Contacts of the strand formed by residues 493 - 503 (chain B) in PDB entry 5ZHU
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 493 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427B VAL 3.2 9.6 - - - +
428B LYS* 4.3 14.4 - - + -
429B LEU 5.1 0.2 - - - -
436B ILE* 3.6 42.0 - - + -
472B PHE* 3.8 27.8 - + + -
474B GLU* 3.5 28.0 - - + -
475B THR 3.4 22.7 - - - -
476B THR* 3.7 15.3 - - + -
477B ALA 5.7 0.2 - - - -
491B ARG* 6.0 2.2 - - + -
492B TYR* 1.3 81.5 - - - +
494B MET* 1.3 62.7 + - - +
517B ARG* 3.5 4.0 - - - -
518B ILE* 2.7 46.1 + - + +
520B VAL* 3.7 19.7 - - + -
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Residues in contact with MET 494 (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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345B GLN* 5.1 8.1 - - - +
426B GLY* 3.3 3.5 - - - -
427B VAL* 2.9 37.4 + - + +
429B LEU* 4.0 24.5 - - + -
432B LEU* 4.4 17.0 - - + -
472B PHE* 5.4 0.7 - - - -
493B PHE* 1.3 81.2 - - - +
495B LEU* 1.3 60.2 + - - +
514B ILE* 3.6 33.4 - - + -
515B SER* 3.1 30.5 - - - +
516B GLU* 3.9 13.0 - - - +
517B ARG* 4.0 4.3 - - - +
518B ILE* 4.7 0.4 - - - -
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Residues in contact with LEU 495 (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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344B TRP* 3.4 20.3 - - + -
376B PHE* 4.5 10.5 - - + -
393B PHE* 3.8 26.9 - - + -
395B VAL* 3.9 18.8 - - + -
424B LEU* 4.7 5.4 - - + -
425B HIS 3.7 21.8 - - - +
438B ILE* 4.1 12.6 - - + -
472B PHE* 4.0 21.8 - - + -
494B MET* 1.3 72.6 - - - +
496B VAL* 1.3 59.2 + - - +
497B VAL* 4.3 7.4 - - + -
514B ILE* 3.2 3.3 - - - -
515B SER* 2.8 45.4 + - - +
518B ILE* 4.1 10.8 - - + +
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Residues in contact with VAL 496 (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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347B HIS* 3.9 24.0 - - + +
423B LYS 3.7 0.7 - - - +
424B LEU* 3.3 6.4 - - - +
425B HIS* 2.8 68.4 + - + +
427B VAL* 4.3 12.1 - - + -
494B MET 4.3 1.3 - - - +
495B LEU* 1.3 77.9 - - - +
497B VAL* 1.3 68.9 + - - +
498B ALA* 4.7 9.4 - - + -
512B ALA* 4.8 2.5 - - + -
513B GLN 3.4 6.5 - - - +
514B ILE* 3.8 27.4 - - + -
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Residues in contact with VAL 497 (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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344B TRP* 3.7 27.8 - - + -
368B TYR* 3.0 20.8 + - - +
370B VAL* 3.7 15.0 - - + -
395B VAL* 4.1 7.6 - - + -
397B VAL* 3.7 24.9 - - + -
422B LEU* 4.3 3.4 - - + -
423B LYS 3.6 2.5 - - - -
424B LEU* 4.0 28.7 - - + -
495B LEU* 4.3 4.5 - - + -
496B VAL* 1.3 77.0 - - - +
498B ALA* 1.3 61.8 + - - +
512B ALA* 3.3 0.4 - - - -
513B GLN 2.9 32.6 + - - +
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Residues in contact with ALA 498 (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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368B TYR* 3.6 3.1 - - - -
422B LEU* 3.5 4.3 - - - +
423B LYS* 2.8 55.7 + - + +
425B HIS* 6.0 1.1 - - + -
496B VAL* 4.7 8.3 - - + -
497B VAL* 1.3 75.7 - - - +
499B LEU* 1.3 61.9 + - - +
500B GLN* 4.9 3.4 - - + +
509B THR* 4.4 12.8 - - + +
511B ALA 3.4 4.7 - - - +
512B ALA* 3.8 17.9 - - + -
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Residues in contact with LEU 499 (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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366B LEU* 4.0 26.2 - - + -
368B TYR* 3.5 19.8 + - + -
399B ILE* 3.8 42.2 - - + -
420B PHE* 4.2 16.6 - - + -
421B TYR 3.5 15.5 - - - +
422B LEU* 4.3 4.3 - - + -
455B VAL* 4.2 6.3 - - + -
457B LEU* 4.0 7.6 - - + -
498B ALA* 1.3 72.2 - - - +
500B GLN* 1.3 69.8 + - - +
509B THR* 3.5 4.3 - - - +
510B LEU* 2.9 37.3 + - + -
511B ALA 2.8 15.1 + - - +
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Residues in contact with GLN 500 (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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420B PHE* 3.3 9.9 - - - +
421B TYR* 2.7 49.6 + - + +
423B LYS* 3.5 45.0 - - + +
452B PRO* 4.7 5.5 - - - +
498B ALA* 4.6 3.8 - - + +
499B LEU* 1.3 78.5 - - - +
501B ALA* 1.3 61.0 + - - +
507B ASN* 3.6 36.5 + - + +
508B TYR 3.3 10.3 - - - +
509B THR* 4.2 17.1 + - - +
510B LEU* 4.4 3.8 - - - -
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Residues in contact with ALA 501 (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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408B VAL* 3.5 30.5 - - + -
417B LEU* 3.7 9.6 - - + -
419B CYS 3.6 4.3 - - - -
420B PHE* 4.3 1.3 - - + -
500B GLN* 1.3 73.5 - - - +
502B HIS* 1.3 61.1 + - - +
507B ASN* 3.4 3.2 - - - -
508B TYR* 2.8 40.0 + - + +
510B LEU* 3.6 26.8 - - + +
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Residues in contact with HIS 502 (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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417B LEU* 4.1 2.3 - - - +
418B ASP* 2.9 50.7 + - + +
419B CYS* 2.8 33.9 + - - +
420B PHE* 4.8 0.2 - - - +
421B TYR* 3.8 14.9 + + + -
500B GLN 4.2 0.8 - - - -
501B ALA* 1.3 69.4 - - - +
503B ALA* 1.3 62.3 + - - +
505B ASN* 3.9 17.0 + - - -
506B GLN* 3.4 26.4 + - - -
507B ASN* 3.2 28.3 + - - +
442C GLN* 6.0 7.0 - - + -
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Residues in contact with ALA 503 (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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408B VAL* 3.6 30.7 - - + -
415B LYS* 4.3 7.2 - - + -
416B PRO 3.3 23.8 - - - +
417B LEU* 4.6 0.9 - - - -
418B ASP* 3.8 4.3 - - - -
501B ALA 3.9 0.4 + - - -
502B HIS* 1.3 76.0 - - - +
504B GLN* 1.3 75.5 + - - +
505B ASN 3.3 1.6 - - - -
506B GLN* 2.8 21.3 + - - +
508B TYR* 3.7 10.4 - - + -
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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