Contacts of the strand formed by residues 558 - 561 (chain F) in PDB entry 6MZL
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 LEU 558 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484F LEU* 3.7 31.2 - - + -
492F SER* 5.3 7.2 - - - +
494F VAL* 5.0 11.7 - - + -
539F LEU* 5.2 4.3 - - + -
549F ALA* 5.7 0.9 - - + -
550F SER 4.2 1.3 - - - -
551F PHE* 3.7 36.3 - - + -
557F TYR* 1.3 77.0 - - - +
559F LEU* 1.3 72.8 + - - +
560F SER* 4.8 7.2 - - - +
569F LEU* 3.3 13.0 - - - +
570F TRP* 3.1 49.3 + - + +
571F SER 4.3 2.9 - - - +
572F LEU* 3.4 21.4 - - + +
575F PHE* 6.2 2.0 - - + -
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Residues in contact with LEU 559 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548F GLY 5.2 0.4 - - - +
549F ALA* 3.3 25.4 - - - +
550F SER* 3.4 16.5 + - - +
558F LEU* 1.3 80.6 - - - +
560F SER* 1.3 83.5 + - - +
561F SER* 3.5 2.5 - - - +
567F VAL* 3.9 11.0 - - + -
568F ARG 3.4 5.8 - - - +
569F LEU* 3.8 13.0 - - + -
570F TRP* 4.7 0.4 - - - -
591F THR* 3.3 31.2 - - + +
593F PHE* 3.6 35.4 - - + +
600F PHE* 3.7 31.0 - - + -
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Residues in contact with SER 560 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492F SER* 3.6 20.8 - - - -
542F HIS* 3.5 28.5 - - - -
546F VAL* 4.5 7.9 - - - -
548F GLY 3.6 4.7 - - - -
549F ALA* 4.8 1.9 - - - +
558F LEU* 4.8 2.6 - - - +
559F LEU* 1.3 81.7 + - - +
561F SER* 1.3 68.0 + - - +
562F SER 4.2 0.7 - - - -
567F VAL* 3.5 13.7 - - - +
568F ARG 3.1 13.5 + - - -
570F TRP* 3.2 21.2 + - - -
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Residues in contact with SER 561 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546F VAL* 3.6 4.0 - - - +
547F TYR* 2.5 36.3 + - - +
548F GLY* 3.0 23.2 + - - -
559F LEU* 3.5 0.2 - - - +
560F SER* 1.3 78.8 + - - +
562F SER* 1.3 59.1 + - - +
566F THR 4.8 4.3 - - - -
567F VAL* 4.4 1.7 - - - +
588F VAL* 3.9 14.8 - - - -
589F TRP 4.0 2.9 - - - -
591F THR* 2.5 40.6 + - - +
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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
------------------------------------------------------------
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