Contacts of the strand formed by residues 526 - 534 (chain B) in PDB entry 1Y8Q
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 TYR 526 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ARG* 3.4 39.5 - - + -
442B TYR* 2.6 48.3 + + - -
443B VAL* 3.8 28.5 - - + -
448B PRO* 4.0 12.8 - - + -
473B PHE* 4.3 4.0 - - + -
475B MET* 3.4 27.5 - - + +
520B ASP* 3.4 3.1 - - - +
521B ASP* 2.9 33.6 + - + +
524B GLN* 3.9 20.0 - - + +
525B ASP* 1.3 76.3 - - - +
527B THR* 1.3 73.3 + - - +
528B LEU* 3.7 14.6 - - + +
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Residues in contact with THR 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B PRO* 3.4 29.3 - - - +
518B GLN* 4.0 28.3 - - + +
519B ALA 3.4 2.5 - - - -
520B ASP* 2.5 23.3 + - - +
525B ASP 5.4 1.2 - - - -
526B TYR* 1.3 77.7 + - - +
528B LEU* 1.3 64.2 + - - +
529B LEU* 5.1 6.3 - - + +
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Residues in contact with LEU 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B TYR* 3.8 8.7 - - + +
448B PRO* 3.7 27.4 - - + -
449B GLU* 3.8 6.1 - - - +
450B VAL* 4.0 16.4 - - + +
473B PHE* 3.8 39.7 - - + -
475B MET* 4.2 7.0 - - + -
518B GLN* 3.7 0.5 - - - -
519B ALA* 2.7 45.5 + - + +
526B TYR* 3.7 30.0 - - + +
527B THR* 1.3 76.3 - - - +
529B LEU* 1.3 71.7 + - - +
530B ILE* 3.6 9.1 + - + +
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Residues in contact with LEU 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447B LYS* 5.3 13.7 - - + +
448B PRO 3.1 19.9 + - - +
449B GLU* 3.4 17.3 - - + +
450B VAL* 3.0 29.8 + - - +
483B GLU* 4.0 16.6 - - - +
516B ARG* 3.6 34.1 - - + +
517B LEU 3.4 3.8 - - - +
518B GLN* 3.8 34.3 - - + +
527B THR* 5.2 4.3 - - + -
528B LEU* 1.3 73.9 - - - +
530B ILE* 1.3 59.3 + - - +
531B ASN* 4.0 0.4 - - - -
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Residues in contact with ILE 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B VAL* 3.6 10.5 - - + -
452B VAL* 3.9 27.6 - - + -
464B LEU* 5.2 8.3 - - + -
468B ILE* 5.2 1.8 - - + -
469B VAL* 4.5 11.7 - - + -
473B PHE* 4.2 22.4 - - + -
480B VAL* 5.7 1.3 - - + -
516B ARG* 3.4 1.7 - - - +
517B LEU* 2.5 56.6 + - + +
519B ALA* 4.0 20.2 - - + -
528B LEU* 3.9 13.2 - - + +
529B LEU* 1.3 77.8 - - - +
531B ASN* 1.3 64.0 + - - +
532B ILE* 3.7 17.9 + - + -
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Residues in contact with ASN 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B GLU* 2.9 37.9 + - - +
450B VAL 2.8 11.1 + - - -
451B THR* 3.3 25.5 + - + +
452B VAL* 2.7 32.6 + - - +
514B GLY 5.6 0.9 - - - +
515B SER 3.7 4.8 - - - +
516B ARG* 3.2 27.9 + - - +
530B ILE* 1.3 74.1 - - - +
532B ILE* 1.3 59.2 + - - +
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Residues in contact with ILE 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451B THR* 5.0 0.2 - - - -
452B VAL* 3.5 7.9 - - + +
454B LEU* 3.4 36.3 - - + -
456B VAL* 4.1 15.3 - - + -
464B LEU* 5.9 3.4 - - + -
506B LEU* 5.6 2.5 - - + -
511B ILE* 4.3 12.8 - - + -
512B ARG 4.2 11.2 - - - +
514B GLY* 3.0 27.8 + - - -
515B SER* 2.8 20.7 + - - +
517B LEU* 4.0 33.0 - - + -
530B ILE* 4.1 13.5 - - + -
531B ASN* 1.3 78.5 - - - +
533B LEU* 1.3 72.2 + - - +
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Residues in contact with LEU 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451B THR* 3.7 26.5 - - + -
452B VAL 2.8 11.9 + - - +
453B ARG* 3.4 22.7 - - + +
454B LEU* 3.0 26.2 + - - +
513B ASN* 3.4 19.5 - - - +
514B GLY* 5.3 1.6 - - - +
532B ILE* 1.3 78.1 - - - +
534B HIS* 1.3 62.6 + - - +
535B SER 3.5 0.2 + - - -
547B VAL* 3.9 17.3 - - + -
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Residues in contact with HIS 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B LEU 3.3 4.2 + - - -
455B ASN* 3.8 19.3 - - - -
456B VAL* 3.4 31.8 + - + -
457B HIS* 4.0 22.3 + + - -
512B ARG* 5.8 1.1 - - + -
513B ASN* 2.8 39.2 + - + +
532B ILE* 4.4 0.2 - - - +
533B LEU* 1.3 71.9 - - - +
535B SER* 1.3 68.1 + - - +
536B GLU* 3.5 39.9 + - + +
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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