Contacts of the strand formed by residues 549 - 555 (chain A) in PDB entry 1U2Z
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 GLU 549 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481A PHE* 6.0 0.7 - - - -
507A LEU* 3.4 24.4 - - - +
533A ARG* 2.7 36.7 + - + +
534A TYR 3.1 17.5 - - - +
535A ASP* 4.5 0.9 - - - -
536A LEU* 3.7 15.6 - - - +
548A GLY* 1.3 77.9 - - - +
550A TYR* 1.3 63.9 + - - +
551A TYR* 2.6 33.4 + - + -
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Residues in contact with TYR 550 (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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379A PHE* 3.5 40.5 - + + -
382A ASP* 5.3 2.3 - - - +
383A VAL* 3.9 9.5 - - + +
386A GLN* 2.5 37.4 + - - -
505A ILE* 4.8 4.3 - - + -
506A SER 3.5 11.9 - - - +
507A LEU* 4.2 6.3 - - + +
533A ARG* 3.7 0.5 - - - +
534A TYR* 3.0 68.5 + + + +
535A ASP 3.5 14.6 - - - -
536A LEU* 3.5 13.7 - - + -
537A LYS* 5.4 1.9 - - + -
549A GLU* 1.3 75.3 - - - +
551A TYR* 1.3 78.4 + - - +
552A ILE* 4.3 6.5 - - + -
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Residues in contact with TYR 551 (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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504A ILE 3.6 0.8 - - - +
505A ILE* 3.3 8.0 - - - +
506A SER* 2.7 44.1 + - - +
507A LEU 4.0 9.0 - - - -
508A LYS* 3.8 6.5 - - - -
509A SER* 3.4 42.1 - - - -
513A LEU* 5.6 8.2 - - + +
531A VAL* 3.7 28.3 - - + -
532A GLN 3.4 3.8 - - - +
533A ARG* 3.6 32.6 - - + -
549A GLU* 2.6 34.1 + - + -
550A TYR* 1.3 81.3 - - - +
552A ILE* 1.3 65.5 + - - +
553A SER* 4.1 4.7 - - - +
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Residues in contact with ILE 552 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383A VAL* 4.9 2.0 - - + +
386A GLN* 3.8 39.5 - - + +
387A CYS* 4.1 26.2 - - - -
503A LYS* 4.4 13.0 - - + +
504A ILE 3.3 5.8 - - - +
505A ILE* 4.5 7.2 - - + -
530A LYS 3.5 2.8 - - - +
532A GLN* 3.1 39.1 + - + +
534A TYR* 3.7 27.8 - - + +
550A TYR* 4.3 8.1 - - + -
551A TYR* 1.3 77.8 - - - +
553A SER* 1.3 61.7 + - - +
554A THR* 4.0 13.4 + - - +
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Residues in contact with SER 553 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502A CYS 3.7 1.0 - - - +
503A LYS* 3.5 2.1 - - - -
504A ILE* 2.8 45.2 + - - +
506A SER* 5.1 0.3 + - - -
510A LEU* 4.0 25.1 + - - +
529A LEU* 3.8 26.6 - - - +
530A LYS 3.1 5.8 - - - -
531A VAL* 3.8 19.7 - - - +
551A TYR* 4.6 4.9 - - - +
552A ILE* 1.3 75.2 + - - +
554A THR* 1.3 62.1 + - - +
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Residues in contact with THR 554 (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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501A GLY* 4.1 13.2 - - - +
502A CYS 3.5 8.7 - - - +
503A LYS* 3.3 34.3 + - - +
529A LEU* 3.2 5.3 - - - -
530A LYS* 2.7 47.9 + - - -
532A GLN* 4.5 7.3 + - - -
552A ILE* 4.4 5.5 - - - +
553A SER* 1.3 74.9 - - - +
555A VAL* 1.3 68.7 + - - +
556A MET* 3.3 22.5 + - - +
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Residues in contact with VAL 555 (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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498A ALA* 4.1 10.3 - - + +
499A LYS 3.3 26.5 - - - +
500A VAL* 3.6 6.4 - - - +
501A GLY* 2.7 28.6 + - - -
502A CYS* 2.9 20.3 + - + +
504A ILE* 4.4 7.4 - - + -
525A ILE* 3.8 28.0 - - + -
528A ARG* 3.2 33.0 - - - +
529A LEU* 4.2 15.9 - - + +
554A THR* 1.3 74.8 - - - +
556A MET* 1.3 59.7 + - - +
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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