Contacts of the strand formed by residues 423 - 429 (chain B) in PDB entry 3KCZ
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 ARG 423 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B PHE* 3.6 33.6 - - + -
417B ARG 5.2 0.6 + - - -
418B GLU* 3.0 43.8 + - - +
420B LEU 4.6 9.7 + - - +
421B HIS 3.3 1.4 - - - -
422B ASN* 1.3 76.2 - - - +
424B MET* 1.3 59.9 + - - +
489B GLU* 4.4 8.6 + - - -
490B VAL 3.3 15.0 - - - +
491B ALA* 4.5 2.9 - - - +
532B ASN 4.4 5.5 + - - -
533B GLY* 4.1 28.6 + - - +
534B SER* 3.1 24.0 - - - +
535B THR* 2.9 26.9 + - - -
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Residues in contact with MET 424 (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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422B ASN* 3.8 17.9 - - - +
423B ARG* 1.3 78.6 - - - +
425B LEU* 1.3 62.0 + - - +
426B LEU* 3.6 17.7 + - + -
465B ASP* 5.4 0.2 - - - +
488B SER 3.4 1.7 - - - +
489B GLU* 3.6 0.5 - - - -
490B VAL* 2.8 33.9 + - - +
492B LEU* 3.6 25.8 - - + -
528B PHE* 4.5 8.3 - - + -
534B SER* 4.1 4.9 - - - -
535B THR* 3.4 25.6 - - + +
537B PRO* 3.9 34.3 - - + -
559B TYR* 4.2 22.7 - - - +
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B VAL* 6.2 0.2 - - + -
382B ILE* 5.1 1.3 - - + -
385B TYR* 2.7 37.0 + - + -
424B MET* 1.3 69.9 - - - +
426B LEU* 1.3 56.6 + - - +
487B LEU* 3.8 33.2 - - + -
488B SER* 3.4 24.9 - - - +
489B GLU* 3.9 18.4 - - + +
531B LEU* 4.2 12.6 - - + +
534B SER* 4.0 8.0 - - - -
535B THR 2.9 14.6 + - - +
536B VAL* 4.1 22.7 - - + -
537B PRO* 3.7 3.5 - - - +
570B ARG* 4.4 2.0 - - + -
571B TYR* 4.1 24.0 - - + -
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Residues in contact with LEU 426 (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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385B TYR* 3.9 6.3 - - - +
424B MET* 3.9 31.6 - - + +
425B LEU* 1.3 85.0 - - - +
427B TRP* 1.3 63.0 - - - +
463B PHE* 3.7 32.9 - - + -
464B ALA 3.6 13.5 - - - +
465B ASP* 4.1 14.4 - - + -
486B LEU 3.6 0.3 - - - +
487B LEU* 3.4 8.6 - - - -
488B SER* 2.9 30.4 + - - +
490B VAL* 4.0 20.0 - - + -
492B LEU* 4.6 1.8 - - + -
537B PRO* 4.4 0.2 - - + -
559B TYR* 3.8 31.9 - - + -
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Residues in contact with TRP 427 (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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382B ILE 4.4 1.8 - - - -
385B TYR* 3.3 46.7 - + - -
386B LEU* 3.6 31.6 - - + -
389B THR* 3.5 0.6 + - - -
426B LEU* 1.3 72.7 - - - +
428B HIS* 1.3 60.2 - - - +
463B PHE* 3.2 11.9 - - - -
464B ALA* 2.9 45.6 + - + +
465B ASP 3.9 1.8 - - - -
466B MET 3.7 3.1 - - - -
467B SER* 3.4 33.4 - - - +
470B SER* 3.2 20.4 + - - +
485B LEU* 3.8 22.2 - - + -
486B LEU 3.4 11.0 - - - -
487B LEU* 3.3 37.5 - - + -
573B LEU* 3.7 29.2 - - + -
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Residues in contact with HIS 428 (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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1B 3AB 3.3 21.9 + - - -
427B TRP* 1.3 75.7 - - - +
429B GLY* 1.3 72.3 + - - +
430B SER* 4.3 12.3 + - - -
435B TRP* 4.0 5.0 - + - -
438B ILE* 4.5 3.6 - - + +
443B LEU* 3.7 37.5 - - + +
461B ILE* 5.0 2.5 - - + -
462B TYR* 2.9 30.1 + - + -
463B PHE* 4.2 12.8 - - + -
470B SER* 3.9 2.9 - - - -
485B LEU* 3.9 1.8 - - - -
486B LEU* 2.9 44.5 + - + +
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Residues in contact with GLY 429 (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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1B 3AB 2.8 30.4 + - - -
428B HIS* 1.3 79.4 + - - +
430B SER* 1.3 64.3 + - - -
435B TRP* 4.6 0.2 - - - -
470B SER* 3.3 23.2 - - - -
473B TYR* 3.8 5.3 - - - +
474B CYS* 4.2 3.6 - - - -
484B LEU 4.6 1.3 - - - -
485B LEU* 3.9 11.4 - - - -
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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