Contacts of the strand formed by residues 488 - 496 (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 PHE 488 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480A LEU* 3.7 40.8 - - + +
481A TRP 3.4 1.3 - - - -
482A LYS* 3.5 44.6 - - + -
486A GLY 4.2 7.0 - - - -
487A ARG* 1.3 80.9 + - - +
489A LYS* 1.3 63.4 + - - +
490A ASP* 4.0 5.0 + - - +
534A GLN* 5.9 0.7 - - - -
552A HIS* 3.5 36.1 - + + -
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Residues in contact with LYS 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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480A LEU* 3.6 2.8 - - - -
481A TRP* 2.9 44.2 + - + +
483A THR* 3.9 17.2 - - + +
485A THR* 6.2 1.0 - - - +
487A ARG* 3.9 1.5 + - - -
488A PHE* 1.3 73.6 - - - +
490A ASP* 1.3 69.3 + - - +
491A VAL* 3.3 6.1 + - + -
504A GLN* 3.1 32.7 - - - +
513A PRO* 5.6 0.2 - - + -
515A LEU* 3.6 34.3 - - + +
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Residues in contact with ASP 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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478A CYS* 6.0 5.9 - - + +
479A LEU 3.7 5.0 - - - +
480A LEU* 3.5 19.6 - - - +
488A PHE 4.8 3.8 - - - +
489A LYS* 1.3 73.1 - - - +
491A VAL* 1.3 65.9 + - - +
504A GLN* 3.9 9.2 - - - +
505A GLU* 3.7 30.0 - - - +
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Residues in contact with VAL 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A CYS* 3.4 8.3 - - - +
479A LEU* 2.9 44.0 + - + +
481A TRP* 4.0 23.6 - - + +
489A LYS* 3.9 17.3 - - + +
490A ASP* 1.3 80.4 - - - +
492A LEU* 1.3 63.3 + - - +
493A VAL* 3.8 18.3 + - + -
502A PHE* 4.0 14.4 - - + -
503A LEU 3.4 14.1 - - - +
504A GLN* 4.3 10.5 - - + +
505A GLU* 4.9 2.2 - - - -
513A PRO* 5.0 7.2 - - + -
515A LEU* 6.2 0.7 - - + -
551A VAL* 5.6 0.4 - - + -
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Residues in contact with LEU 492 (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* 3.8 18.2 - - - +
445A ILE* 4.5 1.6 - - + -
476A ASP* 4.4 4.0 - - - +
477A GLY* 3.9 26.0 - - - +
478A CYS* 4.5 11.9 - - - +
491A VAL* 1.3 70.0 - - - +
493A VAL* 1.3 66.0 + - - +
494A LEU* 3.9 21.3 + - + -
501A VAL 3.7 1.9 - - - +
502A PHE* 3.7 1.2 - - - -
503A LEU* 2.9 50.4 + - + +
504A GLN* 5.1 1.5 - - - +
505A GLU* 5.2 4.7 + - + +
510A TYR* 3.7 41.3 - - + +
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Residues in contact with VAL 493 (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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476A ASP* 3.1 6.9 - - - +
477A GLY 2.9 37.0 + - - +
479A LEU* 3.8 24.9 - - + -
491A VAL* 3.8 12.6 - - + +
492A LEU* 1.3 76.7 - - - +
494A LEU* 1.3 65.4 + - - +
500A LEU* 3.8 26.5 - - + -
501A VAL 3.4 6.7 - - - +
502A PHE* 3.7 32.5 - - + -
540A LEU* 6.4 1.1 - - + -
562A TRP* 3.4 19.3 - - + -
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Residues in contact with LEU 494 (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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442A LEU* 4.8 1.3 - - + -
445A ILE* 3.8 29.8 - - + -
468A LEU* 4.1 25.6 - - + -
473A LEU* 3.8 16.8 - - + -
475A HIS 3.7 3.6 - - - -
476A ASP* 4.1 5.8 - - + -
492A LEU* 3.9 18.6 - - + +
493A VAL* 1.3 78.4 - - - +
495A LEU* 1.3 59.9 + - - +
496A MET* 3.8 13.8 + - + +
499A VAL 3.9 0.2 - - - +
500A LEU* 3.3 9.9 - - - +
501A VAL* 2.9 44.4 + - + -
503A LEU* 3.9 23.8 - - + -
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Residues in contact with LEU 495 (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* 3.9 1.8 - - - +
474A ILE* 2.8 32.2 + - + +
475A HIS* 2.7 22.5 + - + +
493A VAL 4.1 0.6 - - - -
494A LEU* 1.3 70.8 - - - +
496A MET* 1.3 57.0 + - - +
499A VAL 4.1 0.2 - - - +
500A LEU* 3.8 21.1 - - + -
523A LEU* 3.7 31.9 - - + -
562A TRP* 4.1 12.0 - - + -
565A VAL* 3.2 49.8 - - + +
566A ILE* 3.9 12.3 - - + +
569A SER* 3.5 14.6 - - - +
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Residues in contact with MET 496 (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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442A LEU* 3.6 31.6 - - + -
463A PHE* 5.2 0.2 - - - -
468A LEU* 3.7 35.0 - - + +
471A ARG* 4.1 21.5 - - + -
472A LYS 3.1 23.1 - - - +
473A LEU* 4.1 11.0 - - + +
474A ILE* 4.1 7.8 - - - +
494A LEU* 4.2 18.2 - - + +
495A LEU* 1.3 80.6 - - - +
497A THR* 1.3 70.0 + - - +
498A ASP 3.3 0.9 - - - -
499A VAL* 2.9 25.8 + - + +
501A VAL* 3.9 11.4 - - + -
523A LEU* 3.2 15.1 - - - +
569A SER* 4.4 0.7 - - - -
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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