Contacts of the strand formed by residues 482 - 491 (chain A) in PDB entry 4EEP
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 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396A PRO* 3.5 31.0 - - + -
397A ARG* 3.9 17.1 - - + +
446A ILE 5.6 0.2 - - - +
449A GLN* 3.7 40.4 - - + +
474A PRO* 3.7 25.8 - - + -
475A MET 3.9 7.6 - - - +
476A ARG* 3.4 15.3 - - + +
477A ASP* 5.2 0.5 - - - +
481A GLU* 1.3 76.5 - - - +
483A GLN* 1.3 60.2 + - - +
484A TYR 3.7 19.1 - - - +
485A PHE* 3.7 15.7 - - + -
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Residues in contact with GLN 483 (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 PRO* 3.3 10.5 - - - +
397A ARG* 2.7 54.8 + - - +
475A MET* 2.8 15.5 + - - +
476A ARG 4.6 2.3 - - - +
477A ASP* 4.0 27.5 + - + +
481A GLU 3.4 5.1 + - - +
482A LEU* 1.3 76.4 - - - +
484A TYR* 1.3 90.3 + - + +
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Residues in contact with TYR 484 (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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393A ILE* 3.7 15.5 - - + -
394A SER 3.4 15.9 - - - +
395A ASP* 4.3 3.4 - - - -
396A PRO* 3.7 3.1 - - - -
397A ARG* 3.3 17.0 + - - -
404A ILE* 3.5 28.0 - - + +
475A MET* 2.8 58.3 + - + +
482A LEU* 3.7 8.3 - - - +
483A GLN* 1.3 123.6 + - + +
485A PHE* 1.3 62.6 + - - +
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Residues in contact with PHE 485 (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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393A ILE* 3.3 7.1 - - - +
394A SER* 2.9 42.7 + - - +
396A PRO* 3.9 15.3 - - + -
401A ASN* 3.9 15.5 - - - -
446A ILE* 3.6 48.9 - - + -
449A GLN* 4.1 7.9 - - + -
472A LEU* 3.7 21.5 - - + -
473A GLN 3.5 1.6 - - - -
474A PRO* 3.7 31.4 - - + -
475A MET* 4.2 3.4 - - - -
482A LEU* 3.7 28.3 - - + -
484A TYR* 1.3 73.8 - - - +
486A ILE* 1.3 59.0 + - - +
1001A FMN 3.6 15.9 - - + +
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Residues in contact with ILE 486 (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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388A GLU* 5.5 5.6 - - + -
391A PHE* 3.9 27.6 - - + -
392A VAL 3.4 5.8 - - - +
393A ILE* 3.6 21.1 - - + -
471A HIS* 3.7 2.2 - - + +
472A LEU* 3.6 3.8 - - - +
473A GLN* 2.9 61.5 + - + +
475A MET* 3.7 22.1 - - + -
485A PHE* 1.3 73.3 - - - +
487A GLY* 1.3 61.8 + - - +
488A VAL* 4.2 13.9 - - + -
1001A FMN 3.9 2.5 - - - -
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Residues in contact with GLY 487 (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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391A PHE* 3.1 4.9 - - - -
392A VAL 2.9 33.7 + - - -
470A PHE* 3.7 16.4 - - - -
471A HIS 3.5 4.9 - - - -
486A ILE* 1.3 73.0 - - - +
488A VAL* 1.3 62.3 + - - -
489A GLN* 3.3 9.3 + - - +
1001A FMN 3.5 15.3 - - - +
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Residues in contact with VAL 488 (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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388A GLU* 3.2 42.8 - - + +
390A ASN 3.5 10.1 - - - +
391A PHE* 3.9 14.4 - - + -
469A LEU 3.5 2.3 - - - +
470A PHE* 3.4 6.2 - - - -
471A HIS* 2.8 57.4 + - + +
486A ILE* 4.2 14.8 - - + -
487A GLY* 1.3 76.1 - - - -
489A GLN* 1.3 68.0 + - - +
490A LEU* 5.2 8.5 - - + -
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Residues in contact with GLN 489 (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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390A ASN* 3.0 36.5 + - + +
391A PHE* 3.6 1.4 - - - -
392A VAL* 3.8 6.7 - - - +
410A PHE* 3.3 34.3 - - + -
413A LEU* 3.7 19.5 - - + -
429A LEU* 5.2 0.7 - - + -
468A ASN* 3.3 20.2 - - - +
470A PHE* 4.0 2.4 - - + -
487A GLY 3.3 23.5 + - - +
488A VAL* 1.3 76.0 - - - +
490A LEU* 1.3 69.2 + - - +
1001A FMN 3.1 43.0 + - - +
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Residues in contact with LEU 490 (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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388A GLU* 5.8 2.7 - - - +
389A LYS* 6.0 4.0 - - + -
390A ASN* 4.2 12.6 - - + +
413A LEU* 5.0 2.5 - - - -
466A PHE* 5.3 0.2 - - - -
467A TRP 3.4 1.9 - - - +
468A ASN* 3.5 3.7 + - - -
469A LEU* 2.8 57.3 + - + +
488A VAL* 5.2 9.4 - - + -
489A GLN* 1.3 83.4 - - - +
491A ASP* 1.3 61.2 + - - +
492A GLY 3.2 3.9 + - - -
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Residues in contact with ASP 491 (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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390A ASN* 4.8 1.6 - - - +
413A LEU* 3.7 25.0 - - + +
466A PHE* 3.6 22.5 - - - +
467A TRP 3.6 3.1 - - - -
469A LEU* 5.0 0.7 - - - +
490A LEU* 1.3 71.6 - - - +
492A GLY* 1.3 58.5 + - - +
493A SER* 2.9 32.7 + - - +
495A HIS* 2.7 27.5 + - - -
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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