Contacts of the strand formed by residues 589 - 592 (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 THR 589 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511F VAL* 3.9 36.6 - - + +
512F ASN* 4.2 1.8 - - - +
559F GLN* 3.4 11.0 - - - +
583F PHE 3.5 0.2 - - - +
584F LEU* 3.7 1.1 - - - -
585F HIS* 2.8 50.3 + - - +
588F LEU* 1.3 94.0 - - - +
590F VAL* 1.3 62.7 + - - +
591F LYS* 4.1 12.8 - - - -
585G HIS* 5.4 3.9 + - - +
586G GLU* 5.2 3.3 + - - +
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Residues in contact with VAL 590 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511F VAL 3.7 3.3 - - - +
512F ASN* 2.9 29.7 + - - +
556F ILE* 4.1 30.1 - - + +
559F GLN* 2.9 33.7 + - + +
560F THR* 3.8 23.3 - - - +
582F ILE* 3.8 24.5 - - + -
583F PHE 3.5 3.1 - - - +
584F LEU* 4.2 15.9 - - + -
588F LEU 4.6 0.9 - - - +
589F THR* 1.3 73.0 - - - +
591F LYS* 1.3 64.9 + - - +
592F ILE* 4.5 5.2 - - + +
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Residues in contact with LYS 591 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510F HIS 5.0 0.2 + - - -
511F VAL* 2.6 35.7 + - - +
512F ASN 3.5 3.1 - - - -
513F ILE 4.5 2.0 + - - +
514F LEU* 4.1 26.2 - - + +
530F GLN* 3.4 26.2 + - - +
532F CYS* 5.4 0.9 - - - -
583F PHE* 2.8 47.8 + - + +
585F HIS* 3.6 37.2 - - + +
589F THR* 4.1 13.6 - - - +
590F VAL* 1.3 74.5 - - - +
592F ILE* 1.3 62.3 + - - +
801F CL 3.4 27.4 - - - +
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Residues in contact with ILE 592 (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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512F ASN 2.8 15.8 + - - +
513F ILE* 3.8 10.7 - - + -
514F LEU* 3.0 21.4 + - - +
559F GLN 5.2 0.2 - - - +
560F THR* 3.7 32.8 - - + +
563F GLY* 4.0 9.4 - - - -
564F MET* 3.6 34.1 - - + +
567F LEU* 4.8 0.4 - - + -
574F HIS* 4.0 28.5 - - + +
577F LEU* 4.2 13.5 - - + -
581F ASN* 3.5 7.2 - - + +
582F ILE* 4.6 4.3 - - + +
590F VAL* 4.7 7.9 - - + -
591F LYS* 1.3 69.9 - - - +
593F GLY* 1.3 60.7 + - - +
595F PHE* 3.4 13.3 - - + -
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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