Contacts of the strand formed by residues 473 - 482 (chain A) in PDB entry 5EFX
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 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439A GLY 4.3 15.8 + - - +
441A ARG* 3.6 33.9 - - + -
442A LEU* 3.7 37.3 - - + +
445A ILE* 4.1 8.7 - - + -
471A ARG 3.9 2.4 + - - -
472A LYS* 1.3 79.3 + - - +
474A ILE* 1.3 61.7 + - - +
475A HIS 3.5 24.2 - - - +
476A ASP* 4.0 12.6 - - + +
494A LEU* 3.8 25.4 - - + -
495A LEU 4.0 4.3 - - - +
496A MET* 4.1 7.7 - - + +
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Residues in contact with ILE 474 (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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472A LYS* 3.4 28.7 + - + +
473A LEU* 1.3 75.6 - - - +
475A HIS* 1.3 61.4 + - - +
495A LEU* 2.8 17.7 + - + +
496A MET 4.1 2.2 - - - +
497A THR* 4.1 24.7 - - + +
565A VAL* 3.9 19.1 - - + +
569A SER* 3.3 30.1 - - - +
572A THR* 6.1 0.9 - - - +
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Residues in contact with HIS 475 (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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473A LEU* 3.5 5.3 - - - +
474A ILE* 1.3 79.9 - - - +
476A ASP* 1.3 88.7 + - - +
477A GLY* 5.1 0.7 - - - -
495A LEU* 2.7 40.6 + - + +
558A ASP* 5.7 0.7 - - - -
561A THR* 4.0 25.8 - - + +
562A TRP* 3.7 35.4 - + + -
565A VAL* 3.8 27.6 - - + -
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Residues in contact with ASP 476 (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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441A ARG* 3.2 45.0 + - - +
445A ILE* 5.1 0.2 - - + -
473A LEU* 4.0 17.4 - - + +
475A HIS* 1.3 96.7 + - - +
477A GLY* 1.3 60.1 + - - +
492A LEU* 4.4 3.6 - - + +
493A VAL 3.1 11.2 - - - +
494A LEU* 4.1 10.8 - - + -
562A TRP* 3.9 0.4 - - - -
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Residues in contact with GLY 477 (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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475A HIS* 5.1 0.9 - - - -
476A ASP* 1.3 76.9 - - - +
478A CYS* 1.3 65.2 + - - -
479A LEU 3.5 0.9 + - - -
492A LEU* 3.9 9.1 - - - +
493A VAL* 2.9 35.2 + - - +
562A TRP* 3.5 15.3 - - - -
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Residues in contact with CYS 478 (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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477A GLY* 1.3 72.8 - - - -
479A LEU* 1.3 73.0 + - - +
490A ASP* 6.0 5.2 - - + +
491A VAL 3.4 12.3 - - - +
492A LEU* 4.5 13.2 - - - +
505A GLU* 5.4 9.2 - - - -
553A THR* 5.5 0.3 - - - -
558A ASP* 4.7 4.9 - - - +
562A TRP* 4.9 0.9 + - - -
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Residues in contact with LEU 479 (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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477A GLY 3.5 1.1 + - - +
478A CYS* 1.3 83.2 - - - +
480A LEU* 1.3 66.2 + - - +
489A LYS 3.7 0.3 - - - +
490A ASP* 3.7 4.2 - - - +
491A VAL* 2.9 34.9 + - + +
493A VAL* 3.8 31.6 - - + -
538A MET* 4.4 14.1 - - + -
540A LEU* 6.2 1.3 - - + -
551A VAL* 4.4 15.3 - - + -
552A HIS 3.8 9.2 - - - +
553A THR* 3.6 26.7 - - + +
558A ASP* 4.4 1.3 - - - +
562A TRP* 3.5 42.8 - - + +
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Residues in contact with LEU 480 (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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479A LEU* 1.3 77.1 - - - +
481A TRP* 1.3 60.1 + - - +
482A LYS 3.8 0.9 + - - -
488A PHE* 3.7 37.5 - - + -
489A LYS 3.6 0.9 - - - +
490A ASP* 3.5 34.5 - - - +
491A VAL* 4.8 0.4 - - - -
551A VAL* 3.1 9.7 - - - -
552A HIS* 2.9 49.8 + - + +
553A THR 5.4 3.6 - - - +
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Residues in contact with TRP 481 (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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479A LEU 4.1 0.4 + - - -
480A LEU* 1.3 70.9 - - - +
482A LYS* 1.3 79.2 + - - +
483A THR* 3.3 11.3 + - + +
487A ARG 3.4 0.3 - - - +
488A PHE* 3.4 2.0 - - - -
489A LYS* 2.9 44.7 + - + +
491A VAL* 4.0 15.0 - - + -
502A PHE* 3.3 57.0 - + + -
513A PRO* 5.6 3.1 - - + -
515A LEU* 2.5 42.2 - - + +
517A LYS* 3.9 28.4 - - + +
518A PRO 4.0 8.3 - - - -
519A SER* 5.1 3.1 - - - -
549A TYR* 3.5 24.2 - + + -
550A GLU 3.7 9.4 - - - +
551A VAL* 4.4 4.3 - - + -
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Residues in contact with LYS 482 (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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480A LEU 3.8 1.6 + - - -
481A TRP* 1.3 80.3 + - - +
483A THR* 1.3 66.1 + - - +
486A GLY* 4.3 17.2 - - - +
487A ARG 3.5 6.7 - - - +
488A PHE* 3.5 43.9 - - + -
517A LYS* 5.4 5.4 - - - -
534A GLN* 5.5 7.8 + - - +
550A GLU* 3.0 59.1 + - + +
552A HIS* 4.9 0.9 - - - -
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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