Contacts of the strand formed by residues 436 - 447 (chain A) in PDB entry 4PKY
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 TRP 436 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399A PHE 5.3 0.2 - - - -
400A CYS 3.8 4.7 - - - -
401A HIS* 3.3 67.1 + + + -
402A PRO* 4.2 7.9 - - + -
428A ARG* 3.9 22.6 - - + +
429A PHE 3.6 5.8 - - - -
430A ARG* 3.5 57.2 - - + +
435A GLU* 1.3 72.5 - - - +
437A LEU* 1.3 64.0 + - - +
438A TRP* 3.8 7.1 + - - -
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Residues in contact with LEU 437 (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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383A THR 3.5 24.2 - - - +
384A VAL* 4.0 12.8 - - + -
428A ARG* 4.3 1.6 - - - -
429A PHE* 2.8 38.4 + - + +
431A SER* 3.6 22.7 - - - -
435A GLU* 3.8 34.3 - - + +
436A TRP* 1.3 72.7 - - - +
438A TRP* 1.3 63.1 + - - +
439A MET* 3.2 11.0 + - - +
463A ASN* 3.8 21.3 - - - +
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Residues in contact with TRP 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ASP* 4.4 6.3 - - - -
426A MET* 3.7 27.1 - - + -
427A PHE* 3.7 35.9 - - - -
428A ARG* 3.5 42.3 - - + +
436A TRP 3.8 5.8 + - - -
437A LEU* 1.3 69.7 - - - +
439A MET* 1.3 58.2 + - - +
463A ASN* 3.0 9.1 + - - +
464A VAL* 2.9 53.3 + - + +
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Residues in contact with MET 439 (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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363A PHE* 4.2 5.4 - - + -
383A THR* 4.1 12.6 - - + -
384A VAL* 4.4 15.9 - - + -
425A VAL 3.5 2.4 - - - +
426A MET* 3.4 5.9 - - - -
427A PHE* 2.7 54.5 + - + +
429A PHE* 3.5 32.5 - - + -
437A LEU* 3.6 6.7 - - - +
438A TRP* 1.3 73.9 - - - +
440A ARG* 1.3 58.8 + - - +
441A THR* 3.8 4.5 - - - +
461A ASN* 3.5 31.6 - - + +
462A THR 3.4 22.0 - - - -
463A ASN* 3.6 25.1 - - - +
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Residues in contact with ARG 440 (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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424A SER* 3.4 29.0 + - - +
425A VAL 3.4 7.9 - - - +
426A MET* 4.1 24.8 - - + +
438A TRP 4.2 0.6 + - - -
439A MET* 1.3 70.5 - - - +
441A THR* 1.3 60.3 + - - +
442A SER* 4.1 0.4 + - - -
460A THR 3.5 3.1 - - - +
462A THR* 2.8 35.5 + - - +
464A VAL* 4.0 21.4 - - + +
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Residues in contact with THR 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ILE* 5.7 2.0 - - + -
412A PHE* 6.5 0.4 - - + -
423A LEU 4.1 0.2 - - - +
424A SER* 3.3 4.9 - - - -
425A VAL* 2.9 40.7 + - + +
427A PHE* 3.5 26.4 - - + -
439A MET* 3.8 2.3 - - - +
440A ARG* 1.3 74.7 - - - +
442A SER* 1.3 61.6 + - - +
443A SER* 3.8 11.4 + - - +
459A CYS* 3.6 24.2 - - + -
460A THR 3.4 4.5 - - - +
461A ASN* 2.9 36.0 + - - +
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Residues in contact with SER 442 (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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422A VAL* 4.1 12.6 - - - -
423A LEU 3.2 10.8 - - - -
424A SER* 4.2 7.6 - - - +
440A ARG* 4.1 1.0 + - - -
441A THR* 1.3 72.1 - - - +
443A SER* 1.3 61.3 + - - +
444A PHE* 5.1 3.4 - - - -
458A ILE 3.9 0.3 - - - +
459A CYS* 3.3 4.2 - - - -
460A THR* 2.9 45.6 + - - -
625C ILE* 4.5 9.2 - - - +
629C GLU* 4.6 13.2 + - - -
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Residues in contact with SER 443 (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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411A SER* 4.5 10.3 + - - -
412A PHE* 5.4 4.0 - - - -
415A VAL* 3.8 20.7 - - - +
422A VAL* 3.3 3.1 - - - +
423A LEU 2.8 33.2 + - - -
425A VAL* 5.4 1.7 - - - +
441A THR* 3.8 8.3 + - - +
442A SER* 1.3 75.0 - - - +
444A PHE* 1.3 69.2 + - - +
457A ILE* 4.2 5.2 - - - -
458A ILE 3.3 5.4 - - - -
459A CYS* 3.0 28.1 - - - -
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Residues in contact with PHE 444 (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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415A VAL* 4.5 5.8 - - - -
420A GLY 3.6 16.4 - - - +
421A GLN 3.7 9.0 - - - +
422A VAL* 4.1 19.1 - - + -
442A SER* 5.1 2.5 - - - -
443A SER* 1.3 82.6 - - - +
445A THR* 1.3 74.2 + - - +
446A PHE* 5.2 1.6 - - + -
457A ILE* 4.3 4.0 - - - +
458A ILE* 3.2 66.9 + - + -
460A THR* 5.4 0.9 - - - -
624B LEU* 4.2 13.7 - - + -
627B LYS* 3.9 22.4 - - + -
625C ILE* 4.3 28.3 - - + -
628C MET* 5.2 11.2 - - + -
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Residues in contact with THR 445 (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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415A VAL* 3.2 29.9 + - + +
416A VAL* 4.0 8.3 - - + -
419A LYS* 3.2 27.0 - - - +
420A GLY 3.4 5.7 + - - +
421A GLN 4.9 0.2 + - - -
444A PHE* 1.3 85.5 - - - +
446A PHE* 1.3 62.3 + - - +
447A GLN* 4.8 2.3 - - - +
454A ILE* 4.1 21.4 - - + +
456A TYR 3.5 8.1 - - - -
457A ILE* 3.9 20.4 - - + +
627B LYS* 3.1 18.6 + - - -
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Residues in contact with PHE 446 (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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444A PHE* 5.2 1.1 - - + -
445A THR* 1.3 75.7 - - - +
447A GLN* 1.3 79.0 + - - +
448A ASN* 4.8 1.6 - - - -
454A ILE* 3.9 4.3 - - - +
455A GLU* 3.3 52.7 + - + -
456A TYR* 3.0 42.3 + + + +
458A ILE* 5.1 4.0 - - + -
623B ASP* 3.0 58.8 - - + -
624B LEU* 5.7 2.2 - - + -
626B SER* 4.7 8.3 - - - -
627B LYS* 3.9 24.0 - - + +
630B LYS* 5.9 1.6 - - - -
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Residues in contact with GLN 447 (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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419A LYS* 3.7 43.4 + - + +
420A GLY* 5.9 0.6 - - - -
445A THR* 4.8 4.9 - - - +
446A PHE* 1.3 100.0 - - - +
448A ASN* 1.3 70.1 + - - +
452A ASP* 4.3 25.3 + - - +
453A GLU 4.0 13.9 - - - +
454A ILE* 5.5 1.1 - - + -
627B LYS* 4.0 13.1 - - - +
630B LYS* 3.9 18.1 + - - +
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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