Contacts of the strand formed by residues 548 - 554 (chain B) in PDB entry 3U0Z
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 548 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484B VAL* 3.5 8.9 - - - +
485B PHE* 3.0 45.3 + - + +
491B ILE* 5.0 2.0 - - + -
504B ILE* 5.5 2.0 - - - -
506B HIS 3.6 1.8 - - - +
507B GLY* 4.2 3.4 - - - -
508B VAL 3.4 39.3 - - - -
509B ALA* 4.5 6.3 - - - -
544B ALA* 4.0 11.0 - - + -
546B THR 3.4 9.4 + - - +
547B TYR* 1.3 70.9 - - - +
549B ARG* 1.3 64.9 + - - +
550B LEU* 3.6 21.1 + - + +
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Residues in contact with ARG 549 (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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426B HIS 5.2 7.1 + - - -
427B ARG 5.8 0.8 + - - -
429B GLN* 4.6 15.6 + - - +
482B PHE* 3.5 33.0 - - + -
483B GLU 3.9 3.6 - - - -
484B VAL* 4.6 8.8 - - + +
504B ILE 4.0 0.2 - - - -
505B GLN* 2.3 79.1 + - - +
506B HIS* 2.6 38.5 + - + +
547B TYR* 5.5 4.0 - - + +
548B CYS* 1.3 76.1 - - - +
550B LEU* 1.3 62.6 + - - +
551B TYR* 5.7 0.6 + - - -
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Residues in contact with LEU 550 (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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482B PHE* 3.4 9.3 - - - -
483B GLU* 2.9 39.5 + - + +
485B PHE* 3.5 31.2 - - + -
491B ILE* 4.3 8.7 - - + -
502B TYR* 3.8 24.0 - - + -
503B PHE 3.3 5.6 - - - +
504B ILE* 3.7 35.7 - - + +
505B GLN 4.5 0.2 - - - +
527B PHE* 4.0 17.3 - - + -
548B CYS* 4.2 18.4 - - + +
549B ARG* 1.3 82.0 - - - +
551B TYR* 1.3 64.9 + - - +
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Residues in contact with TYR 551 (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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455B CYS* 4.9 19.6 - - - -
458B LEU* 5.3 9.9 - - + -
480B LEU* 3.8 38.4 - - + -
481B ARG 3.5 4.3 - - - -
482B PHE* 3.6 49.6 - + + +
502B TYR* 3.3 1.4 - - - -
503B PHE* 2.6 50.0 + - + +
505B GLN* 4.3 33.2 + - + -
549B ARG* 5.7 0.3 + - - -
550B LEU* 1.3 75.2 - - - +
552B SER* 1.3 60.8 + - - +
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Residues in contact with SER 552 (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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479B LYS 4.0 1.2 - - - +
480B LEU* 3.4 8.4 - - - -
481B ARG* 2.9 42.2 + - - +
483B GLU* 2.8 29.2 + - - +
500B LYS* 4.4 9.9 - - - +
501B MET 3.1 10.3 - - - -
502B TYR* 3.6 17.9 - - - -
550B LEU 4.2 0.4 - - - -
551B TYR* 1.3 75.2 - - - +
553B LEU* 1.3 61.3 + - - +
554B SER 4.4 0.2 + - - -
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Residues in contact with LEU 553 (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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476B MET* 3.9 36.1 - - + +
479B LYS* 3.8 26.7 - - + +
480B LEU* 4.2 12.6 - - + -
500B LYS* 3.5 2.1 - - - -
501B MET* 2.7 46.6 + - + +
503B PHE* 4.4 7.0 - - + -
532B LEU* 4.6 1.7 - - - +
552B SER* 1.3 74.2 - - - +
554B SER* 1.3 68.7 + - - +
557B ASN* 3.6 27.4 - - + +
558B PHE* 4.0 28.5 - - + +
561B VAL* 5.9 0.2 - - + -
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Residues in contact with SER 554 (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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479B LYS 5.2 0.6 + - - -
499B LYS 3.5 11.0 - - - -
500B LYS* 4.4 5.8 - - - +
552B SER 4.2 0.8 + - - -
553B LEU* 1.3 76.0 - - - +
555B VAL* 1.3 66.9 + - - +
556B ASP* 3.9 4.6 + - - +
557B ASN* 3.0 29.6 + - - +
558B PHE* 2.9 19.5 + - - +
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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