Contacts of the strand formed by residues 364 - 371 (chain A) in PDB entry 4RA4
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 LEU 364 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A LEU* 3.7 30.7 - - + -
355A LEU* 4.4 9.9 - - + -
356A ALA 3.9 2.7 - - - +
357A ASP* 3.8 13.7 - - + -
362A GLU 3.4 9.7 + - - +
363A GLU* 1.4 69.5 - - - +
365A TYR* 1.4 75.3 + - - +
418A GLU* 5.4 0.3 - - - -
419A TYR* 4.2 38.2 + - + +
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Residues in contact with TYR 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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339A PHE* 4.2 14.1 - + + -
354A MET 3.6 0.7 - - - +
355A LEU* 3.4 6.4 - - - +
356A ALA* 2.8 40.9 + - - +
358A ARG* 3.3 20.5 + - + -
363A GLU* 3.0 49.3 + - + -
364A LEU* 1.4 79.3 - - - +
366A ALA* 1.4 59.0 + - - +
367A ILE* 3.9 7.0 - - + -
404A HIS* 3.6 25.9 - + + -
416A VAL* 4.0 20.6 - - + -
417A MET 3.6 16.4 - - - +
418A GLU* 4.8 1.3 - - - -
419A TYR* 4.0 8.3 - - - +
663A PHE* 3.8 17.3 - + - -
665A HIS* 3.3 20.5 + - - -
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Residues in contact with ALA 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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345A LEU* 3.9 19.5 - - + -
353A VAL* 4.3 5.4 - - + -
354A MET 3.4 5.6 - - - -
365A TYR* 1.4 70.6 - - - +
367A ILE* 1.3 61.9 + - - +
368A LYS 3.8 0.2 + - - -
417A MET* 3.0 35.1 + - - +
418A GLU 4.0 0.7 - - - +
419A TYR* 3.8 11.7 - - + +
701A 3KZ 3.4 35.3 - - + +
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Residues in contact with ILE 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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339A PHE* 3.9 31.9 - - + -
341A PHE* 3.9 12.6 - - + -
352A LYS 3.6 0.2 - - - +
353A VAL* 3.4 3.3 - - - -
354A MET* 2.7 48.1 + - + +
356A ALA* 3.8 24.9 - - + -
365A TYR* 4.5 8.7 - - + -
366A ALA* 1.3 74.2 - - - +
368A LYS* 1.3 61.5 + - - +
369A ILE* 3.5 23.5 + - + +
407A PHE* 5.6 1.8 - - + -
414A TYR* 3.9 21.3 - - + -
415A PHE 3.3 11.9 - - - +
416A VAL* 4.5 13.9 - - + -
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Residues in contact with LYS 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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350A PHE* 4.9 8.0 - - + +
352A LYS 3.6 8.3 - - - +
353A VAL* 4.5 4.9 - - + +
366A ALA 3.8 2.2 + - - -
367A ILE* 1.3 69.6 - - - +
369A ILE* 1.3 59.5 + - - +
370A LEU* 4.1 22.4 - - + -
387A GLU* 2.7 43.3 + - - -
413A LEU 3.7 1.6 - - - +
414A TYR* 3.5 3.6 - - - -
415A PHE* 2.9 58.8 + - + +
417A MET* 4.8 3.4 - - + -
481A ASP* 3.7 23.6 + - - +
701A 3KZ 4.2 34.9 - - + +
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Residues in contact with ILE 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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341A PHE* 4.2 14.6 - - + -
351A GLY* 3.8 2.6 - - - -
352A LYS* 2.8 43.0 + - + +
354A MET* 3.7 37.0 - - + +
367A ILE* 3.7 9.9 - - + +
368A LYS* 1.3 72.0 - - - +
370A LEU* 1.4 63.4 + - - +
371A LYS* 4.4 1.7 + - + +
412A ARG* 3.7 28.9 - - + +
413A LEU 3.5 5.6 - - - +
414A TYR* 3.5 40.4 - - + -
637A LEU* 4.5 10.1 - - + -
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Residues in contact with LEU 370 (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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350A PHE* 3.2 36.3 - - + +
351A GLY* 4.4 1.6 - - - +
368A LYS* 4.2 22.4 - - + -
369A ILE* 1.4 76.8 - - - +
371A LYS* 1.3 61.9 + - - +
375A VAL* 3.8 20.0 - - + -
384A THR* 3.6 23.6 - - - +
387A GLU* 5.1 2.7 - - - +
412A ARG* 3.3 5.1 - - - +
413A LEU* 2.8 41.4 + - + +
415A PHE* 4.1 25.4 - - + -
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Residues in contact with LYS 371 (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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350A PHE 5.2 1.4 + - - -
351A GLY* 5.7 1.4 - - - -
369A ILE* 4.4 2.2 + - + +
370A LEU* 1.3 72.0 - - - +
372A LYS* 1.4 59.0 + - - +
373A ASP* 3.3 24.5 + - - +
374A VAL* 3.2 22.7 + - + +
375A VAL* 2.9 30.4 + - - +
411A ASP* 3.4 9.4 + - + +
412A ARG* 3.4 44.3 - - + +
638A TPO 4.0 30.6 + - - +
639A PRO 5.2 1.4 + - - -
640A PRO* 5.3 5.3 - - - +
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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