Contacts of the strand formed by residues 460 - 465 (chain A) in PDB entry 6X70
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 460 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A PHE* 3.9 29.2 - - + -
343A ASN* 5.6 1.1 - - - +
348A THR* 4.4 15.7 - - - +
349A LYS* 5.5 0.2 - - - -
350A ILE* 3.9 27.1 - - + +
458A PHE* 3.4 1.1 - - - +
459A ASN* 1.3 81.2 - - - +
461A ILE* 1.3 69.0 + - - +
462A LEU* 3.9 25.1 - - + -
471A CYS* 3.5 2.4 - - - -
472A VAL* 2.7 57.3 + - + +
610A ILE 4.5 0.9 - - - +
611A LEU* 4.1 14.8 - - + +
614A PRO* 4.2 8.5 - - + -
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Residues in contact with ILE 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PHE* 3.4 21.6 - - - -
449A TYR* 4.4 28.3 - - + +
452A LEU* 3.9 36.8 - - + +
453A LYS* 3.9 14.8 - - + +
458A PHE* 3.9 24.5 - - + +
460A LEU* 1.3 79.3 - - - +
462A LEU* 1.3 60.6 + - - +
463A PRO* 3.5 5.9 - - + +
469A ALA* 4.8 1.1 - - + -
470A VAL 3.9 2.0 - - - -
471A CYS* 4.2 13.2 - - - -
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Residues in contact with LEU 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PHE* 4.2 7.4 - - + -
460A LEU* 3.9 26.9 - - + -
461A ILE* 1.3 72.5 - - - +
463A PRO* 1.3 68.8 - - + +
464A ILE* 3.3 2.7 + - + +
469A ALA* 3.3 4.4 - - - -
470A VAL* 2.8 55.8 + - + +
472A VAL* 4.6 0.9 - - + -
610A ILE* 3.8 47.3 - - + +
611A LEU* 4.3 9.6 - - + -
614A PRO* 3.6 29.8 - - + -
618A LEU* 4.6 7.9 - - + -
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Residues in contact with PRO 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A LEU* 3.8 43.3 - - + +
336A LYS* 4.6 10.0 - - + +
339A PHE* 4.0 18.6 - - + -
449A TYR* 3.3 31.9 - - + +
461A ILE* 3.5 10.3 - - + +
462A LEU* 1.3 81.4 - - + +
464A ILE* 1.3 66.1 + - - +
610A ILE* 5.9 0.2 - - - +
618A LEU* 4.4 21.1 - - + +
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Residues in contact with ILE 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A LYS* 3.8 22.0 - - - +
336A LYS* 5.4 1.0 - - - -
360A HIS* 4.6 1.6 - - + +
462A LEU 3.3 4.2 + - - +
463A PRO* 1.3 79.9 - - - +
465A SER* 1.3 61.6 + - - +
468A GLU* 2.9 43.2 + - + +
469A ALA* 4.2 1.1 - - - -
470A VAL* 3.6 40.6 - - + +
610A ILE* 4.7 18.4 - - + -
12P G 4.2 24.2 - - - +
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Residues in contact with SER 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A LEU* 5.7 5.6 - - - -
332A LYS* 4.9 12.1 - - - -
335A LEU* 3.5 10.1 - - - +
449A TYR* 2.7 23.0 + - - -
463A PRO 3.7 0.6 - - - -
464A ILE* 1.3 77.9 - - - +
466A ILE* 1.3 64.5 + - - +
467A ASP* 2.6 31.0 + - - -
468A GLU* 2.9 15.7 + - - +
12P G 3.6 20.0 + - - -
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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