Contacts of the strand formed by residues 585 - 590 (chain A) in PDB entry 5ULM
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 585 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577A ILE* 3.6 6.1 - - - +
578A ASN* 2.8 57.6 + - - +
580A GLU* 4.2 15.3 + - + +
583A GLU* 3.7 10.5 - - + +
584A LYS* 1.3 82.8 - - - +
586A ILE* 1.3 64.1 + - - +
603A ASN* 3.9 22.6 + - - +
604A PHE 3.2 13.5 - - - +
605A SER* 4.0 10.5 - - - -
606A ALA 4.7 0.4 - - - +
653A ILE* 5.3 1.1 - - - -
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Residues in contact with ILE 586 (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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575A LEU* 4.5 9.0 - - + -
576A SER 3.4 8.7 - - - +
577A ILE* 4.0 12.6 - - + -
585A THR* 1.3 77.6 - - - +
587A SER* 1.3 63.0 + - - +
588A ILE* 4.0 25.6 - - + -
602A TRP 4.0 0.5 - - - +
603A ASN* 3.3 4.3 + - - -
604A PHE* 2.7 48.5 + - + +
606A ALA* 6.5 0.2 - - - -
609A VAL* 4.1 19.3 - - + -
624A LEU* 4.2 16.2 - - + -
646A PHE* 4.8 1.1 - - + -
650A VAL* 3.9 31.0 - - + -
653A ILE* 4.0 19.3 - - + -
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Residues in contact with SER 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A LEU* 3.2 5.4 - - - +
576A SER* 2.8 41.1 + - - +
578A ASN* 2.8 20.0 + - - +
586A ILE* 1.3 69.1 - - - +
588A ILE* 1.3 66.1 + - - +
589A TRP* 4.1 15.0 - - - -
602A TRP 3.5 6.1 - - - -
603A ASN* 2.4 29.8 + - - -
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Residues in contact with ILE 588 (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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561A VAL* 5.8 0.9 - - + -
563A ILE* 3.6 30.1 - - + -
573A SER* 5.0 1.8 - - - -
574A TYR 3.4 8.7 - - - +
575A LEU* 4.1 18.2 - - + -
586A ILE* 4.0 11.9 - - + -
587A SER* 1.3 81.1 - - - +
589A TRP* 1.3 67.5 + - - +
601A GLU* 3.5 1.9 - - - +
602A TRP* 2.9 51.0 + - + +
604A PHE* 4.3 11.0 - - + -
624A LEU* 3.8 28.9 - - + -
633A PHE* 4.3 14.6 - - + -
635A ILE* 4.5 4.5 - - + -
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Residues in contact with TRP 589 (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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558A ARG* 3.6 32.5 - - + +
573A SER* 3.1 4.1 - - - -
574A TYR* 2.8 81.3 + + + +
575A LEU 5.0 0.4 - - - -
576A SER* 4.1 12.8 - - - -
587A SER* 4.1 21.3 - - - -
588A ILE* 1.3 85.5 - - - +
590A HIS* 1.3 77.5 + - - +
591A VAL* 3.7 2.3 + - + +
600A HIS 3.4 9.2 - - - +
601A GLU* 3.7 26.5 - - + +
602A TRP* 5.1 0.2 - - - -
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Residues in contact with HIS 590 (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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563A ILE* 3.8 13.9 - - + +
565A GLU* 3.7 20.7 + - - -
571A GLN* 3.6 32.9 - - + +
572A PRO 3.6 3.6 - - - -
573A SER* 3.2 10.1 + - - -
589A TRP* 1.3 83.9 - - - +
591A VAL* 1.3 61.3 + - - +
592A LEU 3.8 1.7 + - - -
593A PRO* 4.3 12.5 - - + +
599A ILE 4.6 0.8 + - - -
600A HIS* 2.9 50.7 + + + +
602A TRP* 3.5 31.5 - + - -
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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