Contacts of the strand formed by residues 541 - 545 (chain F) in PDB entry 1ZM9
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 ALA 541 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510F GLY 3.0 9.7 + - - +
511F PHE* 3.8 20.0 - - + -
512F TYR* 3.0 28.4 + - - -
531F ILE* 4.3 1.4 - - - +
537F LEU* 3.8 4.7 - - - -
540F ASP* 1.3 74.8 - - - +
542F ILE* 1.3 60.7 + - - +
554F THR* 4.4 3.6 - - + -
555F ILE 3.4 10.8 - - - +
556F LEU* 3.5 33.0 - - + -
560F LEU* 4.0 2.9 - - + +
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Residues in contact with ILE 542 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466F TRP* 4.7 1.3 - - + -
512F TYR* 3.4 26.7 - - + +
513F ARG* 3.8 9.6 - - - +
514F THR* 4.0 17.3 - - + -
518F LEU* 4.2 19.2 - - + +
527F VAL* 4.0 27.8 - - + -
530F LEU* 4.5 9.0 - - + -
531F ILE* 4.7 2.0 - - + -
537F LEU* 3.8 30.3 - - + +
541F ALA* 1.3 75.5 - - - +
543F THR* 1.3 69.8 + - - +
553F GLU 4.0 0.9 - - - +
554F THR* 3.4 2.0 - - - +
555F ILE* 2.9 35.0 + - + +
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Residues in contact with THR 543 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511F PHE* 5.3 1.4 - - - -
512F TYR 2.9 12.5 + - - -
513F ARG* 3.3 7.8 + - + +
514F THR 3.1 24.4 + - - +
542F ILE* 1.3 78.2 - - - +
544F GLY* 1.3 60.9 + - - +
552F LEU* 4.2 26.6 - - + +
553F GLU 3.4 7.6 - - - +
554F THR* 2.6 30.5 + - - +
600F TYR* 3.3 30.2 - - + -
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Residues in contact with GLY 544 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514F THR* 3.5 7.4 - - - -
516F LEU 4.3 0.9 - - - -
518F LEU* 3.5 19.5 - - - +
542F ILE 4.2 0.2 - - - -
543F THR* 1.3 76.9 - - - +
545F PRO* 1.3 78.7 - - - +
552F LEU* 4.2 8.5 - - - -
553F GLU* 3.1 27.1 + - - +
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Residues in contact with PRO 545 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514F THR 3.6 9.9 - - - +
515F SER* 3.8 15.7 - - - +
516F LEU 3.4 14.8 - - - +
517F THR* 3.5 14.4 - - + -
518F LEU* 3.1 18.5 - - - +
544F GLY* 1.3 80.1 - - - -
546F GLU* 1.3 67.0 + - - +
547F GLU 3.2 19.0 + - - +
549F GLY 5.1 2.7 - - - +
550F GLY 4.5 8.3 - - - +
551F ARG 3.6 8.3 - - - +
552F LEU* 4.3 10.7 - - + -
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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