Contacts of the strand formed by residues 457 - 463 (chain A) in PDB entry 6PAI
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 457 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408A LYS 5.6 0.2 - - - +
411A TRP* 3.1 35.5 - - + -
426A VAL* 4.8 1.3 - - + -
428A SER* 3.3 12.3 + - - -
433A THR* 2.8 31.9 + - - +
456A GLN* 1.3 75.8 - - - +
458A PHE* 1.3 57.5 + - - +
459A PHE 3.3 32.3 - - - +
460A CYS* 4.0 13.5 - - + -
470A GLN* 3.0 25.0 + - + +
471A ILE 3.7 4.7 - - - +
472A THR* 4.4 2.4 - - - +
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Residues in contact with PHE 458 (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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411A TRP* 3.4 15.4 + - - -
456A GLN* 3.2 42.2 - - + -
457A THR* 1.3 76.0 - - - +
459A PHE* 1.3 63.8 + - - +
471A ILE 2.7 12.8 + - - +
472A THR 4.5 2.2 - - - +
473A SER* 3.8 27.1 - - - -
498A ILE* 3.5 18.4 - - + -
499A SER 3.3 29.8 - - - -
500A VAL* 4.5 2.7 - - - -
501A ALA* 3.9 27.7 - - + +
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Residues in contact with PHE 459 (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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411A TRP* 3.6 23.1 - + - +
457A THR* 3.3 8.0 - - - +
458A PHE* 1.3 81.1 - - - +
460A CYS* 1.3 95.3 + - - +
461A GLY* 4.2 3.8 - - - -
462A ASN 5.9 1.3 - - - -
463A VAL* 5.7 0.9 - - + -
469A ILE* 4.1 7.2 - - + -
471A ILE* 2.9 44.0 + - + -
501A ALA* 5.0 8.5 - - + +
502A SER* 5.7 1.6 - - - -
503A CYS* 3.5 53.2 - - + -
504A ASN* 5.2 1.8 - - - -
639A ARG* 6.0 2.0 - - - -
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Residues in contact with CYS 460 (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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411A TRP* 3.6 31.7 - - - +
412A PRO* 4.7 1.6 - - - +
413A LEU* 5.3 2.2 - - - -
426A VAL* 3.6 45.1 - - - -
451A PHE* 3.8 14.4 - - + -
457A THR* 4.0 6.1 - - + -
459A PHE* 1.3 96.8 - - - +
461A GLY* 1.3 60.2 + - - +
469A ILE 3.1 17.5 - - - +
470A GLN* 3.9 3.4 - - - -
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Residues in contact with GLY 461 (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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412A PRO 4.3 8.7 - - - -
413A LEU* 3.7 23.9 - - - +
451A PHE* 4.9 0.2 - - - -
459A PHE* 4.8 4.0 - - - -
460A CYS* 1.3 79.3 - - - +
462A ASN* 1.3 63.1 + - - -
463A VAL* 4.8 0.2 - - - -
468A LEU* 3.7 1.1 - - - -
469A ILE* 3.0 35.6 + - - +
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Residues in contact with ASN 462 (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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412A PRO 4.8 1.3 + - - +
413A LEU* 3.8 5.4 - - - +
414A ARG* 3.0 73.6 + - - +
417A PRO* 5.9 3.6 - - - +
422A ASP* 5.3 0.3 - - - +
459A PHE* 5.9 1.7 - - - -
461A GLY* 1.3 71.2 - - - -
463A VAL* 1.3 64.5 + - - +
467A GLN 4.7 2.2 + - - -
468A LEU* 3.3 22.8 - - - +
504A ASN 5.1 0.9 - - - +
505A SER* 4.4 9.4 - - - -
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Residues in contact with VAL 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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459A PHE* 5.7 0.7 - - + -
461A GLY 4.0 0.2 - - - +
462A ASN* 1.3 79.0 + - - +
464A ALA* 1.3 66.2 + - - +
465A HIS 4.0 0.2 + - - -
466A GLN* 4.1 3.6 + - - -
467A GLN* 3.0 48.1 + - + +
468A LEU 3.9 2.9 - - - +
469A ILE* 3.4 31.0 - - + -
478A LEU* 3.8 16.8 - - + -
503A CYS* 4.4 0.2 - - - -
504A ASN 4.0 11.2 - - - +
505A SER* 3.4 15.9 - - - +
521A ILE* 3.8 21.8 - - + -
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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