Contacts of the strand formed by residues 364 - 369 (chain A) in PDB entry 3PE7
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 GLN 364 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLN* 6.1 0.6 - - - +
24A THR* 5.7 3.6 + - - -
358A PHE* 3.5 8.5 - - - -
359A THR* 3.0 48.0 + - + +
361A ASP* 4.8 5.5 - - - +
362A ASP 3.5 0.4 - - - -
363A LYS* 1.3 89.8 - - + +
365A ILE* 1.3 66.2 + - - +
379A LEU* 3.8 34.2 + - + +
380A ALA 3.1 13.0 - - - +
381A THR* 3.9 20.3 + - + +
382A LEU* 4.4 3.1 - - - +
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Residues in contact with ILE 365 (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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298A VAL* 4.0 22.9 - - + -
322A LEU* 3.9 33.4 - - + -
324A VAL* 4.6 0.2 - - + -
335A VAL* 3.9 24.9 - - + -
356A PRO* 5.0 2.5 - - + -
357A SER 3.3 12.8 - - - +
358A PHE* 3.7 26.0 - - + -
364A GLN* 1.3 80.1 - - - +
366A LEU* 1.3 61.5 + - - +
367A PHE* 3.9 2.9 - - + -
378A TYR 3.6 1.2 - - - +
379A LEU* 3.2 8.3 - - - -
380A ALA* 2.9 50.5 + - + +
382A LEU* 4.0 10.3 - - + -
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Residues in contact with LEU 366 (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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26A LEU* 4.4 2.5 - - + -
35A ARG* 3.3 42.2 + - + +
42A CYS* 4.0 3.6 - - - -
43A PHE* 3.8 17.5 - - + -
50A LEU* 3.7 44.2 - - + -
356A PRO* 3.3 22.9 - - - +
357A SER 3.0 11.2 + - - +
359A THR 5.2 0.4 - - - +
364A GLN 4.4 0.2 + - - -
365A ILE* 1.3 73.2 - - - +
367A PHE* 1.3 65.0 + - - +
377A LEU* 4.0 14.8 - - + -
378A TYR 3.3 17.3 - - - +
379A LEU* 3.8 21.7 - - + +
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Residues in contact with PHE 367 (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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23A VAL* 4.7 7.9 - - + -
35A ARG* 4.6 5.8 - - - -
322A LEU* 3.6 25.4 - - + -
336A ALA* 5.6 0.9 - - + -
337A ARG 3.8 10.8 - - - -
338A HIS* 3.7 33.9 - - + -
354A PRO* 3.2 21.8 - - + +
356A PRO* 4.4 7.4 - - + -
365A ILE* 3.9 8.7 - - + -
366A LEU* 1.3 81.1 - - - +
368A THR* 1.3 72.4 + - - +
369A SER* 4.3 0.7 - - - -
377A LEU* 3.6 4.1 - - - +
378A TYR* 2.9 72.3 + + + -
380A ALA* 3.9 22.0 - - + -
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Residues in contact with THR 368 (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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33A CYS 4.0 6.5 - - - +
34A HIS* 3.7 3.5 - - + +
35A ARG* 3.0 34.7 + - - +
351A VAL 3.4 21.7 + - - +
352A THR* 4.2 3.0 - - - +
353A HIS 3.6 14.6 + - - -
354A PRO* 3.0 32.2 + - - +
367A PHE* 1.3 76.4 - - - +
369A SER* 1.3 68.5 + - - +
375A PRO* 3.9 19.3 - - + -
376A ALA 3.2 13.4 + - - +
377A LEU* 4.9 0.3 - - - +
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Residues in contact with SER 369 (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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338A HIS 2.6 30.9 + - - -
339A ASP 3.5 0.2 - - - -
340A THR* 3.4 17.7 + - - -
352A THR* 5.7 0.2 - - - -
367A PHE* 4.3 2.9 - - - -
368A THR* 1.3 78.3 - - - +
370A ASP* 1.3 61.0 + - - +
371A VAL* 3.1 16.6 + - - +
374A LYS 3.8 0.9 - - - +
375A PRO* 4.1 2.5 - - - -
376A ALA 2.8 29.7 + - - +
378A TYR* 3.4 24.0 + - - -
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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