL* 5.6 2.0 - - + -
372B LEU* 5.7 1.6 - - + -
380B ILE* 3.9 27.1 - - + -
392B ILE* 3.5 32.1 - - + -
393B PHE* 1.3 76.3 - - - +
395B GLY* 1.3 60.8 + - - +
396B ALA* 4.1 1.1 + - - -
406B MET* 4.3 4.0 - - - -
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Residues in contact with GLY 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B VAL* 3.4 1.6 - - - -
319B ALA* 2.8 34.9 + - - +
348B GLY 5.3 3.4 - - - -
349B LEU* 5.0 1.3 - - - -
394B PHE* 1.3 73.7 - - - +
396B ALA* 1.3 58.3 + - - -
402B VAL* 3.4 14.0 - - - +
405B ALA* 6.4 0.7 - - - -
406B MET* 3.7 25.2 - - - -
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Residues in contact with ALA 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B VAL* 3.5 28.2 - - + +
307B PHE* 3.7 26.5 - - + -
310B PRO* 3.3 14.1 - - - +
317B ARG 3.4 7.0 - - - -
318B VAL* 3.7 15.5 - - + +
347B LYS* 4.7 5.5 + - - -
394B PHE 4.0 1.6 + - - -
395B GLY* 1.3 72.1 - - - -
397B ASP* 1.3 61.7 + - - +
402B VAL* 4.0 0.4 - - - +
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Residues in contact with ASP 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B PRO* 3.8 10.7 - - - +
316B GLY* 3.3 4.4 - - - -
317B ARG 2.9 26.8 + - - +
345B GLY 3.5 7.8 - - - +
346B ALA* 5.7 0.9 - - - -
347B LYS* 2.7 36.1 + - - +
396B ALA* 1.3 74.3 - - - +
398B ASN* 1.3 80.9 + - - +
401B ILE* 3.2 40.1 - - + +
402B VAL* 3.1 12.9 - - + +
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Residues in contact with ASN 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B LYS* 3.1 21.9 - - - +
316B GLY* 4.1 1.6 - - - -
317B ARG 4.6 0.2 - - - -
397B ASP* 1.3 90.0 + - - +
399B LYS* 1.3 63.5 + - - +
400B LYS* 2.7 45.5 + - - +
401B ILE* 2.7 27.2 + - + +
402B VAL* 3.0 8.9 + - - +
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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