Contacts of the strand formed by residues 516 - 520 (chain F) in PDB entry 4MNE
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 516 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450F TRP* 3.9 24.0 - + + -
502F VAL* 4.2 22.9 - - + -
505F LEU* 3.6 43.7 - - + +
506F ARG* 3.8 28.5 - - + -
508F THR* 4.8 1.5 + - - +
514F LEU 3.3 5.5 + - - -
515F LEU* 1.3 77.9 - - - +
517F MET* 1.3 61.1 + - - +
518F GLY* 3.3 37.0 - - - -
519F TYR* 4.1 3.1 - + + -
527F ILE* 3.9 14.4 - - + -
528F VAL 3.9 2.5 - - - -
529F THR* 4.3 5.4 - - - +
509G ARG* 3.2 50.1 + - - +
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Residues in contact with MET 517 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450F TRP* 3.6 22.0 - - - +
452F ILE* 5.2 0.2 - - - +
476F TRP* 4.4 27.6 - - + +
477F HIS 5.7 1.3 - - - +
479F ASP 5.0 4.0 - - - +
480F VAL* 4.2 22.4 - - + -
515F LEU* 3.7 12.6 - - + +
516F PHE* 1.3 82.1 - - - +
518F GLY* 1.3 57.4 + - - +
528F VAL* 2.8 23.6 + - + +
529F THR 4.1 0.2 - - - -
530F GLN* 3.5 35.2 - - + +
509G ARG* 3.9 21.1 - - - +
510G HIS* 4.4 27.4 - - + -
511G VAL* 4.4 10.8 - - + +
566G TYR* 5.1 1.0 + - - -
570G LYS* 5.1 0.7 + - - -
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Residues in contact with GLY 518 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450F TRP* 3.1 14.8 - - - -
452F ILE* 3.9 15.3 - - - -
516F PHE* 3.3 20.2 - - - -
517F MET* 1.3 81.5 - - - +
519F TYR* 1.3 56.2 + - - +
527F ILE 3.7 0.2 - - - -
528F VAL* 2.7 31.3 + - - +
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Residues in contact with TYR 519 (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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449F ASP* 4.1 9.4 + - - -
450F TRP* 3.0 18.6 + - + -
451F GLU* 3.5 47.6 + - + +
452F ILE* 2.8 32.9 + - - +
498F PHE* 3.7 22.7 - + + -
502F VAL* 3.6 41.1 - - + -
506F ARG* 5.2 7.0 + - - -
516F PHE* 4.2 4.0 - + - -
518F GLY* 1.3 75.9 - - - +
520F SER* 1.3 62.8 + - - +
521F THR* 4.7 4.5 - - - -
526F ALA 3.1 13.2 - - - +
527F ILE* 4.6 0.7 - - - -
528F VAL* 4.6 1.3 - - - +
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Residues in contact with SER 520 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451F GLU* 5.2 0.9 - - - -
452F ILE 3.5 16.0 + - - +
453F PRO 5.2 0.2 + - - -
454F ASP* 5.2 1.0 + - - -
457F ILE* 3.8 26.2 - - - +
498F PHE* 3.7 9.5 - - - -
519F TYR* 1.3 77.3 - - - +
521F THR* 1.3 60.0 + - - +
522F LYS 3.1 22.3 + - - -
523F PRO* 4.9 1.5 - - - +
524F GLN 3.4 9.5 - - - +
525F LEU* 3.4 3.8 - - - -
526F ALA* 2.8 32.8 + - - -
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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