Contacts of the strand formed by residues 584 - 588 (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 PRO 584 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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552B LEU* 3.7 48.2 - - + +
576B VAL* 4.0 8.1 - - + -
577B ILE 3.5 6.5 - - - +
578B ARG* 3.7 18.6 - - + +
582B GLY 3.5 8.5 - - - +
583B SER* 1.3 88.3 - - - +
585B GLN* 1.3 60.7 + - - +
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Residues in contact with GLN 585 (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* 5.1 0.7 - - - -
576B VAL* 3.7 2.0 - - - -
577B ILE* 2.9 49.9 + - + +
583B SER 3.7 1.7 + - - +
584B PRO* 1.3 73.9 - - - +
586B ILE* 1.3 82.2 + - - +
587B GLU* 4.1 16.1 + - - +
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Residues in contact with ILE 586 (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* 4.9 5.8 - - + -
548B THR* 4.0 27.8 - - + +
551B LEU* 3.4 41.3 - - + -
552B LEU* 3.8 18.6 - - + +
575B HIS 3.5 11.0 - - - +
576B VAL* 3.8 20.9 - - + -
585B GLN* 1.3 84.6 - - - +
587B GLU* 1.3 70.2 - - - +
588B ASN* 4.4 13.3 - - - +
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Residues in contact with GLU 587 (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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642A VAL* 4.1 29.9 - - + +
574B ALA* 3.6 1.4 - - - -
575B HIS* 3.0 62.6 + - + +
577B ILE* 3.7 23.8 - - + +
585B GLN* 4.0 11.0 + - - +
586B ILE* 1.3 73.9 - - - +
588B ASN* 1.3 67.3 + - - +
589B ILE* 4.0 4.0 - - - +
650B VAL* 3.6 23.1 - - - +
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Residues in contact with ASN 588 (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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640A GLY 3.8 10.1 + - - +
641A PTR 3.2 21.9 - - + -
642A VAL* 2.7 32.7 + - - +
544B LYS* 3.4 33.2 + - - +
547B VAL* 4.9 4.1 - - - +
548B THR* 5.6 1.0 + - - -
562B ARG* 4.7 5.9 - - - +
572B THR* 4.8 1.4 + - - -
573B ILE 3.5 3.4 + - - +
574B ALA* 3.3 29.5 - - - +
586B ILE* 4.4 10.3 - - - +
587B GLU* 1.3 76.7 - - - +
589B ILE* 1.3 54.9 + - - +
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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