Contacts of the strand formed by residues 396 - 405 (chain A) in PDB entry 4Y05
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 GLU 396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A LYS* 4.6 2.0 - - - +
394A GLY 4.5 8.7 - - - +
395A LEU* 1.3 76.3 - - - +
397A VAL* 1.3 62.1 + - - +
398A TYR* 3.4 32.8 + - + +
438A LEU* 3.9 15.0 - - + -
477A ILE 3.8 0.7 - - - +
478A LEU* 3.6 5.9 - - - +
479A ARG* 2.9 39.3 + - - +
480A ALA 5.1 2.3 - - - +
481A LYS* 5.1 3.6 - - - -
482A GLY* 4.1 16.0 + - - -
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Residues in contact with VAL 397 (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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381A VAL* 4.0 8.5 - - + -
382A PHE* 3.8 23.1 - - + -
385A LYS* 3.5 32.7 - - + +
396A GLU* 1.3 75.1 - - - +
398A TYR* 1.3 65.5 + - - +
399A VAL* 4.8 2.7 - - + -
438A LEU* 3.4 7.7 - - - +
439A VAL* 3.0 46.2 + - + +
445A VAL* 5.6 0.2 - - + -
476A ILE* 3.9 25.6 - - + -
477A ILE 3.6 3.6 - - - +
478A LEU* 3.8 14.6 - - + -
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Residues in contact with TYR 398 (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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396A GLU* 3.4 39.5 + - + -
397A VAL* 1.3 74.9 - - - +
399A VAL* 1.3 70.7 + - - +
436A GLU* 3.5 37.0 - - + +
437A HIS 3.2 6.1 - - - -
438A LEU* 3.7 44.2 - - + +
476A ILE* 3.7 0.9 - - - -
477A ILE* 2.9 39.4 + - + +
479A ARG* 3.8 34.1 - - + -
482A GLY* 5.7 1.9 - - - -
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Residues in contact with VAL 399 (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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397A VAL* 4.8 2.9 - - + -
398A TYR* 1.3 81.8 - - - +
400A THR* 1.3 75.5 + - - +
401A PHE* 5.3 0.2 - - + -
413A LEU* 4.4 11.9 - - + -
436A GLU* 3.5 0.6 - - - -
437A HIS* 2.8 40.8 + - + +
439A VAL* 4.0 21.5 - - + -
445A VAL* 4.1 10.1 - - + -
448A MET* 4.7 13.0 - - + -
474A PHE* 3.3 37.2 - - + -
475A GLN 3.3 9.6 - - - +
476A ILE* 4.6 6.5 - - + -
477A ILE* 5.1 0.7 - - - -
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Residues in contact with THR 400 (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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399A VAL* 1.3 81.9 - - - +
401A PHE* 1.3 64.6 + - - +
402A PHE* 3.9 3.3 - - - -
413A LEU* 4.2 4.9 - - - -
434A LEU* 4.0 27.6 - - + -
435A GLN 3.8 16.8 - - - +
436A GLU* 3.9 20.0 - - + -
473A CYS 4.4 0.2 - - - -
474A PHE* 3.4 7.6 - - - -
475A GLN* 2.8 57.6 + - - +
477A ILE* 4.1 9.4 - - + -
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Residues in contact with PHE 401 (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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374A TYR* 4.1 20.9 - + - -
399A VAL* 5.3 0.2 - - + -
400A THR* 1.3 78.0 - - - +
402A PHE* 1.3 61.2 + - - +
411A ASP* 3.5 9.3 + - - +
412A LEU* 3.0 39.3 + - + +
413A LEU* 3.7 22.1 + - + +
434A LEU* 5.3 0.8 - - - +
448A MET* 5.0 0.7 - - + -
449A ILE* 3.7 34.8 - - + -
452A GLY* 3.7 19.1 - - - -
453A SER* 3.7 18.8 - - - -
472A ALA* 4.2 18.4 - - + -
473A CYS 3.3 17.7 - - - -
474A PHE* 3.7 25.1 - + + -
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Residues in contact with PHE 402 (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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400A THR* 3.9 4.5 - - - -
401A PHE* 1.3 78.4 - - - +
403A GLU* 1.3 59.0 + - - +
404A ILE* 4.2 14.4 - - + -
409A LEU* 3.8 26.0 - - + -
410A PHE 3.2 18.8 - - - +
411A ASP* 4.3 3.6 - - - -
412A LEU* 3.8 6.9 - - - +
419A LEU* 4.5 7.2 - - + -
434A LEU* 3.8 27.6 - - + -
472A ALA* 3.5 2.1 - - - -
473A CYS* 2.8 65.2 + - + +
475A GLN* 3.6 26.5 - - - -
547A VAL* 3.6 31.9 - - + -
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Residues in contact with GLU 403 (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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402A PHE* 1.3 75.1 - - - +
404A ILE* 1.3 63.4 + - - +
405A TYR* 4.1 10.0 - - - +
408A LYS 3.7 0.5 - - - +
409A LEU* 3.3 5.0 - - - +
410A PHE* 2.9 51.9 + - + -
412A LEU* 3.9 20.6 - - + +
416A LYS* 3.2 28.8 + - - -
456A ARG* 3.5 21.5 - - - +
457A THR 3.9 7.8 + - - +
470A SER* 3.4 21.6 + - - -
471A HIS 3.1 13.7 - - - +
472A ALA* 4.3 3.2 - - + +
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Residues in contact with ILE 404 (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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402A PHE* 4.2 20.4 - - + -
403A GLU* 1.3 77.4 - - - +
405A TYR* 1.3 62.2 + - - +
407A GLY* 4.6 2.0 - - - +
408A LYS 3.3 12.6 - - - +
409A LEU* 3.7 19.3 - - + -
469A ARG 4.6 0.2 - - - +
470A SER* 3.3 6.6 - - - -
471A HIS* 2.8 53.4 + - + +
473A CYS* 5.6 1.8 - - + -
543A LYS* 4.0 23.6 - - + +
544A LEU* 3.8 42.6 - - + +
547A VAL* 5.0 2.5 - - + -
704A SO4 4.4 8.1 - - - +
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Residues in contact with TYR 405 (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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403A GLU* 4.1 9.6 - - - +
404A ILE* 1.3 73.8 - - - +
406A ASN* 1.3 93.4 + - + +
407A GLY 3.3 1.3 - - - -
408A LYS* 2.9 26.7 + - - +
410A PHE* 3.9 19.9 - + + -
457A THR 5.8 2.0 - - - -
466A ASN 4.9 8.1 - - - -
469A ARG* 3.1 68.5 + - + -
470A SER* 4.0 10.5 - - - -
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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