Contacts of the strand formed by residues 469 - 478 (chain A) in PDB entry 3L5J
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 CYS 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437A VAL* 3.6 4.5 - - - +
438A LEU* 2.8 47.3 + - + +
468A LYS* 1.3 69.3 - - - +
470A TYR* 1.3 62.1 + - - +
489A LYS* 4.1 26.5 - - - -
490A ALA 4.0 1.3 - - - -
491A TYR* 3.1 42.5 - - - +
522A VAL* 4.3 20.6 + - + +
528A PHE* 4.4 5.2 - - - -
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Residues in contact with TYR 470 (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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417A LEU* 4.6 12.1 - - + -
435A TRP* 3.7 24.0 - + + -
436A CYS* 3.4 8.3 - - - -
437A VAL* 3.2 29.6 - - + +
438A LEU* 4.8 1.6 - - - -
460A LEU* 5.5 0.2 - - + -
463A ASN 4.3 3.1 + - - -
464A LEU* 3.3 29.8 - - + -
465A ALA* 2.7 50.4 + - - +
468A LYS* 3.4 22.8 + - + -
469A CYS* 1.3 73.0 - - - +
471A LEU* 1.3 59.3 + - - +
472A ILE* 3.8 14.3 + - + +
488A ILE 3.7 0.7 - - - +
489A LYS* 3.3 5.9 - - - -
490A ALA 2.9 39.2 + - - +
492A LEU* 4.8 4.3 - - + -
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Residues in contact with LEU 471 (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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434A GLU 3.8 0.7 - - - +
435A TRP* 3.3 19.4 - - - -
436A CYS* 2.8 17.0 + - - +
438A LEU* 3.5 34.1 - - + -
444A CYS* 4.9 10.8 - - - -
469A CYS 3.9 0.6 + - - -
470A TYR* 1.3 70.9 - - - +
472A ILE* 1.3 62.6 + - - +
473A THR* 4.5 5.6 + - - +
487A SER* 3.8 25.4 - - - +
488A ILE 3.6 17.9 - - - +
489A LYS* 3.9 17.3 - - + +
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Residues in contact with ILE 472 (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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408A LEU* 5.5 0.2 - - - -
410A ALA* 3.8 17.7 - - + -
417A LEU* 3.9 14.8 - - + -
419A VAL* 3.7 35.0 - - + -
433A LEU* 5.1 2.5 - - + -
434A GLU 3.4 9.4 - - - +
435A TRP* 4.0 4.0 - - + -
460A LEU* 3.7 31.9 - - + -
470A TYR* 4.5 9.0 - - + +
471A LEU* 1.3 71.5 - - - +
473A THR* 1.3 72.5 + - - +
474A VAL* 4.6 9.2 - - + -
486A GLU 3.9 0.2 - - - +
487A SER* 3.0 5.9 - - - -
488A ILE* 2.8 48.9 + - + +
490A ALA* 4.8 4.0 - - + -
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Residues in contact with THR 473 (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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432A ILE 3.4 2.4 - - - +
433A LEU* 3.4 4.9 - - - -
434A GLU* 2.8 50.5 + - + +
471A LEU* 4.5 8.0 + - - +
472A ILE* 1.3 74.9 - - - +
474A VAL* 1.3 63.8 + - - +
475A THR* 4.0 10.2 + - - +
485A PRO* 3.9 24.2 - - + -
486A GLU 3.3 7.2 - - - +
487A SER* 2.7 25.0 + - - +
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Residues in contact with VAL 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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405A VAL* 4.1 22.4 - - + +
408A LEU* 4.0 15.5 - - + -
419A VAL* 3.9 28.5 - - + -
421A TRP* 4.0 16.6 - - + -
431A TYR* 4.0 26.0 - - + -
432A ILE 3.6 4.7 - - - +
433A LEU* 4.1 11.4 - - + -
472A ILE* 4.6 4.3 - - + -
473A THR* 1.3 75.5 - - - +
475A THR* 1.3 63.5 + - - +
476A PRO* 3.8 4.8 - - - +
485A PRO* 3.8 1.4 - - - +
486A GLU* 2.9 33.5 + - - +
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Residues in contact with THR 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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311A TRP* 4.4 15.9 + - + -
430A LYS 4.1 0.2 - - - +
431A TYR* 3.7 1.8 - - - -
432A ILE* 2.9 44.3 + - - +
434A GLU* 5.4 5.2 - - - -
473A THR* 4.0 13.9 + - - +
474A VAL* 1.3 80.5 + - - +
476A PRO* 1.3 75.6 - - - +
477A VAL* 3.6 3.3 + - - +
482A PRO* 4.3 12.1 - - + -
483A GLY 4.0 14.6 - - - +
485A PRO* 4.4 11.9 - - + +
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Residues in contact with PRO 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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403A HIS 3.5 18.6 - - - +
404A PRO 4.1 0.2 - - - -
405A VAL* 3.7 26.7 - - + +
424A PRO* 5.8 1.1 - - + -
428A VAL* 4.4 4.7 - - + -
430A LYS 4.3 2.7 - - - +
431A TYR* 4.4 10.5 - - + -
474A VAL 3.8 5.6 - - - +
475A THR* 1.3 91.3 - - + +
477A VAL* 1.3 63.4 + - - +
478A TYR* 3.6 28.0 - - + +
483A GLY* 2.8 25.2 + - - -
484A SER 3.5 20.0 - - - +
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Residues in contact with VAL 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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311A TRP* 3.6 37.0 - - + -
392A LEU* 6.2 0.7 - - + -
428A VAL* 3.2 4.5 - - - +
429A LYS* 2.9 32.6 + - + +
430A LYS* 3.0 44.1 + - + +
432A ILE* 4.2 9.2 - - + -
475A THR* 4.1 5.8 - - + +
476A PRO* 1.3 79.0 - - - +
478A TYR* 1.3 70.8 + - - +
481A GLY 4.2 3.4 - - - +
482A PRO* 4.7 3.6 - - + -
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Residues in contact with TYR 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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1A EDO 3.4 30.3 - - - +
393A THR* 5.8 0.7 - - - -
403A HIS* 3.2 40.3 + + + +
424A PRO* 4.4 10.7 - - - +
426A GLU* 4.1 17.2 - - + +
427A SER 3.5 20.0 - - - -
428A VAL* 3.7 25.9 - - + +
429A LYS* 3.9 6.3 - - + -
476A PRO* 3.6 26.2 - - + +
477A VAL* 1.3 80.6 - - - +
479A ALA* 1.3 65.8 + - - +
480A ASP* 3.0 1.5 + - + +
481A GLY 2.9 30.2 + - - +
483A GLY* 4.1 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