Contacts of the strand formed by residues 461 - 465 (chain F) in PDB entry 6T8G
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 HIS 461 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468A THR* 6.1 0.2 - - - -
456F LEU* 6.1 0.2 - - - -
459F MET* 3.7 7.4 - - - +
460F PRO* 1.3 105.6 + - + +
462F LEU* 1.3 66.0 + - - +
615F ILE* 5.1 1.8 - - + -
616F ALA* 4.3 28.8 + - + -
619F ALA* 4.1 24.2 + - + -
620F ARG* 4.7 1.2 + - - +
624F ILE 3.8 8.5 - - - -
625F HIS* 3.7 17.5 - + - -
626F LEU* 3.1 34.4 + - + +
645F ASN 4.5 8.7 - - - -
646F ILE* 3.6 26.1 - - + +
648F THR* 3.3 22.9 - - - -
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Residues in contact with LEU 462 (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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441F LEU* 4.1 2.7 - - + -
459F MET* 3.7 20.4 - - + -
461F HIS* 1.3 80.3 - - - +
463F LEU* 1.3 69.6 + - - +
464F VAL* 4.3 4.5 - - + -
479F MET* 3.6 38.4 - - + -
626F LEU 3.0 3.9 + - - +
627F ILE* 3.7 26.2 - - + -
628F LEU* 2.9 32.4 + - - +
646F ILE* 3.5 4.4 - - - +
648F THR* 3.5 32.3 - - + +
650F ILE* 3.7 24.2 - - + -
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Residues in contact with LEU 463 (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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462F LEU* 1.3 75.3 - - - +
464F VAL* 1.3 63.7 + - - +
465F ALA* 6.3 0.9 - - + -
597F PHE* 5.9 1.8 - - + -
628F LEU* 3.4 37.0 - - + +
630F THR* 5.1 10.3 - - + -
638F ILE* 4.3 29.4 - - + -
642F ILE* 4.4 21.3 - - + +
646F ILE* 4.3 10.5 - - + -
648F THR 3.3 6.7 + - - -
649F ARG* 3.6 39.4 - - + +
650F ILE* 2.6 32.9 + - - +
663F ILE* 5.3 6.1 - - + -
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Residues in contact with VAL 464 (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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462F LEU* 4.3 8.7 - - + -
463F LEU* 1.3 81.1 - - - +
465F ALA* 1.3 65.8 + - - +
472F LYS* 4.6 15.0 - - + +
475F GLY 6.4 0.2 - - - -
476F VAL* 5.4 4.3 - - + +
479F MET* 4.1 24.2 - - + -
627F ILE* 5.3 4.3 - - + -
628F LEU 3.4 6.1 + - - -
629F ALA* 3.4 13.9 - - + -
630F THR* 2.8 30.1 + - - +
650F ILE* 3.2 19.5 - - + +
652F PHE* 3.7 33.0 - - + -
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Residues in contact with ALA 465 (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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463F LEU* 6.3 0.7 - - + -
464F VAL* 1.3 79.1 - - - +
466F GLY* 1.3 57.2 + - - +
472F LYS* 5.4 1.6 - - - +
630F THR* 3.3 26.2 - - + +
633F PRO* 4.1 10.3 - - + -
638F ILE* 4.9 1.1 - - + -
650F ILE 3.3 5.9 + - - -
651F ALA* 3.7 2.1 - - - -
652F PHE* 2.7 36.9 + - - +
654F VAL* 4.6 2.5 - - - +
663F ILE* 3.6 28.5 - - + -
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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