Contacts of the strand formed by residues 571 - 578 (chain B) in PDB entry 4Y5U
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 571 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524B LEU* 4.1 6.7 - - + +
529B LEU* 4.1 11.2 - - + -
538B ILE* 3.6 42.0 - - + -
561B LEU* 4.1 13.7 - - + -
562B ARG 3.0 21.1 - - - +
563B PHE* 4.1 10.5 - - + -
570B GLY* 1.3 75.0 - - - +
572B THR* 1.3 64.4 + - - +
591B PRO* 3.9 0.9 - - - -
592B PHE* 2.7 47.3 + - + +
597B LEU* 4.0 26.9 - - + -
602B LEU* 4.3 13.5 - - + -
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Residues in contact with THR 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A PTR 3.7 14.3 - - + +
561B LEU* 3.7 5.5 - - - +
562B ARG* 2.9 64.4 + - + +
564B SER 4.2 8.7 - - - +
571B ILE* 1.3 78.4 - - - +
573B ILE* 1.3 67.3 + - - +
574B ALA 4.1 0.2 - - - -
588B ASN* 4.7 1.8 + - - +
589B ILE 2.4 29.0 + - - -
590B GLN 4.6 1.1 - - - -
591B PRO* 3.7 18.8 - - + -
592B PHE* 5.2 0.2 - - - -
602B LEU* 6.4 0.2 - - - -
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Residues in contact with ILE 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B PHE* 4.3 11.0 - - + -
560B LEU 3.8 4.7 - - - +
561B LEU* 3.8 16.6 - - + -
572B THR* 1.3 78.9 + - - +
574B ALA* 1.3 71.7 + - - +
575B HIS* 4.4 4.5 - - + -
587B GLU 3.9 0.7 - - - +
588B ASN* 3.5 1.7 - - - -
589B ILE* 2.9 60.2 + - + +
592B PHE* 4.0 27.0 - - + -
602B LEU* 4.7 2.7 - - + -
605B ARG* 5.7 0.2 - - + -
606B ILE* 4.2 23.6 - - + +
609B LEU* 4.8 4.3 - - + -
612B LEU* 4.2 21.1 - - + -
648B MET* 4.9 2.9 - - + -
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Residues in contact with ALA 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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547B VAL* 3.5 26.5 - - + -
551B LEU* 4.0 2.4 - - + +
559B PHE* 3.3 1.9 - - - +
560B LEU* 3.0 42.0 + - + -
562B ARG* 4.5 7.0 - - - -
572B THR 4.0 0.8 + - - -
573B ILE* 1.3 73.9 - - - +
575B HIS* 1.3 67.6 + - - +
586B ILE* 5.3 0.4 - - + -
587B GLU 3.6 4.5 - - - -
588B ASN* 3.3 21.3 - - - +
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Residues in contact with HIS 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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551B LEU* 3.8 9.5 - - - +
557B GLY* 5.4 0.8 - - - -
558B THR 3.5 6.3 - - - +
559B PHE* 3.4 19.5 - - + -
573B ILE* 4.4 2.7 - - + -
574B ALA* 1.3 79.3 - - - +
576B VAL* 1.3 61.4 + - - +
577B ILE* 3.6 29.8 + - + +
586B ILE* 3.5 4.3 - - - +
587B GLU* 3.0 69.1 + - + +
589B ILE* 4.2 21.7 - - + +
609B LEU* 6.2 0.7 - - + -
611B GLN* 3.8 21.7 + - + -
612B LEU* 3.8 19.7 - - + +
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Residues in contact with VAL 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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551B LEU* 3.3 27.7 - - + +
552B LEU* 4.6 0.2 - - - -
554B GLU* 3.6 15.3 - - + +
555B PRO 3.4 23.1 - - - +
556B ASP* 4.6 0.2 - - - -
557B GLY* 2.9 30.9 + - - -
558B THR* 3.1 23.6 + - - +
575B HIS* 1.3 74.9 + - - +
577B ILE* 1.3 65.7 + - - +
578B ARG* 4.2 1.8 - - - +
584B PRO* 4.0 22.4 - - + -
585B GLN 3.7 9.9 - - - +
586B ILE* 3.8 12.3 - - + -
611B GLN* 3.9 2.8 - - - +
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Residues in contact with ILE 577 (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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556B ASP* 3.5 6.3 - - - +
575B HIS* 3.6 25.8 - - + -
576B VAL* 1.3 72.2 - - - +
578B ARG* 1.3 65.3 + - - +
583B SER 3.9 0.3 - - - +
584B PRO* 3.5 0.7 - - - +
585B GLN* 2.9 53.0 + - + +
587B GLU* 3.7 28.5 - - + +
611B GLN* 3.5 28.5 - - + +
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Residues in contact with ARG 578 (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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552B LEU 2.6 27.4 + - - -
553B ASN* 3.4 10.9 - - - +
554B GLU 2.7 29.5 + - - -
555B PRO* 4.8 1.2 - - - +
556B ASP* 3.0 39.6 + - + +
576B VAL* 4.4 2.2 - - + +
577B ILE* 1.3 78.9 - - - +
579B GLY* 1.3 68.8 + - - +
582B GLY* 3.8 21.5 + - - -
583B SER 3.7 12.8 - - - +
584B PRO* 3.7 26.1 - - + +
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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