Contacts of the strand formed by residues 570 - 576 (chain B) in PDB entry 2YA6
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 ILE 570 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B VAL* 3.7 28.9 - - + -
408B ASP* 3.8 21.8 - - + +
415B PHE* 4.1 16.6 - - + -
559B ILE 3.5 7.2 - - - +
560B VAL* 4.0 15.7 - - + +
568B GLY 4.1 7.0 - - - +
569B ARG* 1.3 73.0 - - - +
571B LEU* 1.3 61.6 + - - +
572B ILE* 3.8 7.2 - - + -
592B ILE 3.8 0.3 - - - +
593B TYR* 3.0 29.1 - - - +
594B SER* 3.0 12.9 + - - +
597B HIS* 3.9 4.0 - - - -
598B GLY* 3.8 26.0 - - - +
601B TRP* 3.8 18.7 - - + -
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Residues in contact with LEU 571 (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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558B GLY* 3.5 8.0 - - - -
559B ILE* 2.9 39.9 + - + +
561B LEU* 3.7 29.8 - - + -
569B ARG* 3.7 19.5 - - + -
570B ILE* 1.3 72.5 - - - +
572B ILE* 1.3 66.2 + - - +
573B PRO* 3.9 2.3 - - - +
591B VAL* 4.0 19.7 - - + -
592B ILE 3.7 0.4 - - - -
593B TYR* 3.6 24.2 - - + -
635B VAL* 3.7 29.3 - - + +
643B VAL* 3.8 12.6 - - + -
662B GLY 3.7 12.3 - - - +
663B GLY* 4.6 0.4 - - - -
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Residues in contact with ILE 572 (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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404B VAL* 4.1 30.5 - - + +
406B VAL* 3.8 26.9 - - + -
417B ILE* 3.6 28.9 - - + -
553B VAL* 4.3 10.8 - - + -
570B ILE* 3.8 6.1 - - + -
571B LEU* 1.3 81.8 - - - +
573B PRO* 1.3 77.2 - - - +
574B VAL* 3.4 1.1 + - + -
591B VAL* 3.3 3.2 - - - -
592B ILE* 3.0 42.4 + - + +
601B TRP* 3.6 24.9 - - + -
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Residues in contact with PRO 573 (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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404B VAL* 4.5 9.4 - - + -
553B VAL* 3.5 3.5 - - - +
554B GLY* 2.9 30.7 + - - +
557B THR 5.3 2.2 - - - +
558B GLY* 4.5 3.8 - - - -
571B LEU 3.9 6.3 - - - +
572B ILE* 1.3 91.8 - - + +
574B VAL* 1.3 63.3 + - - +
590B ARG 3.7 6.7 - - - +
591B VAL* 3.9 4.7 - - + -
633B SER* 3.4 37.7 - - - +
634B THR* 4.5 0.9 - - - -
635B VAL* 3.8 32.1 - - + +
645B LEU* 4.8 0.2 - - + -
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Residues in contact with VAL 574 (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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521B LEU* 4.5 6.5 - - + -
551B LEU* 4.0 20.0 - - + -
552B GLY 3.2 18.2 - - - +
553B VAL* 4.1 6.1 - - + -
554B GLY* 3.7 2.9 - - - +
572B ILE* 3.8 10.1 - - + +
573B PRO* 1.3 79.3 - - - +
575B TYR* 1.3 67.5 + - - +
589B SER* 3.5 3.5 - - - -
590B ARG* 2.9 60.8 + - + +
592B ILE* 4.0 33.9 - - + +
631B THR 4.2 1.7 - - - +
633B SER* 4.8 1.7 + - - -
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Residues in contact with TYR 575 (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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402B ASP* 4.8 1.4 + - - -
427B ILE* 5.0 0.7 - - + -
550B PHE* 3.5 36.3 - + - -
551B LEU* 3.4 3.3 - - - +
552B GLY 2.8 36.2 + - - +
553B VAL 3.4 22.7 - - - -
574B VAL* 1.3 79.1 - - - +
576B THR* 1.3 64.1 + - - +
587B GLN* 3.6 30.3 - - + -
588B SER 3.1 17.7 - - - +
590B ARG 4.7 0.2 - - - +
631B THR* 3.4 29.2 - - - +
632B GLU* 3.6 26.7 + - + +
1777B DAN 2.7 40.1 + - - -
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Residues in contact with THR 576 (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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547B TRP* 3.6 18.9 - - - -
548B MET* 3.6 37.0 - - + -
550B PHE* 3.1 14.4 - - - +
551B LEU* 3.8 13.7 - - + -
575B TYR* 1.3 78.1 - - - +
577B THR* 1.3 70.3 + - - +
586B SER 3.5 1.1 - - - +
587B GLN* 3.2 7.4 - - - -
588B SER* 3.0 42.2 + - - -
590B ARG* 4.1 13.9 + - - +
620B SER 4.9 0.3 + - - -
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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