Contacts of the strand formed by residues 488 - 493 (chain A) in PDB entry 3Q8A
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 488 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A ALA* 3.7 26.5 - - - +
257A ALA* 4.6 3.8 - - + -
484A ILE* 2.8 27.9 + - + +
485A GLN 4.3 3.1 - - - +
487A THR* 1.3 85.2 - - - +
489A ALA* 1.3 59.7 + - - +
504A ARG* 3.1 43.8 + - - +
505A ILE 3.4 15.9 - - - +
506A ALA* 4.4 8.1 - - - +
507A ALA 4.5 1.6 - - - +
585A ALA* 4.0 1.5 - - - +
586A LYS* 3.2 19.2 + - - -
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Residues in contact with ALA 489 (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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488A THR* 1.3 71.9 - - - +
490A ARG* 1.3 62.9 + - - +
491A ILE* 4.5 1.3 - - + +
504A ARG* 3.5 2.3 - - - -
505A ILE* 2.9 34.5 + - - +
507A ALA* 4.0 13.4 - - + +
583A LEU* 4.4 16.1 - - + +
584A ASN 3.3 22.2 - - - +
585A ALA* 4.4 0.8 - - - +
587A MET* 3.5 20.9 - - + +
589A ILE* 5.8 1.6 - - + -
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Residues in contact with ARG 490 (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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299A HIS* 3.3 21.4 + - - -
323A GLY 2.8 29.5 + - - -
324A PHE 3.9 3.6 + - - -
325A SER 3.0 22.5 + - - -
326A ASN* 4.4 6.6 + - - +
327A SER 5.9 0.8 + - - -
489A ALA* 1.3 73.1 - - - +
491A ILE* 1.3 71.8 + - - +
492A ILE* 3.9 12.4 - - + +
502A GLU* 3.0 39.0 + - + -
503A ARG 3.4 14.1 - - - +
504A ARG* 3.4 29.2 - - - +
587A MET 2.7 11.8 + - - +
588A ASN* 3.2 27.5 + - - +
589A ILE* 3.0 26.4 + - - +
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Residues in contact with ILE 491 (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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489A ALA* 4.5 1.8 - - + +
490A ARG* 1.3 81.8 - - - +
492A ILE* 1.3 71.9 + - - +
493A PHE* 4.6 2.0 - - + +
501A VAL 3.6 0.7 - - - +
502A GLU* 3.3 3.8 - - - -
503A ARG* 2.9 30.6 + - - +
505A ILE* 3.4 28.7 - - + -
523A LEU* 5.0 5.6 - - + -
526A ALA* 4.0 20.4 - - + +
527A LEU* 4.5 14.4 - - + -
531A PHE* 3.8 24.2 - - + -
583A LEU* 4.8 7.4 - - + -
589A ILE* 3.9 20.9 - - + -
591A ILE* 4.4 21.1 - - + -
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Residues in contact with ILE 492 (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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299A HIS* 3.6 46.2 - - + +
322A ALA* 6.0 0.4 - - + -
490A ARG* 3.9 23.6 - - - +
491A ILE* 1.3 82.6 - - - +
493A PHE* 1.3 60.8 + - - +
500A LEU* 3.4 38.6 - - + -
501A VAL 3.4 8.7 - - - +
502A GLU* 4.2 9.6 - - + +
588A ASN* 6.3 0.7 - - + -
589A ILE 3.1 18.0 + - - +
590A LEU* 3.5 7.8 - - + +
591A ILE* 2.8 30.0 + - - +
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Residues in contact with PHE 493 (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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491A ILE* 4.7 2.9 - - + -
492A ILE* 1.3 76.2 - - - +
494A ASN* 1.3 58.7 + - - +
495A GLY* 3.4 29.6 - - - -
496A LYS* 4.8 2.4 + - + -
499A ASN 3.1 1.9 - - - +
500A LEU* 4.7 1.1 - - - -
501A VAL* 3.0 32.3 + - - +
531A PHE* 3.4 41.7 - + + -
533A PHE* 3.8 17.9 - + - -
542A TYR* 3.6 38.6 - + - -
550A PHE* 3.5 25.8 - + - -
591A ILE* 3.1 40.8 - - + -
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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