Contacts of the strand formed by residues 353 - 359 (chain A) in PDB entry 2PE8
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 VAL 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A LEU 3.8 8.7 - - - +
310A ARG* 4.1 10.0 - - - -
311A ASN 4.2 5.9 + - - -
312A MET* 5.0 1.9 + - - +
313A VAL* 3.5 22.7 + - + +
314A GLY 3.4 31.9 - - - +
315A ALA* 4.0 0.9 - - - +
316A GLY* 5.1 1.6 - - - -
317A GLU 5.9 3.1 - - - +
322A LEU* 5.2 3.8 - - + -
341A ILE* 4.0 24.7 - - + -
342A PHE 3.8 2.5 - - - +
343A GLU* 3.8 21.3 - - + +
349A ASP 5.0 0.4 + - - -
350A ASP 5.5 0.6 - - - -
351A GLU 3.3 3.6 - - - +
352A ALA* 1.3 80.7 - - - +
354A ARG* 1.3 63.4 + - - +
355A ILE* 4.0 18.7 + - + +
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Residues in contact with ARG 354 (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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308A LEU* 3.5 27.0 - - + +
309A LEU 3.7 3.8 - - - -
310A ARG* 4.3 17.1 - - + +
340A VAL 3.7 0.7 - - - +
341A ILE* 3.5 3.1 - - - +
342A PHE* 2.7 47.0 + - + +
344A ILE* 3.9 22.8 - - + +
351A GLU* 4.4 10.7 + - - +
352A ALA 3.8 0.2 + - - -
353A VAL* 1.3 75.8 - - - +
355A ILE* 1.3 61.9 - - - +
356A PHE* 3.7 10.3 - - + -
387A TYR* 3.8 11.7 - - - -
397A LEU 2.8 36.5 + - - -
398A ALA 3.5 4.9 + - - -
399A GLU 2.9 36.2 + - - +
400A GLN* 4.7 2.4 + - - +
401A VAL* 4.3 16.4 - - - +
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Residues in contact with ILE 355 (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 VAL 3.7 1.0 - - - +
308A LEU* 3.5 3.4 - - - +
309A LEU* 2.7 48.0 + - + +
312A MET* 3.9 37.5 - - + -
313A VAL* 5.4 1.6 - - + +
322A LEU* 4.0 24.5 - - + -
326A THR* 4.0 25.8 - - + +
339A CYS* 4.0 17.0 - - - -
340A VAL 3.6 2.2 - - - -
341A ILE* 4.0 14.8 - - + -
353A VAL* 4.2 13.5 - - + +
354A ARG* 1.3 76.5 - - - +
356A PHE* 1.3 62.3 + - - +
357A LEU* 4.3 7.6 - - + -
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Residues in contact with PHE 356 (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* 4.2 11.4 - - + -
307A VAL 3.3 4.7 - - - +
308A LEU* 3.8 21.1 - - + -
339A CYS* 3.2 9.0 - - - -
340A VAL* 2.8 45.0 + - + +
342A PHE* 4.0 6.7 - - + -
354A ARG* 3.7 21.3 - - + -
355A ILE* 1.3 75.8 - - - +
357A LEU* 1.3 61.0 + - - +
358A GLU 4.2 0.4 - - - -
387A TYR* 3.7 34.3 - + - -
392A PHE* 3.5 33.1 - + + -
397A LEU* 3.5 51.6 - - + -
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Residues in contact with LEU 357 (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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305A LYS 3.5 2.6 - - - +
306A VAL* 3.4 4.5 - - - -
307A VAL* 2.9 41.2 + - + +
309A LEU* 3.7 35.2 - - + -
326A THR* 4.1 6.3 - - + -
327A LYS* 4.0 10.8 - - - +
330A CYS* 3.8 32.3 - - + -
336A VAL* 4.0 14.4 - - + -
338A LYS 3.5 2.7 - - - +
339A CYS* 4.0 24.7 - - + -
355A ILE* 4.3 3.4 - - + +
356A PHE* 1.3 78.5 - - - +
358A GLU* 1.3 60.8 + - - +
359A PHE* 3.7 19.6 + - + -
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Residues in contact with GLU 358 (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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305A LYS* 3.6 14.6 + - + +
306A VAL* 3.9 20.2 - - + +
336A VAL* 3.5 3.0 - - - -
337A GLY* 2.6 36.9 + - - -
338A LYS* 2.9 40.7 + - + +
356A PHE 4.2 0.4 - - - -
357A LEU* 1.3 70.1 - - - +
359A PHE* 1.3 61.0 + - - +
360A GLU* 5.3 4.0 - - - +
392A PHE* 3.7 20.1 - - + -
393A ARG* 3.0 38.0 + - - -
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Residues in contact with PHE 359 (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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305A LYS* 2.8 39.2 + - - +
307A VAL* 3.8 19.5 - - + -
330A CYS* 3.4 37.7 - - + -
333A TYR* 4.0 10.1 - - + -
334A GLY 3.8 5.2 - - - -
335A LYS 3.5 13.7 - - - +
336A VAL* 3.6 11.0 - - + -
337A GLY* 4.1 0.7 - - - +
357A LEU* 3.8 20.6 - - + -
358A GLU* 1.3 79.3 - - - +
360A GLU* 1.3 64.9 + - - +
361A ARG 3.3 19.3 - - - +
364A SER* 3.4 18.6 - - - -
365A ALA* 3.7 13.7 - - + +
368A ALA* 3.8 22.4 - - + -
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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