Contacts of the strand formed by residues 336 - 343 (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 336 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A LYS* 2.9 51.7 + - + +
330A CYS* 3.7 15.0 - - + +
331A GLU* 3.4 21.4 + - - +
334A GLY 3.3 2.0 + - - +
335A LYS* 1.3 71.3 - - - +
337A GLY* 1.3 60.3 + - - +
338A LYS 3.4 26.0 - - - +
357A LEU* 4.0 11.7 - - + -
358A GLU 3.7 7.6 - - - +
359A PHE* 3.6 29.2 - - + +
360A GLU* 4.6 1.6 - - - -
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Residues in contact with GLY 337 (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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327A LYS* 4.3 4.2 + - - -
335A LYS 3.9 3.8 + - - -
336A VAL* 1.3 73.8 - - - +
338A LYS* 1.3 63.0 + - - +
358A GLU* 2.6 20.3 + - - -
359A PHE 4.9 0.2 - - - -
360A GLU* 3.9 25.6 - - - +
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Residues in contact with LYS 338 (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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327A LYS* 4.8 5.4 - - - +
336A VAL* 3.4 12.7 - - - +
337A GLY* 1.3 78.4 - - - +
339A CYS* 1.3 60.8 + - - +
340A VAL* 4.1 21.7 - - - +
357A LEU* 3.5 0.5 - - - -
358A GLU* 2.9 57.1 + - + +
392A PHE* 4.1 14.5 - - + -
395A LEU* 5.4 7.7 - - - +
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Residues in contact with CYS 339 (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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323A GLU* 3.1 45.9 - - + +
326A THR* 4.6 1.6 - - - -
327A LYS* 4.1 15.8 - - + +
338A LYS* 1.3 78.4 - - - +
340A VAL* 1.3 68.1 + - - +
341A ILE* 3.5 24.9 - - - -
355A ILE* 4.0 8.5 - - - -
356A PHE 3.2 13.0 - - - +
357A LEU* 4.0 20.9 - - + -
392A PHE* 6.0 0.2 - - - -
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Residues in contact with VAL 340 (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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323A GLU* 4.0 4.3 - - - +
338A LYS* 4.1 16.6 - - - +
339A CYS* 1.3 77.8 - - - +
341A ILE* 1.3 73.0 + - - +
342A PHE* 4.7 1.1 - - + +
355A ILE* 3.6 1.0 - - - -
356A PHE* 2.8 50.4 + - + -
392A PHE* 3.8 26.2 - - + -
395A LEU* 5.2 9.2 - - + -
397A LEU* 4.0 24.9 - - + -
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Residues in contact with ILE 341 (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 GLU 5.5 4.5 - - - +
322A LEU* 4.2 19.7 - - + +
323A GLU* 3.6 33.1 + - + +
326A THR* 5.5 0.2 - - - +
339A CYS* 3.5 28.9 - - - -
340A VAL* 1.3 79.9 - - - +
342A PHE* 1.3 64.6 + - - +
343A GLU* 4.3 4.3 + - + +
353A VAL* 4.0 22.0 - - + -
354A ARG 3.5 2.7 - - - -
355A ILE* 4.0 19.3 - - + -
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Residues in contact with PHE 342 (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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340A VAL* 3.9 0.9 + - + -
341A ILE* 1.3 75.9 - - - +
343A GLU* 1.3 71.1 + - - +
344A ILE* 3.8 26.9 + - + -
345A PRO* 5.7 2.7 - - + -
352A ALA 3.7 0.9 - - - +
353A VAL* 3.8 0.2 - - - -
354A ARG* 2.7 46.3 + - - +
356A PHE* 4.0 7.4 - - + -
395A LEU 6.0 0.9 - - - -
397A LEU* 3.8 59.7 - - + -
398A ALA* 4.4 9.2 - - + -
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Residues in contact with GLU 343 (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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315A ALA* 2.9 38.6 - - + +
316A GLY* 4.3 4.2 - - - -
341A ILE* 4.2 5.0 + - + +
342A PHE* 1.3 86.4 - - - +
344A ILE* 1.3 67.2 + - - +
345A PRO* 3.4 17.0 - - + +
352A ALA* 3.4 11.4 - - + +
353A VAL* 3.8 13.8 - - + +
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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