Contacts of the strand formed by residues 469 - 477 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437B VAL* 3.5 4.0 - - - -
438B LEU* 2.9 53.2 + - + +
468B LYS* 1.3 70.9 - - - +
470B TYR* 1.3 62.7 + - - +
489B LYS* 4.1 27.6 - - - -
490B ALA 4.1 1.1 - - - -
491B TYR* 3.3 41.6 + - + +
522B VAL* 4.3 18.5 + - + -
528B PHE* 4.5 3.6 - - - -
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Residues in contact with TYR 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B LEU* 5.0 5.8 - - + -
435B TRP* 4.3 23.1 - + + -
436B CYS* 3.4 17.0 - - - +
437B VAL* 3.3 26.0 - - + +
438B LEU* 5.2 0.2 - - - -
460B LEU* 6.0 0.2 - - + -
463B ASN 4.8 1.4 + - - -
464B LEU* 3.6 23.5 - - + -
465B ALA* 2.7 53.6 + - + +
468B LYS* 3.5 20.4 + - + -
469B CYS* 1.3 75.6 - - - +
471B LEU* 1.3 59.3 + - - +
472B ILE* 3.6 14.8 + - + +
489B LYS* 3.4 4.7 - - - +
490B ALA 2.8 46.2 + - - +
492B LEU* 4.7 8.7 - - + -
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Residues in contact with LEU 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434B GLU 3.6 1.6 - - - +
435B TRP* 3.6 3.6 - - - -
436B CYS* 2.8 42.2 + - - +
438B LEU* 4.0 31.9 - - + -
444B CYS* 5.1 3.6 - - - -
469B CYS 4.1 0.8 + - - -
470B TYR* 1.3 70.4 - - - +
472B ILE* 1.3 62.8 + - - +
473B THR* 3.9 8.7 + - - +
487B SER* 4.0 26.9 - - - +
488B ILE 3.9 11.9 - - - +
489B LYS* 4.3 14.1 - - + +
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Residues in contact with ILE 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B ALA* 4.0 5.8 - - + -
417B LEU* 3.7 29.6 - - + -
419B VAL* 3.7 38.1 - - + -
433B LEU* 5.3 1.6 - - + -
434B GLU 3.4 9.4 - - - +
435B TRP* 4.3 13.2 - - + +
460B LEU* 4.1 12.3 - - + -
470B TYR* 4.3 10.1 - - + +
471B LEU* 1.3 70.6 - - - +
473B THR* 1.3 74.1 + - - +
474B VAL* 4.6 4.5 - - + -
487B SER* 3.4 1.0 - - - -
488B ILE* 2.9 48.5 + - + +
490B ALA* 4.0 13.5 - - + -
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Residues in contact with THR 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B ILE 3.5 3.6 - - - +
433B LEU* 3.5 0.7 - - - -
434B GLU* 2.7 58.2 + - - +
471B LEU* 3.9 12.0 + - - +
472B ILE* 1.3 78.2 + - - +
474B VAL* 1.3 62.0 + - - +
475B THR* 4.6 0.9 - - - +
485B PRO* 3.8 26.2 - - + -
486B GLU 3.4 9.6 - - - +
487B SER* 3.5 23.7 + - - +
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Residues in contact with VAL 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405B VAL* 4.0 22.6 - - + +
408B LEU* 4.0 33.6 - - + +
419B VAL* 4.0 11.7 - - + -
421B TRP* 4.1 15.5 - - + -
431B TYR* 4.2 17.9 - - + -
432B ILE 3.5 5.2 - - - +
433B LEU* 3.8 21.5 - - + -
472B ILE* 4.6 3.8 - - + -
473B THR* 1.3 73.2 - - - +
475B THR* 1.3 65.7 + - - +
476B PRO* 4.0 3.9 - - - +
484B SER 4.6 0.2 - - - +
485B PRO* 3.9 1.4 - - - +
486B GLU* 3.2 31.1 + - - +
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Residues in contact with THR 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B TRP* 4.8 15.9 - - + -
431B TYR* 3.4 4.0 - - - -
432B ILE* 2.7 49.2 + - - +
434B GLU* 3.5 20.5 + - - -
473B THR* 4.4 0.5 + - - +
474B VAL* 1.3 78.1 + - - +
476B PRO* 1.3 70.4 - - + +
477B VAL* 4.0 1.2 + - - +
482B PRO* 4.9 6.3 - - + -
483B GLY 3.5 24.0 - - - +
485B PRO* 4.2 20.0 - - + +
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Residues in contact with PRO 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B HIS 3.9 17.3 - - - +
405B VAL* 3.5 25.1 - - + +
424B PRO* 5.6 1.6 - - + -
428B VAL* 4.5 4.9 - - + -
430B LYS 3.8 4.7 - - - +
431B TYR* 4.2 15.3 - - + -
474B VAL 4.0 3.4 - - - +
475B THR* 1.3 92.4 - - + +
477B VAL* 1.3 58.3 + - - +
478B TYR* 3.8 22.8 + - + +
482B PRO* 3.5 2.1 - - - +
483B GLY* 2.7 35.5 + - - +
484B SER 3.9 14.6 - - - +
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Residues in contact with VAL 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B TRP* 3.8 34.1 - - + -
391B VAL 5.7 2.9 - - - +
392B LEU* 5.7 2.9 - - + -
393B THR 6.3 0.4 - - - +
428B VAL* 3.7 2.5 - - - +
429B LYS* 2.9 33.2 + - + +
430B LYS* 2.8 45.4 + - + +
432B ILE* 4.6 3.4 - - + -
475B THR 4.5 6.1 - - - +
476B PRO* 1.3 75.7 - - - +
478B TYR* 1.3 70.0 + - - +
481B GLY* 3.9 12.3 - - - +
482B PRO* 4.4 4.0 - - + -
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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