Contacts of the strand formed by residues 411 - 421 (chain A) in PDB entry 5TYZ
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 SER 411 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A PRO* 3.7 3.8 - - - +
396A GLN* 2.8 24.9 + - - +
397A PRO 3.1 6.2 - - - -
410A GLY* 1.3 81.0 - - - +
412A TRP* 1.3 92.0 + - - +
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Residues in contact with TRP 412 (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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282A HIS* 5.0 7.0 - + - -
285A ASP* 4.5 7.6 - - - +
361A LEU* 3.6 36.6 - - + -
393A ARG* 3.1 57.4 - - + +
394A LEU 3.0 22.2 - - - +
395A PRO* 3.9 2.5 - - + -
396A GLN* 3.5 10.5 - - - +
411A SER* 1.3 98.3 + - - +
413A LYS* 1.3 82.9 + - - +
414A ALA* 4.0 8.7 - - + -
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Residues in contact with LYS 413 (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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285A ASP* 3.5 20.4 - - - +
288A THR* 4.5 20.2 + - + +
289A PRO 3.4 21.4 + - - -
290A VAL* 4.3 4.0 - - - +
291A LEU* 5.2 2.0 - - - +
294A ASP* 3.1 27.3 + - - -
394A LEU* 2.8 44.8 + - + +
396A GLN* 3.7 34.3 + - + +
412A TRP* 1.3 83.5 - - - +
414A ALA* 1.3 65.6 + - - +
415A VAL* 4.0 14.3 - - + +
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Residues in contact with ALA 414 (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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282A HIS* 3.7 26.0 - - + +
285A ASP* 2.9 38.1 + - + +
286A LEU* 3.7 7.8 - - + +
361A LEU* 3.7 7.2 - - + -
391A ILE* 3.6 20.9 - - + -
392A PHE 3.3 6.7 - - - -
412A TRP* 4.0 2.5 - - + -
413A LYS* 1.3 75.2 - - - +
415A VAL* 1.3 65.5 + - - +
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Residues in contact with VAL 415 (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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286A LEU* 4.1 5.2 - - - -
290A VAL* 3.7 30.1 - - + -
298A LEU* 4.0 23.8 - - + -
331A VAL* 4.3 1.6 - - + -
391A ILE* 3.4 1.9 - - - +
392A PHE* 2.6 41.5 + - + +
394A LEU* 3.8 35.4 - - + -
413A LYS* 3.9 14.8 - - + +
414A ALA* 1.3 81.0 - - - +
416A ARG* 1.3 74.4 + - - +
417A VAL* 3.5 0.9 + - + -
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Residues in contact with ARG 416 (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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244A PHE* 3.4 36.5 - - + -
286A LEU* 3.8 28.5 - - + +
329A HIS 4.1 8.0 + - - +
330A ASP* 3.2 21.8 + - + -
331A VAL 3.0 23.4 + - - -
389A PHE* 3.7 2.9 - - - +
390A CYS 3.1 27.5 + - - +
391A ILE* 3.9 19.7 - - + +
415A VAL* 1.3 74.9 - - - +
417A VAL* 1.3 72.0 + - - +
418A ASP* 2.8 34.7 + - - -
3P T 3.7 7.5 + - - -
4P A 2.9 27.5 + - - -
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Residues in contact with VAL 417 (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 LEU* 4.0 22.9 - - + -
302A VAL* 5.2 0.9 - - + -
331A VAL* 3.2 10.8 - - + +
333A PHE* 3.8 28.5 - - + -
388A SER 3.7 0.5 - - - +
390A CYS* 2.8 37.0 + - - +
392A PHE* 3.4 45.8 - - + -
415A VAL 3.8 2.0 - - - +
416A ARG* 1.3 80.6 + - - +
418A ASP* 1.3 65.9 + - - +
419A LEU* 3.9 14.6 - - + -
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Residues in contact with ASP 418 (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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330A ASP* 3.6 0.7 - - - -
331A VAL 2.8 9.2 + - - +
332A ASP* 3.1 13.1 - - - +
333A PHE 2.8 28.8 + - - +
388A SER 3.4 3.6 - - - +
389A PHE* 3.3 19.8 - - + -
416A ARG* 2.8 30.1 + - - -
417A VAL* 1.3 72.0 - - - +
419A LEU* 1.3 63.5 + - - +
420A VAL* 4.6 1.1 - - + +
434A TRP* 4.2 14.1 - - + -
502A MN 2.1 32.8 + - - -
4P A 3.1 16.8 - - - +
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Residues in contact with LEU 419 (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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302A VAL* 4.1 16.8 - - + -
333A PHE* 3.8 30.5 - - + -
335A ILE* 4.5 6.3 - - + -
347A LEU* 3.9 17.0 - - + +
350A VAL* 4.2 11.9 - - + -
351A MET* 3.8 27.1 - - - -
354A LEU* 3.8 19.5 - - + -
387A ARG* 3.4 2.9 - - - -
388A SER* 2.8 41.2 + - - +
390A CYS* 4.9 4.3 - - - -
392A PHE* 4.7 5.6 - - + -
417A VAL* 3.9 11.4 - - + -
418A ASP* 1.3 78.9 - - - +
420A VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 420 (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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333A PHE 3.1 14.6 + - - +
334A LEU* 3.5 14.3 - - + -
335A ILE* 2.7 35.9 + - - +
386A GLU* 3.3 11.0 - - + +
387A ARG* 4.1 13.7 - - + +
389A PHE* 6.0 0.2 - - + -
418A ASP* 4.6 1.1 - - + +
419A LEU* 1.3 83.6 - - - +
421A VAL* 1.3 67.9 + - - +
430A ALA* 5.7 1.8 - - + -
434A TRP* 3.3 60.1 - - + +
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Residues in contact with VAL 421 (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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334A LEU* 4.6 0.4 - - - -
335A ILE* 3.3 24.9 - - + +
343A GLU* 3.9 38.6 - - + +
346A LEU* 4.5 8.1 - - + -
347A LEU* 4.0 39.9 - - + +
385A PHE 5.5 0.2 - - - +
386A GLU* 2.9 35.0 + - + +
420A VAL* 1.3 83.5 - - - +
422A ALA* 1.3 66.2 + - - +
423A PRO* 4.8 0.3 - - - +
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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