Contacts of the strand formed by residues 359 - 370 (chain A) in PDB entry 5H65
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 359 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A GLN* 1.3 80.8 - - - +
360A TYR* 1.3 73.0 + - - +
606A PHE* 5.9 0.9 - - + -
607A ILE 3.4 4.3 - - - -
608A LYS* 4.0 12.0 - - + +
625A PHE* 3.4 41.6 - - + -
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Residues in contact with TYR 360 (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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346A THR* 4.1 17.3 - - + -
351A ILE* 3.6 57.0 + - + -
354A GLN* 2.6 41.8 + - - +
355A LYS 4.4 1.7 + - - -
358A GLN* 3.3 39.9 + - + +
359A GLN* 1.3 80.6 - - - +
361A ARG* 1.3 60.2 + - - +
362A ILE* 3.9 5.2 + - + -
606A PHE* 3.2 10.1 - - - +
607A ILE* 2.8 46.0 + - + +
609A SER* 4.1 12.1 + - - -
625A PHE* 4.8 0.6 - - - -
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Residues in contact with ARG 361 (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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343A LEU* 3.9 31.3 - - + +
344A GLU 3.7 20.6 - - - +
345A ARG* 3.5 7.2 - - + +
346A THR* 2.9 30.3 + - - -
360A TYR* 1.3 70.1 - - - +
362A ILE* 1.3 78.9 + - - +
604A GLU* 2.7 46.5 + - - +
605A CYS* 3.5 12.9 - - - +
606A PHE* 3.8 39.2 - - + -
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Residues in contact with ILE 362 (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 ARG* 4.7 2.7 - - - -
346A THR 3.6 14.1 - - - +
348A LEU* 4.1 14.4 - - + -
351A ILE* 3.4 32.3 - - + -
360A TYR* 4.1 6.7 - - + -
361A ARG* 1.3 99.8 + - - +
363A ARG* 1.3 63.6 + - - +
364A ALA* 4.6 8.5 - - + -
548A LEU* 3.9 22.0 - - + -
605A CYS* 2.8 51.6 + - - +
607A ILE* 4.0 21.1 - - + -
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Residues in contact with ARG 363 (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 ARG* 3.7 25.6 - - + +
346A THR 5.0 1.7 + - - +
348A LEU* 5.6 0.2 - - - +
362A ILE* 1.3 75.3 - - - +
364A ALA* 1.3 64.2 + - - +
550A ASP* 3.4 18.2 - - - +
602A TRP* 3.2 71.5 - - + +
603A LEU 3.4 4.9 - - - +
604A GLU* 3.0 35.3 + - - +
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Residues in contact with ALA 364 (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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348A LEU* 4.2 6.3 - - + -
362A ILE* 4.3 9.8 - - + +
363A ARG* 1.3 77.3 - - - +
365A LYS* 1.3 57.8 + - - +
548A LEU* 4.0 16.2 - - + -
549A ASP 3.6 25.8 - - - +
550A ASP* 3.9 4.9 - - + -
602A TRP* 3.7 11.9 - - - -
603A LEU* 2.8 41.0 + - - +
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Residues in contact with LYS 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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364A ALA* 1.3 76.1 - - - +
366A LEU* 1.3 61.2 + - - +
367A ARG 3.1 3.3 + - - -
548A LEU* 3.4 5.8 - - - -
549A ASP* 2.8 39.8 + - - +
597A ILE* 3.3 35.9 + - + +
598A ASP* 2.9 30.5 + - - +
600A TYR* 2.9 25.9 + - + +
601A PRO 3.9 13.9 - - - +
602A TRP* 3.4 44.5 - - + +
603A LEU 4.8 0.2 - - - +
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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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364A ALA 4.1 1.4 + - - -
365A LYS* 1.3 68.6 - - - +
367A ARG* 1.3 65.6 + - - +
368A SER 3.2 25.1 - - - +
369A TYR* 4.0 15.3 - - + -
546A PHE* 3.4 48.9 - - + -
547A THR 3.7 5.2 - - - +
548A LEU* 4.2 8.2 - - + +
587A MET* 4.9 7.6 - - + +
590A PHE* 4.2 32.0 + - + +
591A CYS* 3.5 23.3 - - + +
600A TYR* 3.3 20.5 - - - -
601A PRO 4.9 1.6 + - - -
603A LEU* 5.3 8.3 - - + +
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Residues in contact with ARG 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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365A LYS 3.1 4.6 + - - -
366A LEU* 1.3 74.7 - - - +
368A SER* 1.3 68.8 + - - +
547A THR* 3.0 27.4 + - + +
549A ASP* 2.9 36.4 + - + -
554A VAL* 5.0 6.5 - - - +
591A CYS* 3.4 9.0 - - - -
597A ILE* 3.8 44.1 - - + +
600A TYR* 3.9 10.1 + - - -
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Residues in contact with SER 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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366A LEU* 3.2 9.2 - - - +
367A ARG* 1.3 85.3 - - - +
369A TYR* 1.3 65.3 + - - +
547A THR* 2.8 45.0 + - - +
591A CYS* 3.8 9.2 - - - -
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Residues in contact with TYR 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A LEU* 4.0 8.7 - - + -
368A SER* 1.3 79.2 - - - +
370A LYS* 1.3 71.3 + - - +
371A PRO 3.3 26.3 - - - -
372A ARG* 4.5 12.4 + - - +
374A LEU* 3.6 25.5 - - + +
544A MET* 5.1 2.7 - - - -
545A THR 3.3 10.8 - - - +
546A PHE* 3.9 19.5 - + + -
547A THR* 5.4 0.7 - - - -
587A MET* 4.0 30.2 + - + +
588A ASP* 5.7 0.3 - - - -
591A CYS* 3.8 40.9 + - + -
593A PRO* 6.0 2.4 - - - +
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Residues in contact with LYS 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A TYR* 1.3 80.8 - - - +
371A PRO* 1.3 71.4 - - + +
372A ARG 5.3 1.3 - - - +
544A MET* 3.4 6.2 - - - +
545A THR* 2.8 54.4 + - - +
547A THR* 4.8 8.3 + - - -
556A GLU* 3.6 22.8 + - - -
306B TYR* 3.7 19.7 - - + -
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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